changeset 0:3de1359b86cc draft default tip

"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit def3e8d4a983ab47ceedde678f585b54c79bb8d1"
author chemteam
date Thu, 27 Jan 2022 17:17:54 +0000
parents
children
files macros.xml parmconv.py template_mmpbsa_mmgbsa.j2 template_parmconv.j2 test-data/1err_desolvated_mini.nc test-data/JZ4.mol2 test-data/LigA.mol2 test-data/LigA.pdb test-data/LigA_output.mol2 test-data/LigA_output.pdb test-data/LigA_output.top test-data/LigA_output.txt test-data/LigA_prmchk.mol2 test-data/ZAFF.frcmod test-data/ZAFF.prep test-data/base_GMX.gro test-data/base_GMX.itp test-data/cid1.inpcrd test-data/cid1.prmtop test-data/complex.prmtop test-data/leap_testfile.txt test-data/ligand.prmtop test-data/receptor.prmtop test-data/sarscov2_helicase_ZincBindingDomain.pdb test-data/solv_ions.gro test-data/topol_solv.top tleap.xml
diffstat 27 files changed, 103781 insertions(+), 0 deletions(-) [+]
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml	Thu Jan 27 17:17:54 2022 +0000
@@ -0,0 +1,582 @@
+<macros>
+	<token name="@TOOL_VERSION@">21.10</token>
+	<xml name="requirements">
+		<requirements>
+			<requirement type="package" version="@TOOL_VERSION@">ambertools</requirement>
+			<yield/>
+		</requirements>
+	</xml>
+	<xml name="builtin_amberfiles">
+		<param name="arg_filename" type="select" label="File">
+			<option value="epASN.prepin">epASN.prepin</option>
+			<option value="epACE.prepin">epACE.prepin</option>
+			<option value="GLYCAM_06j-1.prep">GLYCAM_06j-1.prep</option>
+			<option value="toyrna.in">toyrna.in</option>
+			<option value="epTRP.prepin">epTRP.prepin</option>
+			<option value="epSER.prepin">epSER.prepin</option>
+			<option value="epALA.prepin">epALA.prepin</option>
+			<option value="epASP.prepin">epASP.prepin</option>
+			<option value="amino12.in">amino12.in</option>
+			<option value="amino10.in">amino10.in</option>
+			<option value="epPHE.prepin">epPHE.prepin</option>
+			<option value="uni_amino03.in">uni_amino03.in</option>
+			<option value="aminoct12.in">aminoct12.in</option>
+			<option value="epTHR.prepin">epTHR.prepin</option>
+			<option value="uni_aminoct03.in">uni_aminoct03.in</option>
+			<option value="epNME.prepin">epNME.prepin</option>
+			<option value="chcl3.in">chcl3.in</option>
+			<option value="all_aminont03.in">all_aminont03.in</option>
+			<option value="epTYR.prepin">epTYR.prepin</option>
+			<option value="epVAL.prepin">epVAL.prepin</option>
+			<option value="epGLU.prepin">epGLU.prepin</option>
+			<option value="meoh.in">meoh.in</option>
+			<option value="all_aminoct03.in">all_aminoct03.in</option>
+			<option value="epHID.prepin">epHID.prepin</option>
+			<option value="all_amino03.in">all_amino03.in</option>
+			<option value="aminont10.in">aminont10.in</option>
+			<option value="epLEU.prepin">epLEU.prepin</option>
+			<option value="GLYCAM_lipids_06h.prep">GLYCAM_lipids_06h.prep</option>
+			<option value="GLYCAM_06EPb.prep">GLYCAM_06EPb.prep</option>
+			<option value="epILE.prepin">epILE.prepin</option>
+			<option value="epHIE.prepin">epHIE.prepin</option>
+			<option value="aminoct10.in">aminoct10.in</option>
+			<option value="epCYS.prepin">epCYS.prepin</option>
+			<option value="epGLN.prepin">epGLN.prepin</option>
+			<option value="epLYS.prepin">epLYS.prepin</option>
+			<option value="epARG.prepin">epARG.prepin</option>
+			<option value="epGLY.prepin">epGLY.prepin</option>
+			<option value="nma.in">nma.in</option>
+			<option value="uni_aminont03.in">uni_aminont03.in</option>
+			<option value="nucleic10.in">nucleic10.in</option>
+			<option value="epMET.prepin">epMET.prepin</option>
+			<option value="dna_nuc94-bsc0_chiOl4-ezOL1.in">dna_nuc94-bsc0_chiOl4-ezOL1.in</option>
+			<option value="aminont12.in">aminont12.in</option>
+			<option value="protonated_nucleic/RGE_noP.pdb">protonated_nucleic/RGE_noP.pdb</option>
+			<option value="protonated_nucleic/DA+_noP.pdb">protonated_nucleic/DA+_noP.pdb</option>
+			<option value="protonated_nucleic/DC+.pdb">protonated_nucleic/DC+.pdb</option>
+			<option value="protonated_nucleic/RC+_noP.pdb">protonated_nucleic/RC+_noP.pdb</option>
+			<option value="protonated_nucleic/DC+_noP.pdb">protonated_nucleic/DC+_noP.pdb</option>
+			<option value="protonated_nucleic/RC+.pdb">protonated_nucleic/RC+.pdb</option>
+			<option value="protonated_nucleic/RGE.pdb">protonated_nucleic/RGE.pdb</option>
+			<option value="protonated_nucleic/DTE_noP.pdb">protonated_nucleic/DTE_noP.pdb</option>
+			<option value="protonated_nucleic/DGE_noP.pdb">protonated_nucleic/DGE_noP.pdb</option>
+			<option value="protonated_nucleic/RG-.pdb">protonated_nucleic/RG-.pdb</option>
+			<option value="protonated_nucleic/RU-_noP.pdb">protonated_nucleic/RU-_noP.pdb</option>
+			<option value="protonated_nucleic/DT-_noP.pdb">protonated_nucleic/DT-_noP.pdb</option>
+			<option value="protonated_nucleic/RA+_noP.pdb">protonated_nucleic/RA+_noP.pdb</option>
+			<option value="protonated_nucleic/DA+.pdb">protonated_nucleic/DA+.pdb</option>
+			<option value="protonated_nucleic/RUE_noP.pdb">protonated_nucleic/RUE_noP.pdb</option>
+			<option value="protonated_nucleic/DTE.pdb">protonated_nucleic/DTE.pdb</option>
+			<option value="protonated_nucleic/DT-.pdb">protonated_nucleic/DT-.pdb</option>
+			<option value="protonated_nucleic/DG-.pdb">protonated_nucleic/DG-.pdb</option>
+			<option value="protonated_nucleic/RG-_noP.pdb">protonated_nucleic/RG-_noP.pdb</option>
+			<option value="protonated_nucleic/DG-_noP.pdb">protonated_nucleic/DG-_noP.pdb</option>
+			<option value="protonated_nucleic/DGE.pdb">protonated_nucleic/DGE.pdb</option>
+			<option value="protonated_nucleic/RU-.pdb">protonated_nucleic/RU-.pdb</option>
+			<option value="protonated_nucleic/RA+.pdb">protonated_nucleic/RA+.pdb</option>
+			<option value="protonated_nucleic/RUE.pdb">protonated_nucleic/RUE.pdb</option>
+			<option value="oldff/all_amino02.r1.in">oldff/all_amino02.r1.in</option>
+			<option value="oldff/all.in">oldff/all.in</option>
+			<option value="oldff/all_amino02.in">oldff/all_amino02.in</option>
+			<option value="oldff/opls_unict.in">oldff/opls_unict.in</option>
+			<option value="oldff/unint.in">oldff/unint.in</option>
+			<option value="oldff/all_aminoct94.in">oldff/all_aminoct94.in</option>
+			<option value="oldff/protein.amberua.in">oldff/protein.amberua.in</option>
+			<option value="oldff/protein.amberua.N.in">oldff/protein.amberua.N.in</option>
+			<option value="oldff/all_amino02EP.in">oldff/all_amino02EP.in</option>
+			<option value="oldff/all_aminont02EP.in">oldff/all_aminont02EP.in</option>
+			<option value="oldff/GLYCAM_06j.prep">oldff/GLYCAM_06j.prep</option>
+			<option value="oldff/opls_uni.in">oldff/opls_uni.in</option>
+			<option value="oldff/protein.amberua.C.in">oldff/protein.amberua.C.in</option>
+			<option value="oldff/all_nuc02.in">oldff/all_nuc02.in</option>
+			<option value="oldff/all_nuc94.in">oldff/all_nuc94.in</option>
+			<option value="oldff/all_amino94.in">oldff/all_amino94.in</option>
+			<option value="oldff/GLYCAM_06h.prep">oldff/GLYCAM_06h.prep</option>
+			<option value="oldff/opls_nacl.in">oldff/opls_nacl.in</option>
+			<option value="oldff/all_aminont94.in">oldff/all_aminont94.in</option>
+			<option value="oldff/allnt.in">oldff/allnt.in</option>
+			<option value="oldff/all_aminoct02EP.in">oldff/all_aminoct02EP.in</option>
+			<option value="oldff/all_aminoct02.in">oldff/all_aminoct02.in</option>
+			<option value="oldff/unict.in">oldff/unict.in</option>
+			<option value="oldff/allct.in">oldff/allct.in</option>
+			<option value="oldff/all_nuc02EP.in">oldff/all_nuc02EP.in</option>
+			<option value="oldff/opls_unint.in">oldff/opls_unint.in</option>
+			<option value="oldff/all_aminont02.in">oldff/all_aminont02.in</option>
+			<option value="oldff/na.amberua.in">oldff/na.amberua.in</option>
+			<option value="oldff/uni.in">oldff/uni.in</option>
+			<option value="nucleic12.redq.lib">nucleic12.redq.lib</option>
+			<option value="all_aminontfb15.lib">all_aminontfb15.lib</option>
+			<option value="ff03ua.cmd">ff03ua.cmd</option>
+			<option value="ff94.log">ff94.log</option>
+			<option value="amino19ipq_0.9_vac.lib">amino19ipq_0.9_vac.lib</option>
+			<option value="fb4box.off">fb4box.off</option>
+			<option value="aminont10.lib">aminont10.lib</option>
+			<option value="all_aminont03.lib">all_aminont03.lib</option>
+			<option value="tip4pbox.off">tip4pbox.off</option>
+			<option value="atomic_ions.cmd">atomic_ions.cmd</option>
+			<option value="8Mureabox.off">8Mureabox.off</option>
+			<option value="parmBSC1.lib">parmBSC1.lib</option>
+			<option value="GLYCAM_amino_06j_12SB.lib">GLYCAM_amino_06j_12SB.lib</option>
+			<option value="all_aminofb15.lib">all_aminofb15.lib</option>
+			<option value="amino14ipq.lib">amino14ipq.lib</option>
+			<option value="ff03.log">ff03.log</option>
+			<option value="aminoct19ipq_0.9.lib">aminoct19ipq_0.9.lib</option>
+			<option value="aminont19ipq_0.9_pol.lib">aminont19ipq_0.9_pol.lib</option>
+			<option value="all_aminont94.lib">all_aminont94.lib</option>
+			<option value="DNA_CI.lib">DNA_CI.lib</option>
+			<option value="all_nucleic94.lib">all_nucleic94.lib</option>
+			<option value="GLYCAM_aminont_06j_12SB.lib">GLYCAM_aminont_06j_12SB.lib</option>
+			<option value="atomic_ions.log">atomic_ions.log</option>
+			<option value="amino19ipq_0.9_pol.lib">amino19ipq_0.9_pol.lib</option>
+			<option value="amino19ipq_0.9.lib">amino19ipq_0.9.lib</option>
+			<option value="phos_amino94.lib">phos_amino94.lib</option>
+			<option value="tip4pewbox.off">tip4pewbox.off</option>
+			<option value="tip4pd.off">tip4pd.off</option>
+			<option value="mod_amino.lib">mod_amino.lib</option>
+			<option value="conste.lib">conste.lib</option>
+			<option value="nucleic10.lib">nucleic10.lib</option>
+			<option value="chcl3box.off">chcl3box.off</option>
+			<option value="aminont12.redq.lib">aminont12.redq.lib</option>
+			<option value="all_aminoct94.lib">all_aminoct94.lib</option>
+			<option value="amino15ipq-vac_10.0.lib">amino15ipq-vac_10.0.lib</option>
+			<option value="residues.RNA.parmCHI_YIL.bsc.lib">residues.RNA.parmCHI_YIL.bsc.lib</option>
+			<option value="tip3pbox.off">tip3pbox.off</option>
+			<option value="solvents.lib">solvents.lib</option>
+			<option value="aminoct12.redq.lib">aminoct12.redq.lib</option>
+			<option value="tip3pfbox.off">tip3pfbox.off</option>
+			<option value="DNA.OL15.lib">DNA.OL15.lib</option>
+			<option value="ff10.cmd">ff10.cmd</option>
+			<option value="aminoct12.lib">aminoct12.lib</option>
+			<option value="aminoct19ipq_0.9_pol.lib">aminoct19ipq_0.9_pol.lib</option>
+			<option value="tip5pbox.off">tip5pbox.off</option>
+			<option value="all_amino03.lib">all_amino03.lib</option>
+			<option value="atomic_ions.lib">atomic_ions.lib</option>
+			<option value="8Murea.readme">8Murea.readme</option>
+			<option value="ff03ua.log">ff03ua.log</option>
+			<option value="all_amino94.lib">all_amino94.lib</option>
+			<option value="uni_aminont03.lib">uni_aminont03.lib</option>
+			<option value="nucleic12.LJbb-RNA.lib">nucleic12.LJbb-RNA.lib</option>
+			<option value="nmabox.off">nmabox.off</option>
+			<option value="RNA.YIL.lib">RNA.YIL.lib</option>
+			<option value="xFPchromophores.lib">xFPchromophores.lib</option>
+			<option value="ff94.cmd">ff94.cmd</option>
+			<option value="nab.lib">nab.lib</option>
+			<option value="terminalphos.LJbb-RNA.lib">terminalphos.LJbb-RNA.lib</option>
+			<option value="opcbox.off">opcbox.off</option>
+			<option value="ff03.cmd">ff03.cmd</option>
+			<option value="music.lib">music.lib</option>
+			<option value="all_prot_nucleic10.lib">all_prot_nucleic10.lib</option>
+			<option value="aminoct19ipq_0.9_vac.lib">aminoct19ipq_0.9_vac.lib</option>
+			<option value="all_aminoAM1.lib">all_aminoAM1.lib</option>
+			<option value="all_amino94ildn.lib">all_amino94ildn.lib</option>
+			<option value="ions94.lib">ions94.lib</option>
+			<option value="all_aminoct03.lib">all_aminoct03.lib</option>
+			<option value="RNA.lib">RNA.lib</option>
+			<option value="spcebox.off">spcebox.off</option>
+			<option value="aminont19ipq_0.9_vac.lib">aminont19ipq_0.9_vac.lib</option>
+			<option value="nucleic12.lib">nucleic12.lib</option>
+			<option value="lipid17.lib">lipid17.lib</option>
+			<option value="terminal_monophosphate.lib">terminal_monophosphate.lib</option>
+			<option value="all_prot_nucleic10.log">all_prot_nucleic10.log</option>
+			<option value="ions94.cmd">ions94.cmd</option>
+			<option value="aminont15ipq_10.0.lib">aminont15ipq_10.0.lib</option>
+			<option value="aminocn15ipq_10.0.lib">aminocn15ipq_10.0.lib</option>
+			<option value="mk_nablib.cmd">mk_nablib.cmd</option>
+			<option value="all_modrna08.lib">all_modrna08.lib</option>
+			<option value="aminont12.lib">aminont12.lib</option>
+			<option value="pol3box.off">pol3box.off</option>
+			<option value="ff15ipq-m.lib">ff15ipq-m.lib</option>
+			<option value="phmd.lib">phmd.lib</option>
+			<option value="RNA_CI.lib">RNA_CI.lib</option>
+			<option value="solvents.log">solvents.log</option>
+			<option value="GLYCAM_aminoct_06j_12SB.lib">GLYCAM_aminoct_06j_12SB.lib</option>
+			<option value="amberdyes.lib">amberdyes.lib</option>
+			<option value="uni_aminoct03.lib">uni_aminoct03.lib</option>
+			<option value="phosaa14SB.lib">phosaa14SB.lib</option>
+			<option value="all_aminoPM3.lib">all_aminoPM3.lib</option>
+			<option value="meohbox.off">meohbox.off</option>
+			<option value="amino19.lib">amino19.lib</option>
+			<option value="fb3box.off">fb3box.off</option>
+			<option value="ff12SB.log">ff12SB.log</option>
+			<option value="Makefile">Makefile</option>
+			<option value="aminont14ipq.lib">aminont14ipq.lib</option>
+			<option value="aminoct10.lib">aminoct10.lib</option>
+			<option value="RNA_Shaw.lib">RNA_Shaw.lib</option>
+			<option value="mk_nablib.log">mk_nablib.log</option>
+			<option value="ff10.log">ff10.log</option>
+			<option value="constph.lib">constph.lib</option>
+			<option value="all_nucleic94.nmr.lib">all_nucleic94.nmr.lib</option>
+			<option value="mod_amino19.lib">mod_amino19.lib</option>
+			<option value="ions94.log">ions94.log</option>
+			<option value="aminoct15ipq_10.0.lib">aminoct15ipq_10.0.lib</option>
+			<option value="ff12SB.cmd">ff12SB.cmd</option>
+			<option value="nucleic12.ROC-RNA.lib">nucleic12.ROC-RNA.lib</option>
+			<option value="lipid14.lib">lipid14.lib</option>
+			<option value="amino10.lib">amino10.lib</option>
+			<option value="amino15ipq_10.0.lib">amino15ipq_10.0.lib</option>
+			<option value="all_aminont94ildn.lib">all_aminont94ildn.lib</option>
+			<option value="all_aminoctfb15.lib">all_aminoctfb15.lib</option>
+			<option value="parmBSC0.lib">parmBSC0.lib</option>
+			<option value="solvents.cmd">solvents.cmd</option>
+			<option value="spcfwbox.off">spcfwbox.off</option>
+			<option value="cph_nucleic_caps.lib">cph_nucleic_caps.lib</option>
+			<option value="opc3box.off">opc3box.off</option>
+			<option value="amino12.redq.lib">amino12.redq.lib</option>
+			<option value="aminont15ipq-vac_10.0.lib">aminont15ipq-vac_10.0.lib</option>
+			<option value="all_prot_nucleic10.cmd">all_prot_nucleic10.cmd</option>
+			<option value="phosaa19SB.lib">phosaa19SB.lib</option>
+			<option value="qspcfwbox.off">qspcfwbox.off</option>
+			<option value="uni_amino03.lib">uni_amino03.lib</option>
+			<option value="all_amino94.nmr.lib">all_amino94.nmr.lib</option>
+			<option value="aminoct14ipq.lib">aminoct14ipq.lib</option>
+			<option value="aminont19ipq_0.9.lib">aminont19ipq_0.9.lib</option>
+			<option value="aminoct15ipq-vac_10.0.lib">aminoct15ipq-vac_10.0.lib</option>
+			<option value="all_aminoct94ildn.lib">all_aminoct94ildn.lib</option>
+			<option value="amino12.lib">amino12.lib</option>
+			<option value="oldff/ff02.log">oldff/ff02.log</option>
+			<option value="oldff/phosphoaa10.lib">oldff/phosphoaa10.lib</option>
+			<option value="oldff/all_nucleic91.lib">oldff/all_nucleic91.lib</option>
+			<option value="oldff/all_aminoct02.lib">oldff/all_aminoct02.lib</option>
+			<option value="oldff/ff02.cmd">oldff/ff02.cmd</option>
+			<option value="oldff/all_nucleic02EP.lib">oldff/all_nucleic02EP.lib</option>
+			<option value="oldff/ions91.lib">oldff/ions91.lib</option>
+			<option value="oldff/dna.amberua.lib">oldff/dna.amberua.lib</option>
+			<option value="oldff/all_aminoct91.lib">oldff/all_aminoct91.lib</option>
+			<option value="oldff/all_aminoct02EP.lib">oldff/all_aminoct02EP.lib</option>
+			<option value="oldff/all_aminont91.lib">oldff/all_aminont91.lib</option>
+			<option value="oldff/all_nucleic02.lib">oldff/all_nucleic02.lib</option>
+			<option value="oldff/protein.amberua.lib">oldff/protein.amberua.lib</option>
+			<option value="oldff/ions91.cmd">oldff/ions91.cmd</option>
+			<option value="oldff/GLYCAM_aminoct_06j_10.lib">oldff/GLYCAM_aminoct_06j_10.lib</option>
+			<option value="oldff/rna.amberua.lib">oldff/rna.amberua.lib</option>
+			<option value="oldff/all_amino02.r1.lib">oldff/all_amino02.r1.lib</option>
+			<option value="oldff/ff02EP.log">oldff/ff02EP.log</option>
+			<option value="oldff/pro-dna91.nmr.off">oldff/pro-dna91.nmr.off</option>
+			<option value="oldff/phosphoaa10.readme">oldff/phosphoaa10.readme</option>
+			<option value="oldff/ff91.log">oldff/ff91.log</option>
+			<option value="oldff/all_aminont2011pol.lib">oldff/all_aminont2011pol.lib</option>
+			<option value="oldff/ff02EP.cmd">oldff/ff02EP.cmd</option>
+			<option value="oldff/all_aminont02.lib">oldff/all_aminont02.lib</option>
+			<option value="oldff/all_amino2011pol.lib">oldff/all_amino2011pol.lib</option>
+			<option value="oldff/ff91.cmd">oldff/ff91.cmd</option>
+			<option value="oldff/all_amino91.lib">oldff/all_amino91.lib</option>
+			<option value="oldff/GLYCAM_aminont_06j_10.lib">oldff/GLYCAM_aminont_06j_10.lib</option>
+			<option value="oldff/lipid11.lib">oldff/lipid11.lib</option>
+			<option value="oldff/all_amino02.lib">oldff/all_amino02.lib</option>
+			<option value="oldff/all_aminoct2011pol.lib">oldff/all_aminoct2011pol.lib</option>
+			<option value="oldff/all_aminont02EP.lib">oldff/all_aminont02EP.lib</option>
+			<option value="oldff/GLYCAM_amino_06j_10.lib">oldff/GLYCAM_amino_06j_10.lib</option>
+			<option value="oldff/all_amino02EP.lib">oldff/all_amino02EP.lib</option>
+			<option value="validate_torsions.py">validate_torsions.py</option>
+			<option value="frcmod.spcfw">frcmod.spcfw</option>
+			<option value="frcmod.ff99SP">frcmod.ff99SP</option>
+			<option value="frcmod.tip4pfb">frcmod.tip4pfb</option>
+			<option value="frcmod.ROC-RNA">frcmod.ROC-RNA</option>
+			<option value="frcmod.constph">frcmod.constph</option>
+			<option value="frcmod.ionsjc_spce">frcmod.ionsjc_spce</option>
+			<option value="frcmod.ions234lm_hfe_tip4pew">frcmod.ions234lm_hfe_tip4pew</option>
+			<option value="frcmod.shaw">frcmod.shaw</option>
+			<option value="frcmod.nma">frcmod.nma</option>
+			<option value="frcmod.ions1lm_iod">frcmod.ions1lm_iod</option>
+			<option value="parm91X.ua.dat">parm91X.ua.dat</option>
+			<option value="frcmod.ionsjc_tip3p">frcmod.ionsjc_tip3p</option>
+			<option value="frcmod.ions234lm_iod_tip3p">frcmod.ions234lm_iod_tip3p</option>
+			<option value="frcmod.ff12SB">frcmod.ff12SB</option>
+			<option value="frcmod.conste">frcmod.conste</option>
+			<option value="lj_1264_pol.dat">lj_1264_pol.dat</option>
+			<option value="frcmod.ions234lm_126_tip4pew">frcmod.ions234lm_126_tip4pew</option>
+			<option value="frcmod.fb15">frcmod.fb15</option>
+			<option value="frcmod.ionslm_126_fb3">frcmod.ionslm_126_fb3</option>
+			<option value="frcmod.phosaa19SB">frcmod.phosaa19SB</option>
+			<option value="frcmod.ff02pol.r1">frcmod.ff02pol.r1</option>
+			<option value="frcmod.ions1lm_1264_tip4pew">frcmod.ions1lm_1264_tip4pew</option>
+			<option value="frcmod.ff99SB">frcmod.ff99SB</option>
+			<option value="frcmod.tip3pfb">frcmod.tip3pfb</option>
+			<option value="frcmod.tip3p">frcmod.tip3p</option>
+			<option value="frcmod.meoh">frcmod.meoh</option>
+			<option value="GLYCAM_06EPb.dat">GLYCAM_06EPb.dat</option>
+			<option value="nucgen.dat">nucgen.dat</option>
+			<option value="frcmod.tip3pf">frcmod.tip3pf</option>
+			<option value="frcmod.opc">frcmod.opc</option>
+			<option value="frcmod.ff19SB_XXX">frcmod.ff19SB_XXX</option>
+			<option value="frcmod.tip4pew">frcmod.tip4pew</option>
+			<option value="frcmod.ff99SB14">frcmod.ff99SB14</option>
+			<option value="frcmod.pol3">frcmod.pol3</option>
+			<option value="frcmod.ff19SB">frcmod.ff19SB</option>
+			<option value="frcmod.ions234lm_hfe_spce">frcmod.ions234lm_hfe_spce</option>
+			<option value="frcmod.ionslm_iod_fb3">frcmod.ionslm_iod_fb3</option>
+			<option value="toyrna.dat">toyrna.dat</option>
+			<option value="frcmod.parmbsc0">frcmod.parmbsc0</option>
+			<option value="frcmod.ff14SB">frcmod.ff14SB</option>
+			<option value="frcmod.tip4pd">frcmod.tip4pd</option>
+			<option value="frcmod.ff03ua">frcmod.ff03ua</option>
+			<option value="frcmod.ionslm_hfe_opc3">frcmod.ionslm_hfe_opc3</option>
+			<option value="opls_parm.dat">opls_parm.dat</option>
+			<option value="frcmod.ionslm_hfe_fb3">frcmod.ionslm_hfe_fb3</option>
+			<option value="frcmod.ff99SBnmr">frcmod.ff99SBnmr</option>
+			<option value="frcmod.ions1lm_1264_tip3p">frcmod.ions1lm_1264_tip3p</option>
+			<option value="frcmod.opc3">frcmod.opc3</option>
+			<option value="frcmod.urea">frcmod.urea</option>
+			<option value="frcmod.phosaa10">frcmod.phosaa10</option>
+			<option value="parmAM1.dat">parmAM1.dat</option>
+			<option value="frcmod.ROC-RNA_const">frcmod.ROC-RNA_const</option>
+			<option value="frcmod.ionslm_hfe_opc">frcmod.ionslm_hfe_opc</option>
+			<option value="frcmod.parmbsc1">frcmod.parmbsc1</option>
+			<option value="parm91.dat">parm91.dat</option>
+			<option value="frcmod.tip5p">frcmod.tip5p</option>
+			<option value="frcmod.ionslm_126_opc">frcmod.ionslm_126_opc</option>
+			<option value="parm10.dat">parm10.dat</option>
+			<option value="parm19ipq.dat">parm19ipq.dat</option>
+			<option value="amberdyes.dat">amberdyes.dat</option>
+			<option value="lipid17.dat">lipid17.dat</option>
+			<option value="frcmod.ionslm_iod_opc3">frcmod.ionslm_iod_opc3</option>
+			<option value="frcmod.ions234lm_1264_tip4pew">frcmod.ions234lm_1264_tip4pew</option>
+			<option value="frcmod.chcl3">frcmod.chcl3</option>
+			<option value="frcmod.parmCHI_YIL">frcmod.parmCHI_YIL</option>
+			<option value="frcmod.ionslm_1264_fb3">frcmod.ionslm_1264_fb3</option>
+			<option value="frcmod.ions1lm_126_spce">frcmod.ions1lm_126_spce</option>
+			<option value="GLYCAM_06j.dat">GLYCAM_06j.dat</option>
+			<option value="frcmod.ff15ipq-m">frcmod.ff15ipq-m</option>
+			<option value="parm99EP.dat">parm99EP.dat</option>
+			<option value="parm94.dat">parm94.dat</option>
+			<option value="parm98.dat">parm98.dat</option>
+			<option value="frcmod.dc4">frcmod.dc4</option>
+			<option value="frcmod.spce">frcmod.spce</option>
+			<option value="frcmod.phosaa14SB">frcmod.phosaa14SB</option>
+			<option value="music.dat">music.dat</option>
+			<option value="parm15ipq_10.3.dat">parm15ipq_10.3.dat</option>
+			<option value="frcmod.ions234lm_126_spce">frcmod.ions234lm_126_spce</option>
+			<option value="frcmod.ions_charmm22">frcmod.ions_charmm22</option>
+			<option value="frcmod.spceb">frcmod.spceb</option>
+			<option value="frcmod.ionslm_iod_fb4">frcmod.ionslm_iod_fb4</option>
+			<option value="frcmod.ionslm_126_fb4">frcmod.ionslm_126_fb4</option>
+			<option value="frcmod.chiOL4">frcmod.chiOL4</option>
+			<option value="gaff.dat">gaff.dat</option>
+			<option value="lipid11.dat">lipid11.dat</option>
+			<option value="all_modrna08.frcmod">all_modrna08.frcmod</option>
+			<option value="frcmod.ions1lm_1264_spce">frcmod.ions1lm_1264_spce</option>
+			<option value="frcmod.ions234lm_1264_tip3p">frcmod.ions234lm_1264_tip3p</option>
+			<option value="frcmod.ff99SBildn">frcmod.ff99SBildn</option>
+			<option value="frcmod.ions1lm_126_tip3p">frcmod.ions1lm_126_tip3p</option>
+			<option value="frcmod.ff14SBmodAA">frcmod.ff14SBmodAA</option>
+			<option value="parm14ipq.dat">parm14ipq.dat</option>
+			<option value="gaff2.dat">gaff2.dat</option>
+			<option value="frcmod.ions234lm_1264_spce">frcmod.ions234lm_1264_spce</option>
+			<option value="frcmod.ionslm_1264_fb4">frcmod.ionslm_1264_fb4</option>
+			<option value="frcmod.ions234lm_iod_tip4pew">frcmod.ions234lm_iod_tip4pew</option>
+			<option value="frcmod.ionsff99_tip3p">frcmod.ionsff99_tip3p</option>
+			<option value="frcmod.vdWall">frcmod.vdWall</option>
+			<option value="frcmod.ions234lm_126_tip3p">frcmod.ions234lm_126_tip3p</option>
+			<option value="frcmod.parmbsc0_ezOL1">frcmod.parmbsc0_ezOL1</option>
+			<option value="frcmod.ionslm_126_opc3">frcmod.ionslm_126_opc3</option>
+			<option value="parm99.dat">parm99.dat</option>
+			<option value="frcmod.ff03">frcmod.ff03</option>
+			<option value="parmPM3.dat">parmPM3.dat</option>
+			<option value="parm96.dat">parm96.dat</option>
+			<option value="lipid14.dat">lipid14.dat</option>
+			<option value="frcmod.ionslm_1264_opc">frcmod.ionslm_1264_opc</option>
+			<option value="parm91X.dat">parm91X.dat</option>
+			<option value="frcmod.DNA.OL15">frcmod.DNA.OL15</option>
+			<option value="frcmod.ions1lm_126_tip4pew">frcmod.ions1lm_126_tip4pew</option>
+			<option value="parm19.dat">parm19.dat</option>
+			<option value="frcmod.ionsjc_tip4pew">frcmod.ionsjc_tip4pew</option>
+			<option value="frcmod.ionslm_hfe_fb4">frcmod.ionslm_hfe_fb4</option>
+			<option value="frcmod.ff99bsc0CG">frcmod.ff99bsc0CG</option>
+			<option value="frcmod.tip4p">frcmod.tip4p</option>
+			<option value="GLYCAM_06h.dat">GLYCAM_06h.dat</option>
+			<option value="frcmod.ions234lm_iod_spce">frcmod.ions234lm_iod_spce</option>
+			<option value="frcmod.ff19SBmodAA">frcmod.ff19SBmodAA</option>
+			<option value="frcmod.protonated_nucleic">frcmod.protonated_nucleic</option>
+			<option value="frcmod.RNA.LJbb">frcmod.RNA.LJbb</option>
+			<option value="opls.info">opls.info</option>
+			<option value="frcmod.phmd">frcmod.phmd</option>
+			<option value="frcmod.ionslm_1264_opc3">frcmod.ionslm_1264_opc3</option>
+			<option value="frcmod.ions234lm_hfe_tip3p">frcmod.ions234lm_hfe_tip3p</option>
+			<option value="frcmod.ionslm_iod_opc">frcmod.ionslm_iod_opc</option>
+			<option value="frcmod.qspcfw">frcmod.qspcfw</option>
+			<option value="frcmod.xFPchromophores">frcmod.xFPchromophores</option>
+			<option value="__pycache__/validate_torsions.cpython-39.pyc">__pycache__/validate_torsions.cpython-39.pyc</option>
+			<option value="leaprc.phosaa10">leaprc.phosaa10</option>
+			<option value="leaprc.protein.ff15ipq">leaprc.protein.ff15ipq</option>
+			<option value="leaprc.phosaa19SB">leaprc.phosaa19SB</option>
+			<option value="leaprc.protein.ff14SB">leaprc.protein.ff14SB</option>
+			<option value="leaprc.water.fb4">leaprc.water.fb4</option>
+			<option value="leaprc.protein.ff19SB_modAA">leaprc.protein.ff19SB_modAA</option>
+			<option value="leaprc.DNA.bsc1">leaprc.DNA.bsc1</option>
+			<option value="leaprc.GLYCAM_06EPb">leaprc.GLYCAM_06EPb</option>
+			<option value="leaprc.amberdyes">leaprc.amberdyes</option>
+			<option value="leaprc.protein.ff15ipq-vac">leaprc.protein.ff15ipq-vac</option>
+			<option value="leaprc.mimetic.ff15ipq">leaprc.mimetic.ff15ipq</option>
+			<option value="leaprc.protein.ff03ua">leaprc.protein.ff03ua</option>
+			<option value="leaprc.gaff2">leaprc.gaff2</option>
+			<option value="leaprc.gaff">leaprc.gaff</option>
+			<option value="leaprc.water.tip3p">leaprc.water.tip3p</option>
+			<option value="leaprc.protein.fb15">leaprc.protein.fb15</option>
+			<option value="leaprc.RNA.YIL">leaprc.RNA.YIL</option>
+			<option value="leaprc.water.tip4pd">leaprc.water.tip4pd</option>
+			<option value="leaprc.lipid17">leaprc.lipid17</option>
+			<option value="leaprc.water.tip4pew">leaprc.water.tip4pew</option>
+			<option value="leaprc.phosaa14SB">leaprc.phosaa14SB</option>
+			<option value="leaprc.lipid14">leaprc.lipid14</option>
+			<option value="leaprc.DNA.OL15">leaprc.DNA.OL15</option>
+			<option value="leaprc.constph">leaprc.constph</option>
+			<option value="leaprc.water.fb3">leaprc.water.fb3</option>
+			<option value="leaprc.water.spce">leaprc.water.spce</option>
+			<option value="leaprc.protein.ff19ipq">leaprc.protein.ff19ipq</option>
+			<option value="leaprc.protein.ff14SB_modAA">leaprc.protein.ff14SB_modAA</option>
+			<option value="leaprc.water.spceb">leaprc.water.spceb</option>
+			<option value="leaprc.ffAM1">leaprc.ffAM1</option>
+			<option value="leaprc.ffPM3">leaprc.ffPM3</option>
+			<option value="leaprc.music">leaprc.music</option>
+			<option value="leaprc.RNA.OL3">leaprc.RNA.OL3</option>
+			<option value="leaprc.conste">leaprc.conste</option>
+			<option value="leaprc.RNA.Shaw">leaprc.RNA.Shaw</option>
+			<option value="leaprc.RNA.LJbb">leaprc.RNA.LJbb</option>
+			<option value="leaprc.modrna08">leaprc.modrna08</option>
+			<option value="leaprc.GLYCAM_06j-1">leaprc.GLYCAM_06j-1</option>
+			<option value="leaprc.protein.ff14SBonlysc">leaprc.protein.ff14SBonlysc</option>
+			<option value="leaprc.water.opc">leaprc.water.opc</option>
+			<option value="leaprc.xFPchromophores">leaprc.xFPchromophores</option>
+			<option value="leaprc.water.opc3">leaprc.water.opc3</option>
+			<option value="leaprc.protein.ff19SB">leaprc.protein.ff19SB</option>
+			<option value="leaprc.protein.ff03.r1">leaprc.protein.ff03.r1</option>
+			<option value="leaprc.RNA.ROC">leaprc.RNA.ROC</option>
+			<option value="oldff/leaprc.ff94.nmr">oldff/leaprc.ff94.nmr</option>
+			<option value="oldff/leaprc.ff84">oldff/leaprc.ff84</option>
+			<option value="oldff/leaprc.ff99SBildn">oldff/leaprc.ff99SBildn</option>
+			<option value="oldff/leaprc.ff99SB">oldff/leaprc.ff99SB</option>
+			<option value="oldff/leaprc.ff98">oldff/leaprc.ff98</option>
+			<option value="oldff/leaprc.ff14SB.redq">oldff/leaprc.ff14SB.redq</option>
+			<option value="oldff/leaprc.rna.ff84">oldff/leaprc.rna.ff84</option>
+			<option value="oldff/leaprc.toyrna">oldff/leaprc.toyrna</option>
+			<option value="oldff/leaprc.rna.ff98">oldff/leaprc.rna.ff98</option>
+			<option value="oldff/leaprc.ff10">oldff/leaprc.ff10</option>
+			<option value="oldff/leaprc.lipid11">oldff/leaprc.lipid11</option>
+			<option value="oldff/leaprc.ff02">oldff/leaprc.ff02</option>
+			<option value="oldff/leaprc.ff02polEP.r0">oldff/leaprc.ff02polEP.r0</option>
+			<option value="oldff/leaprc.ff99">oldff/leaprc.ff99</option>
+			<option value="oldff/leaprc.ff99bsc0">oldff/leaprc.ff99bsc0</option>
+			<option value="oldff/leaprc.GLYCAM_06h-1">oldff/leaprc.GLYCAM_06h-1</option>
+			<option value="oldff/leaprc.rna.ff02EP">oldff/leaprc.rna.ff02EP</option>
+			<option value="oldff/leaprc.rna.ff94">oldff/leaprc.rna.ff94</option>
+			<option value="oldff/leaprc.GLYCAM_06j_10">oldff/leaprc.GLYCAM_06j_10</option>
+			<option value="oldff/leaprc.rna.ff99">oldff/leaprc.rna.ff99</option>
+			<option value="oldff/leaprc.ff86">oldff/leaprc.ff86</option>
+			<option value="oldff/leaprc.ff02polEP.r1">oldff/leaprc.ff02polEP.r1</option>
+			<option value="oldff/leaprc.DNA.bsc0">oldff/leaprc.DNA.bsc0</option>
+			<option value="oldff/leaprc.ff94">oldff/leaprc.ff94</option>
+			<option value="oldff/leaprc.parmbsc0_chiOL4_ezOL1">oldff/leaprc.parmbsc0_chiOL4_ezOL1</option>
+			<option value="oldff/leaprc.ff14SB">oldff/leaprc.ff14SB</option>
+			<option value="oldff/leaprc.GLYCAM_06EP">oldff/leaprc.GLYCAM_06EP</option>
+			<option value="oldff/leaprc.GLYCAM_04">oldff/leaprc.GLYCAM_04</option>
+			<option value="oldff/leaprc.ff02pol.r0">oldff/leaprc.ff02pol.r0</option>
+			<option value="oldff/leaprc.GLYCAM_06h-12SB">oldff/leaprc.GLYCAM_06h-12SB</option>
+			<option value="oldff/leaprc.rna.ff02">oldff/leaprc.rna.ff02</option>
+			<option value="oldff/leaprc.ff14ipq">oldff/leaprc.ff14ipq</option>
+			<option value="oldff/leaprc.GLYCAM_06h">oldff/leaprc.GLYCAM_06h</option>
+			<option value="oldff/leaprc.ff96">oldff/leaprc.ff96</option>
+			<option value="oldff/leaprc.GLYCAM_06">oldff/leaprc.GLYCAM_06</option>
+			<option value="oldff/leaprc.ff99SBnmr">oldff/leaprc.ff99SBnmr</option>
+			<option value="oldff/leaprc.ff02pol.r1">oldff/leaprc.ff02pol.r1</option>
+			<option value="oldff/leaprc.ff03">oldff/leaprc.ff03</option>
+		</param>
+	</xml>
+	<xml name="addingions">
+		<param name="arg_variable" label="Variable name of UNIT:" type="text" value="" help="The variable name that your system's components are assigned to."/>
+		<param name="arg_ion1" label="ion1 type" type="text" value="" help="Atom type for ion, as written in your chosen forcefield file. For example, choose Cl- for chloride."/>
+		<param name="arg__ion1" label="# of ion1 atoms to add" type="text" value="" help="Type 0 if you want to add enough ions to neutralize (if using the conventional 'addIons' command)."/>
+		<param name="arg_ion2" label="ion2 type" type="text" value="" help="Atom type for ion, as written in your chosen forcefield file. For example, choose Na+ for sodium."/>
+		<param name="arg__ion2" label="# of ion1 atoms to add" type="text" value="" help="Type 0 if you want to add enough ions to neutralize (if using the conventional 'addIons' command)."/>
+	</xml>
+	<xml name="unitvariable">
+		<param name="arg_unit" label="Variable name of UNIT:" type="text" value="" help="This is the variable name for the target UNIT, which can be a protein, ligand, or any other unique molecular component of the system, that is loaded into LEaP. "/>
+	</xml>
+	<xml name="container">
+		<param name="arg_container" label="container value" type="text" value="" help="UNIT/RESIDUE/ATOM to apply this to"/>
+	</xml>
+	<xml name="create">
+		<param name="createVar_assign" label="Assign to variable named" type="text" value=""/>
+		<param name="arg_name" label="name" type="text" value="" help="STRING"/>
+	</xml>
+	<xml name="object">
+		<param name="arg_obj" label="obj value" type="text" value="" help="The object can be an entire UNIT, or use periods to choose specific RESIDUES (UNIT.RESIDUE#) and/or ATOMS (UNIT.RESIDUE#.ATOMname) within it." />
+	</xml>
+	<xml name="newfile">
+		<param name="newfile" label="new file to save data into" type="text" />
+	</xml>
+	<xml name="loadfile" token_data_format="txt">
+		<param name="arg_filename" label="File" type="data" format="@DATA_FORMAT@" />
+	</xml>
+	<xml name="defaultsettings">
+		<param name="settingsvariable" label="Parameter to adjust" type="select" value="" help="">
+			<option value="PdbWriteCharges">PdbWriteCharges</option>
+			<option value="OldPrmtopFormat">OldPrmtopFormat</option>
+			<option value="Gibbs">Gibbs</option>
+			<option value="UseResIds">UseResIds</option>
+			<option value="Charmm">Charmm</option>
+			<option value="DeleteExtraPointAngles">DeleteExtraPointAngles</option>
+			<option value="FlexibleWater">FlexibleWater</option>
+			<option value="PBRadii">PBRadii</option>
+			<option value="Dielectric">Dielectric</option>
+			<option value="dipole_damp_factor">dipole_damp_factor</option>
+			<option value="sceescalefactor">sceescalefactor</option>
+			<option value="scnbscalefactor">scnbscalefactor</option>
+			<option value="CMAP">CMAP</option>
+			<option value="PHIPSIMAP">PHIPSIMAP</option>
+			<option value="ipol">ipol</option>
+			<option value="nocenter">nocenter</option>
+			<option value="reorder_residues">reorder_residues</option>
+		</param>
+	</xml>
+	<xml name="settingoptions">
+		<param name="usersetting" label="setting" type="select" help="If unsure of what to choose, please refer to the 'help' message for this command by scrolling down this page, to see which settings apply to each command.">
+			<option value="on">ON</option>
+			<option value="off">OFF</option>
+			<option value="bondi">bondi</option>
+			<option value="mbondi">mbondi</option>
+			<option value="mbondi2">mbondi2</option>
+			<option value="mbondi3">mbondi3</option>
+			<option value="parse">parse</option>
+			<option value="pbamber">pbamber</option>
+			<option value="amber6">amber6</option>
+			<option value="distance">distance</option>
+			<option value="constant">constant</option>
+			<option value="real">real</option>
+			<option value="integer">integer</option>
+		</param>
+	</xml>
+	<xml name="solvateparams">
+		<param name="arg_solute" label="solute UNIT" type="text" value="" help="This is the variable name for the target UNIT, which can be a protein, ligand, or any other unique molecular component of the system that is loaded into LEaP and you are now trying to solvate. "/>
+		<param name="arg_solvent" label="solvent UNIT" type="text" value="" help="The UNIT name for the water model you would like to use. Options include TIP3PBOX, TIP4PBOX, TIP4PEWBOX, and TIP5PBOX. "/>
+		<param name="arg_buffer" label="buffer value" type="text" value="" help="object"/>
+		<param name="arg_closeness" label="closeness value" type="text" value="" help="This is used to control the extent to which solvent atoms overlap solute atoms. The default value is 1.0, which allows no overlap. "/>
+	</xml>
+	<xml name="amberfiles_conditional">
+		<conditional name="file_source">
+			<param name="file_source_selector" type="select" label="Select file source">
+				<option value="history">From history</option>
+				<option value="builtin">From Built-in AmberTools data</option>
+			</param>
+			<when value="history">
+				<expand macro="loadfile" />
+			</when>
+			<when value="builtin">
+				<expand macro="builtin_amberfiles" />
+			</when>
+		</conditional>
+	</xml>
+	<xml name="citations">
+		<citations>
+			<citation type="doi">10.1002/jcc.20290</citation>
+			<citation type="bibtex">
+        @misc{ambertools, author = {D.A. Case, I.Y. Ben-Shalom, S.R. Brozell, D.S. Cerutti, T.E. Cheatham, III, V.W.D. Cruzeiro, T.A. Darden, R.E. Duke, D. Ghoreishi, M.K. Gilson, H. Gohlke, A.W. Goetz, D. Greene, R Harris, N. Homeyer, S. Izadi, A.
+        Kovalenko, T. Kurtzman, T.S. Lee, S. LeGrand, P. Li, C. Lin, J. Liu, T. Luchko, R. Luo, D.J. Mermelstein, K.M. Merz, Y. Miao, G. Monard, C. Nguyen, H. Nguyen, I. Omelyan, A. Onufriev, F. Pan, R. Qi, D.R. Roe, A. Roitberg, C. Sagui, S. Schott-Verdugo,
+        J. Shen, C.L. Simmerling, J. Smith, R. Salomon-Ferrer, J. Swails, R.C. Walker, J. Wang, H. Wei, R.M. Wolf, X. Wu, L. Xiao, D.M. York and P.A. Kollman }, year = {2018}, title = {AMBER 2018}, publisher = {University of California, San Francisco}, url =
+        {http://ambermd.org/CiteAmber.php}, }</citation>
+			<yield/>
+		</citations>
+	</xml>
+	<xml name="mmpbsa_citation">
+		<citation type="doi">10.1021/ct300418h</citation>
+	</xml>
+</macros>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/parmconv.py	Thu Jan 27 17:17:54 2022 +0000
@@ -0,0 +1,82 @@
+import argparse
+import io
+import sys
+from contextlib import redirect_stdout
+
+import parmed
+from parmed import amber, gromacs
+from parmed.tools.changeradii import ChRad
+
+
+def parse_command_line(argv):
+    parser = argparse.ArgumentParser()
+    parser.add_argument('--istr', help='input structure', required=True)
+    parser.add_argument('--itop', help='input topology file', required=True)
+    parser.add_argument('--istripmask', help='stripmask')
+    parser.add_argument('--iradii', required=True, help='parmed radii are \
+                        GB_RADII amber6,bondi, mbondi, mbondi2, mbondi3')
+    parser.add_argument('--removedihe', action='store_true',
+                        default=False, help='remove dihedrals with zero \
+                        periodicity')
+    parser.add_argument('--removebox', action='store_true',
+                        default=False, help='remove periodic box info')
+    parser.add_argument('--o_prmtop', help='AMBER output topology',
+                        required=True)
+    return parser.parse_args()
+
+
+def get_ids(dihedrals):
+    """
+    goes through dihedrals and looks for any with per=0.
+    returns a reverse sorted list of ids to be removed.
+    """
+    indices = []
+    for k, v in enumerate(dihedrals):
+        f = io.StringIO()
+        with redirect_stdout(f):
+            print(v)
+        if f.getvalue().find("per=0") != -1:
+            indices.append(k)
+    indices.sort(reverse=True)
+    return indices
+
+
+args = parse_command_line(sys.argv)
+
+gmx_top = gromacs.GromacsTopologyFile(args.itop)
+gmx_gro = gromacs.GromacsGroFile.parse(args.istr)
+
+if not args.removebox:
+    # keep box info
+    gmx_top.box = gmx_gro.box
+    gmx_top.positions = gmx_gro.positions
+
+
+if args.removedihe:
+    ids_to_remove = get_ids(gmx_top.dihedrals)
+    print("Original number of dihedrals %i" % len(gmx_top.dihedrals))
+    for i in ids_to_remove:
+        gmx_top.dihedrals.pop(i)
+    print("Update number of dihedrals %i" % len(gmx_top.dihedrals))
+
+if args.istripmask is not None:
+    if args.istripmask == "":
+        pass
+    else:
+        gmx_top.strip(args.istripmask)
+
+radii = str(args.iradii)
+parmed.tools.changeRadii(gmx_top, radii)
+amb_prm = amber.AmberParm.from_structure(gmx_top)
+parmed.tools.changeRadii(amb_prm, radii)
+
+if args.removebox:
+    amb_prm.pointers['IFBOX'] = 0
+
+ChRad(amb_prm, radii)
+for i, atom in enumerate(amb_prm.atoms):
+    amb_prm.parm_data['RADII'][i] = atom.solvent_radius
+    amb_prm.parm_data['SCREEN'][i] = atom.screen
+
+
+amb_prm.write_parm(args.o_prmtop)
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/template_mmpbsa_mmgbsa.j2	Thu Jan 27 17:17:54 2022 +0000
@@ -0,0 +1,21 @@
+# Template for mmpbsa in Galaxy
+#  
+&general
+startframe={{ allparams.startframe }}, endframe={{ allparams.endframe }}, interval={{ allparams.interval }},
+verbose=2, keep_files={{ allparams.keep_files | int }}, strip_mask={{ allparams.strip_mask }}, use_sander={{ allparams.use_sander | int }}, entropy={{ allparams.entropy | int }}, netcdf=1
+/
+{% if calcdetails.gb_pb_calc.calctype == 'gb' %}
+&gb
+igb={{ calcdetails.gb_pb_calc.igb }}, saltcon={{ calcdetails.gb_pb_calc.saltcon }}, surfoff={{ calcdetails.gb_pb_calc.surfoff }}, molsurf={{ calcdetails.gb_pb_calc.molsurf | int}}, probe={{ calcdetails.gb_pb_calc.probe }}, msoffset={{ calcdetails.gb_pb_calc.msoffset }}
+/
+{% elif calcdetails.gb_pb_calc.calctype == 'pb' %}
+&pb
+istrng={{ calcdetails.gb_pb_calc.istrng }}, fillratio={{ calcdetails.gb_pb_calc.fillratio }}, inp={{ calcdetails.gb_pb_calc.inp }}, radiopt={{ calcdetails.gb_pb_calc.radiopt }}, cavity_offset={{ calcdetails.gb_pb_calc.cavity_offset }}, scale={{ calcdetails.gb_pb_calc.scale }}, linit={{ calcdetails.gb_pb_calc.linit }}, prbrad={{ calcdetails.gb_pb_calc.prbrad }}
+/
+{% endif %}
+{% if calcdetails.decomposition.decomposition == 'yes' %}
+&decomp
+csv_format={{ calcdetails.decomposition.csv_format | int }}, dec_verbose={{ calcdetails.decomposition.dec_verbose }}, idecomp={{ calcdetails.decomposition.idecomp }}, 
+/
+{% endif %}
+
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/template_parmconv.j2	Thu Jan 27 17:17:54 2022 +0000
@@ -0,0 +1,14 @@
+# Template for parmconv in Galaxy
+{% if fmt == 'AMBER' %}
+parm {{ top_in }}
+{% elif fmt == 'GROMACS' %}
+gromber {{ top_in }} {{str_in}}
+{% elif fmt == 'CHARMM' %}
+chamber {{ top_in }} {{str_in}}
+{% else %}
+parm {{ top_in }}
+{% endif %}
+strip {{ stripmask }}
+summary
+outparm {{ prmtop_out }}
+quit
Binary file test-data/1err_desolvated_mini.nc has changed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/JZ4.mol2	Thu Jan 27 17:17:54 2022 +0000
@@ -0,0 +1,52 @@
+@<TRIPOS>MOLECULE
+/data/dnb02/galaxy_db/files/009/501/dataset_9501918.dat
+ 22 22 0 0 0
+SMALL
+GASTEIGER
+
+@<TRIPOS>ATOM
+      1  C4         0.7939    1.3702    2.1983 C.3   167  JZ4167     -0.0650
+      2  C7         6.5984    0.4172    2.4451 C.ar  167  JZ4167     -0.0613
+      3  C8         7.3182    0.9119    1.3612 C.ar  167  JZ4167     -0.0583
+      4  C9         6.6461    1.3322    0.2147 C.ar  167  JZ4167     -0.0199
+      5  C10        5.2522    1.2617    0.1608 C.ar  167  JZ4167      0.1200
+      6  C11        5.2053    0.3427    2.3837 C.ar  167  JZ4167     -0.0551
+      7  C12        4.5084    0.7745    1.2426 C.ar  167  JZ4167     -0.0060
+      8  C13        3.0004    0.6682    1.1973 C.3   167  JZ4167     -0.0245
+      9  C14        2.3079    1.4796    2.2975 C.3   167  JZ4167     -0.0518
+     10  OAB        4.5987    1.6713   -0.9677 O.3   167  JZ4167     -0.5065
+     11 H           0.3197    1.9287    3.0114 H     167  JZ4167      0.0230
+     12 H           0.4705    0.3267    2.2700 H     167  JZ4167      0.0230
+     13 H           0.4322    1.7786    1.2494 H     167  JZ4167      0.0230
+     14 H           7.1195    0.0849    3.3395 H     167  JZ4167      0.0618
+     15 H           8.4028    0.9664    1.4088 H     167  JZ4167      0.0619
+     16 H           7.2222    1.7087   -0.6246 H     167  JZ4167      0.0654
+     17 H           4.6638   -0.0590    3.2368 H     167  JZ4167      0.0621
+     18 H           2.7296   -0.3918    1.2845 H     167  JZ4167      0.0314
+     19 H           2.6172    0.9976    0.2247 H     167  JZ4167      0.0314
+     20 H           2.6004    2.5342    2.2276 H     167  JZ4167      0.0266
+     21 H           2.6177    1.1288    3.2886 H     167  JZ4167      0.0266
+     22 H           5.2561    1.9626   -1.6199 H     167  JZ4167      0.2921
+@<TRIPOS>BOND
+     1     4     3   ar
+     2     4     5   ar
+     3     3     2   ar
+     4    10     5    1
+     5     5     7   ar
+     6     2     6   ar
+     7     7     6   ar
+     8     7     8    1
+     9     8     9    1
+    10     9     1    1
+    11     1    11    1
+    12     1    12    1
+    13     1    13    1
+    14     2    14    1
+    15     3    15    1
+    16     4    16    1
+    17     6    17    1
+    18     8    18    1
+    19     8    19    1
+    20     9    20    1
+    21     9    21    1
+    22    10    22    1
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/LigA.mol2	Thu Jan 27 17:17:54 2022 +0000
@@ -0,0 +1,61 @@
+@<TRIPOS>MOLECULE
+LigA
+24 24 1 0 0 
+SMALL
+USER_CHARGES
+
+
+@<TRIPOS>ATOM
+  1 C       49.2110    26.9920    85.5530 C.2   1 <1>  -0.3000 
+  2 H       49.1050    28.0330    85.7020 H     1 <1>   0.1500 
+  3 H       48.8320    26.6060    84.6410 H     1 <1>   0.1500 
+  4 C       49.8460    26.1960    86.4430 C.2   1 <1>  -0.1733 
+  5 C       50.0590    24.7460    86.2630 C.2   1 <1>   1.0500 
+  6 O       50.4810    24.0440    87.2160 O.co2 1 <1>  -0.9000 
+  7 O       49.8330    24.2110    85.1490 O.co2 1 <1>  -0.9000 
+  8 O       50.3730    26.8140    87.5890 O.3   1 <1>  -0.3567 
+  9 C       51.7280    27.3660    87.5930 C.3   1 <1>   0.3382 
+ 10 H       51.8840    27.9250    88.5040 H     1 <1>   0.0800 
+ 11 C       51.8170    28.2920    86.3980 C.2   1 <1>  -0.2882 
+ 12 H       51.3990    29.2560    86.5300 H     1 <1>   0.1500 
+ 13 C       52.1840    27.8630    85.1670 C.2   1 <1>  -0.2500 
+ 14 C       52.8190    26.5610    85.0450 C.2   1 <1>  -0.1500 
+ 15 H       53.0370    26.2220    84.0630 H     1 <1>   0.1500 
+ 16 C       53.1170    25.8090    86.1190 C.2   1 <1>  -0.2882 
+ 17 H       53.5700    24.8590    86.0130 H     1 <1>   0.1500 
+ 18 C       52.7610    26.1980    87.5410 C.3   1 <1>   0.3382 
+ 19 H       52.3530    25.3480    88.0710 H     1 <1>   0.0800 
+ 20 O       54.0020    26.6280    88.1730 O.3   1 <1>  -0.6800 
+ 21 H       54.4570    27.1880    87.5220 H     1 <1>   0.4000 
+ 22 C       51.9410    28.6780    83.9640 C.2   1 <1>   1.0500 
+ 23 O       51.9100    29.9280    84.0860 O.co2 1 <1>  -0.9000 
+ 24 O       51.8570    28.1570    82.8230 O.co2 1 <1>  -0.9000 
+@<TRIPOS>BOND
+  1   1   2  1   
+  2   1   3  1   
+  3   1   4  2   
+  4   4   5  1   
+  5   4   8  1   
+  6   5   6  ar  
+  7   5   7  ar  
+  8   8   9  1   
+  9   9  10  1   
+ 10   9  11  1   
+ 11   9  18  1   
+ 12  11  12  1   
+ 13  11  13  2   
+ 14  13  14  1   
+ 15  13  22  1   
+ 16  14  15  1   
+ 17  14  16  2   
+ 18  16  17  1   
+ 19  16  18  1   
+ 20  18  19  1   
+ 21  18  20  1   
+ 22  20  21  1   
+ 23  22  23  ar  
+ 24  22  24  ar  
+@<TRIPOS>SUBSTRUCTURE
+  1 ****  13 GROUP 4 **** **** 0
+
+# MOE 2016.08 (io_trps.svl 2016.04)
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/LigA.pdb	Thu Jan 27 17:17:54 2022 +0000
@@ -0,0 +1,26 @@
+CRYST1    0.000    0.000    0.000  90.00  90.00  90.00 P 1           1
+ATOM      1  C   <1> X   1      49.211  26.992  85.553  0.00  0.00            
+ATOM      2  H   <1> X   1      49.105  28.033  85.702  0.00  0.00            
+ATOM      3  H   <1> X   1      48.832  26.606  84.641  0.00  0.00            
+ATOM      4  C   <1> X   1      49.846  26.196  86.443  0.00  0.00            
+ATOM      5  C   <1> X   1      50.059  24.746  86.263  0.00  0.00            
+ATOM      6  O   <1> X   1      50.481  24.044  87.216  0.00  0.00            
+ATOM      7  O   <1> X   1      49.833  24.211  85.149  0.00  0.00            
+ATOM      8  O   <1> X   1      50.373  26.814  87.589  0.00  0.00            
+ATOM      9  C   <1> X   1      51.728  27.366  87.593  0.00  0.00            
+ATOM     10  H   <1> X   1      51.884  27.925  88.504  0.00  0.00            
+ATOM     11  C   <1> X   1      51.817  28.292  86.398  0.00  0.00            
+ATOM     12  H   <1> X   1      51.399  29.256  86.530  0.00  0.00            
+ATOM     13  C   <1> X   1      52.184  27.863  85.167  0.00  0.00            
+ATOM     14  C   <1> X   1      52.819  26.561  85.045  0.00  0.00            
+ATOM     15  H   <1> X   1      53.037  26.222  84.063  0.00  0.00            
+ATOM     16  C   <1> X   1      53.117  25.809  86.119  0.00  0.00            
+ATOM     17  H   <1> X   1      53.570  24.859  86.013  0.00  0.00            
+ATOM     18  C   <1> X   1      52.761  26.198  87.541  0.00  0.00            
+ATOM     19  H   <1> X   1      52.353  25.348  88.071  0.00  0.00            
+ATOM     20  O   <1> X   1      54.002  26.628  88.173  0.00  0.00            
+ATOM     21  H   <1> X   1      54.457  27.188  87.522  0.00  0.00            
+ATOM     22  C   <1> X   1      51.941  28.678  83.964  0.00  0.00            
+ATOM     23  O   <1> X   1      51.910  29.928  84.086  0.00  0.00            
+ATOM     24  O   <1> X   1      51.857  28.157  82.823  0.00  0.00            
+END
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/LigA_output.mol2	Thu Jan 27 17:17:54 2022 +0000
@@ -0,0 +1,59 @@
+@<TRIPOS>MOLECULE
+MOL
+   24    24     1     0     0
+SMALL
+bcc
+
+
+@<TRIPOS>ATOM
+      1 C           49.2110    26.9920    85.5530 c2         1 MOL      -0.311000
+      2 H           49.1050    28.0330    85.7020 ha         1 MOL       0.109500
+      3 H1          48.8320    26.6060    84.6410 ha         1 MOL       0.109500
+      4 C1          49.8460    26.1960    86.4430 ce         1 MOL       0.022900
+      5 C2          50.0590    24.7460    86.2630 ce         1 MOL       0.384200
+      6 O           50.4810    24.0440    87.2160 o          1 MOL      -0.575500
+      7 O1          49.8330    24.2110    85.1490 o          1 MOL      -0.575500
+      8 O2          50.3730    26.8140    87.5890 os         1 MOL      -0.351900
+      9 C3          51.7280    27.3660    87.5930 c3         1 MOL       0.157300
+     10 H2          51.8840    27.9250    88.5040 h1         1 MOL       0.051700
+     11 C4          51.8170    28.2920    86.3980 c2         1 MOL      -0.174200
+     12 H3          51.3990    29.2560    86.5300 ha         1 MOL       0.141000
+     13 C5          52.1840    27.8630    85.1670 ce         1 MOL      -0.149200
+     14 C6          52.8190    26.5610    85.0450 ce         1 MOL      -0.081000
+     15 H4          53.0370    26.2220    84.0630 ha         1 MOL       0.142000
+     16 C7          53.1170    25.8090    86.1190 c2         1 MOL      -0.248200
+     17 H5          53.5700    24.8590    86.0130 ha         1 MOL       0.104000
+     18 C8          52.7610    26.1980    87.5410 c3         1 MOL       0.131300
+     19 H6          52.3530    25.3480    88.0710 h1         1 MOL       0.151700
+     20 O3          54.0020    26.6280    88.1730 oh         1 MOL      -0.611800
+     21 H7          54.4570    27.1880    87.5220 ho         1 MOL       0.374000
+     22 C9          51.9410    28.6780    83.9640 ce         1 MOL       0.376200
+     23 O4          51.9100    29.9280    84.0860 o          1 MOL      -0.587000
+     24 O5          51.8570    28.1570    82.8230 o          1 MOL      -0.587000
+@<TRIPOS>BOND
+     1     1     2 1   
+     2     1     3 1   
+     3     1     4 2   
+     4     4     5 1   
+     5     4     8 1   
+     6     5     6 2   
+     7     5     7 1   
+     8     8     9 1   
+     9     9    10 1   
+    10     9    11 1   
+    11     9    18 1   
+    12    11    12 1   
+    13    11    13 2   
+    14    13    14 1   
+    15    13    22 1   
+    16    14    15 1   
+    17    14    16 2   
+    18    16    17 1   
+    19    16    18 1   
+    20    18    19 1   
+    21    18    20 1   
+    22    20    21 1   
+    23    22    23 2   
+    24    22    24 1   
+@<TRIPOS>SUBSTRUCTURE
+     1 MOL         1 TEMP              0 ****  ****    0 ROOT
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/LigA_output.pdb	Thu Jan 27 17:17:54 2022 +0000
@@ -0,0 +1,24 @@
+ATOM      1  C   MOL     1      49.211  26.992  85.553  1.00  0.00           C
+ATOM      2  H   MOL     1      49.105  28.033  85.702  1.00  0.00           H
+ATOM      3  H1  MOL     1      48.832  26.606  84.641  1.00  0.00           H
+ATOM      4  C1  MOL     1      49.846  26.196  86.443  1.00  0.00           C
+ATOM      5  C2  MOL     1      50.059  24.746  86.263  1.00  0.00           C
+ATOM      6  O   MOL     1      50.481  24.044  87.216  1.00  0.00           O
+ATOM      7  O1  MOL     1      49.833  24.211  85.149  1.00  0.00           O
+ATOM      8  O2  MOL     1      50.373  26.814  87.589  1.00  0.00           O
+ATOM      9  C3  MOL     1      51.728  27.366  87.593  1.00  0.00           C
+ATOM     10  H2  MOL     1      51.884  27.925  88.504  1.00  0.00           H
+ATOM     11  C4  MOL     1      51.817  28.292  86.398  1.00  0.00           C
+ATOM     12  H3  MOL     1      51.399  29.256  86.530  1.00  0.00           H
+ATOM     13  C5  MOL     1      52.184  27.863  85.167  1.00  0.00           C
+ATOM     14  C6  MOL     1      52.819  26.561  85.045  1.00  0.00           C
+ATOM     15  H4  MOL     1      53.037  26.222  84.063  1.00  0.00           H
+ATOM     16  C7  MOL     1      53.117  25.809  86.119  1.00  0.00           C
+ATOM     17  H5  MOL     1      53.570  24.859  86.013  1.00  0.00           H
+ATOM     18  C8  MOL     1      52.761  26.198  87.541  1.00  0.00           C
+ATOM     19  H6  MOL     1      52.353  25.348  88.071  1.00  0.00           H
+ATOM     20  O3  MOL     1      54.002  26.628  88.173  1.00  0.00           O
+ATOM     21  H7  MOL     1      54.457  27.188  87.522  1.00  0.00           H
+ATOM     22  C9  MOL     1      51.941  28.678  83.964  1.00  0.00           C
+ATOM     23  O4  MOL     1      51.910  29.928  84.086  1.00  0.00           O
+ATOM     24  O5  MOL     1      51.857  28.157  82.823  1.00  0.00           O
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/LigA_output.top	Thu Jan 27 17:17:54 2022 +0000
@@ -0,0 +1,239 @@
+; base_GMX.itp created by acpype (v: 2020-10-24T12:16:34CEST) on Tue Feb 16 21:55:09 2021
+
+[ atomtypes ]
+;name   bond_type     mass     charge   ptype   sigma         epsilon       Amb
+ c2       c2          0.00000  0.00000   A     3.39967e-01   3.59824e-01 ; 1.91  0.0860
+ ha       ha          0.00000  0.00000   A     2.59964e-01   6.27600e-02 ; 1.46  0.0150
+ ce       ce          0.00000  0.00000   A     3.39967e-01   3.59824e-01 ; 1.91  0.0860
+ c        c           0.00000  0.00000   A     3.39967e-01   3.59824e-01 ; 1.91  0.0860
+ o        o           0.00000  0.00000   A     2.95992e-01   8.78640e-01 ; 1.66  0.2100
+ os       os          0.00000  0.00000   A     3.00001e-01   7.11280e-01 ; 1.68  0.1700
+ c3       c3          0.00000  0.00000   A     3.39967e-01   4.57730e-01 ; 1.91  0.1094
+ h1       h1          0.00000  0.00000   A     2.47135e-01   6.56888e-02 ; 1.39  0.0157
+ oh       oh          0.00000  0.00000   A     3.06647e-01   8.80314e-01 ; 1.72  0.2104
+ ho       ho          0.00000  0.00000   A     0.00000e+00   0.00000e+00 ; 0.00  0.0000
+
+[ moleculetype ]
+;name            nrexcl
+ base             3
+
+[ atoms ]
+;   nr  type  resi  res  atom  cgnr     charge      mass       ; qtot   bond_type
+     1   c2     1   MOL     C    1    -0.311000     12.01000 ; qtot -0.311
+     2   ha     1   MOL     H    2     0.109500      1.00800 ; qtot -0.202
+     3   ha     1   MOL    H1    3     0.109500      1.00800 ; qtot -0.092
+     4   ce     1   MOL    C1    4     0.022900     12.01000 ; qtot -0.069
+     5    c     1   MOL    C2    5     0.384200     12.01000 ; qtot 0.315
+     6    o     1   MOL     O    6    -0.575500     16.00000 ; qtot -0.260
+     7    o     1   MOL    O1    7    -0.575500     16.00000 ; qtot -0.836
+     8   os     1   MOL    O2    8    -0.351900     16.00000 ; qtot -1.188
+     9   c3     1   MOL    C3    9     0.157300     12.01000 ; qtot -1.031
+    10   h1     1   MOL    H2   10     0.051700      1.00800 ; qtot -0.979
+    11   c2     1   MOL    C4   11    -0.174200     12.01000 ; qtot -1.153
+    12   ha     1   MOL    H3   12     0.141000      1.00800 ; qtot -1.012
+    13   ce     1   MOL    C5   13    -0.149200     12.01000 ; qtot -1.161
+    14   ce     1   MOL    C6   14    -0.081000     12.01000 ; qtot -1.242
+    15   ha     1   MOL    H4   15     0.142000      1.00800 ; qtot -1.100
+    16   c2     1   MOL    C7   16    -0.248200     12.01000 ; qtot -1.348
+    17   ha     1   MOL    H5   17     0.104000      1.00800 ; qtot -1.244
+    18   c3     1   MOL    C8   18     0.131300     12.01000 ; qtot -1.113
+    19   h1     1   MOL    H6   19     0.151700      1.00800 ; qtot -0.961
+    20   oh     1   MOL    O3   20    -0.614800     16.00000 ; qtot -1.576
+    21   ho     1   MOL    H7   21     0.374000      1.00800 ; qtot -1.202
+    22    c     1   MOL    C9   22     0.376200     12.01000 ; qtot -0.826
+    23    o     1   MOL    O4   23    -0.587000     16.00000 ; qtot -1.413
+    24    o     1   MOL    O5   24    -0.587000     16.00000 ; qtot -2.000
+
+[ bonds ]
+;   ai     aj funct   r             k
+     1      2   1    1.0879e-01    2.8711e+05 ;      C - H     
+     1      3   1    1.0879e-01    2.8711e+05 ;      C - H1    
+     1      4   1    1.3461e-01    4.5798e+05 ;      C - C1    
+     4      5   1    1.4825e-01    2.9665e+05 ;     C1 - C2    
+     4      8   1    1.3710e-01    3.1372e+05 ;     C1 - O2    
+     5      6   1    1.2183e-01    5.3363e+05 ;     C2 - O     
+     5      7   1    1.2183e-01    5.3363e+05 ;     C2 - O1    
+     8      9   1    1.4316e-01    2.5824e+05 ;     O2 - C3    
+     9     10   1    1.0969e-01    2.7665e+05 ;     C3 - H2    
+     9     11   1    1.5095e-01    2.7347e+05 ;     C3 - C4    
+     9     18   1    1.5375e-01    2.5179e+05 ;     C3 - C8    
+    11     12   1    1.0879e-01    2.8711e+05 ;     C4 - H3    
+    11     13   1    1.3461e-01    4.5798e+05 ;     C4 - C5    
+    13     14   1    1.4574e-01    3.2033e+05 ;     C5 - C6    
+    13     22   1    1.4825e-01    2.9665e+05 ;     C5 - C9    
+    14     15   1    1.0883e-01    2.8660e+05 ;     C6 - H4    
+    14     16   1    1.3461e-01    4.5798e+05 ;     C6 - C7    
+    16     17   1    1.0879e-01    2.8711e+05 ;     C7 - H5    
+    16     18   1    1.5095e-01    2.7347e+05 ;     C7 - C8    
+    18     19   1    1.0969e-01    2.7665e+05 ;     C8 - H6    
+    18     20   1    1.4233e-01    2.6501e+05 ;     C8 - O3    
+    20     21   1    9.7300e-02    3.1079e+05 ;     O3 - H7    
+    22     23   1    1.2183e-01    5.3363e+05 ;     C9 - O4    
+    22     24   1    1.2183e-01    5.3363e+05 ;     C9 - O5    
+
+[ pairs ]
+;   ai     aj    funct
+     1      6      1 ;      C - O     
+     1      7      1 ;      C - O1    
+     1      9      1 ;      C - C3    
+     2      5      1 ;      H - C2    
+     2      8      1 ;      H - O2    
+     3      5      1 ;     H1 - C2    
+     3      8      1 ;     H1 - O2    
+     4     10      1 ;     C1 - H2    
+     4     11      1 ;     C1 - C4    
+     4     18      1 ;     C1 - C8    
+     5      9      1 ;     C2 - C3    
+     6      8      1 ;      O - O2    
+     7      8      1 ;     O1 - O2    
+     8     12      1 ;     O2 - H3    
+     8     13      1 ;     O2 - C5    
+     8     16      1 ;     O2 - C7    
+     8     19      1 ;     O2 - H6    
+     8     20      1 ;     O2 - O3    
+     9     14      1 ;     C3 - C6    
+     9     17      1 ;     C3 - H5    
+     9     21      1 ;     C3 - H7    
+     9     22      1 ;     C3 - C9    
+    10     12      1 ;     H2 - H3    
+    10     13      1 ;     H2 - C5    
+    10     16      1 ;     H2 - C7    
+    10     19      1 ;     H2 - H6    
+    10     20      1 ;     H2 - O3    
+    11     15      1 ;     C4 - H4    
+    11     16      1 ;     C4 - C7    
+    11     19      1 ;     C4 - H6    
+    11     20      1 ;     C4 - O3    
+    11     23      1 ;     C4 - O4    
+    11     24      1 ;     C4 - O5    
+    12     14      1 ;     H3 - C6    
+    12     18      1 ;     H3 - C8    
+    12     22      1 ;     H3 - C9    
+    13     17      1 ;     C5 - H5    
+    13     18      1 ;     C5 - C8    
+    14     19      1 ;     C6 - H6    
+    14     20      1 ;     C6 - O3    
+    14     23      1 ;     C6 - O4    
+    14     24      1 ;     C6 - O5    
+    15     17      1 ;     H4 - H5    
+    15     18      1 ;     H4 - C8    
+    15     22      1 ;     H4 - C9    
+    16     21      1 ;     C7 - H7    
+    16     22      1 ;     C7 - C9    
+    17     19      1 ;     H5 - H6    
+    17     20      1 ;     H5 - O3    
+    19     21      1 ;     H6 - H7    
+
+[ angles ]
+;   ai     aj     ak    funct   theta         cth
+     1      4      5      1    1.2042e+02    5.4810e+02 ;      C - C1     - C2    
+     1      4      8      1    1.2370e+02    5.8660e+02 ;      C - C1     - O2    
+     2      1      3      1    1.1690e+02    3.1882e+02 ;      H - C      - H1    
+     2      1      4      1    1.2045e+02    4.1422e+02 ;      H - C      - C1    
+     3      1      4      1    1.2045e+02    4.1422e+02 ;     H1 - C      - C1    
+     4      5      6      1    1.2320e+02    5.7572e+02 ;     C1 - C2     - O     
+     4      5      7      1    1.2320e+02    5.7572e+02 ;     C1 - C2     - O1    
+     4      8      9      1    1.1609e+02    5.2718e+02 ;     C1 - O2     - C3    
+     5      4      8      1    1.1467e+02    5.7404e+02 ;     C2 - C1     - O2    
+     6      5      7      1    1.3025e+02    6.5187e+02 ;      O - C2     - O1    
+     8      9     10      1    1.0978e+02    4.2509e+02 ;     O2 - C3     - H2    
+     8      9     11      1    1.0856e+02    5.7321e+02 ;     O2 - C3     - C4    
+     8      9     18      1    1.0797e+02    5.6902e+02 ;     O2 - C3     - C8    
+     9     11     12      1    1.1568e+02    3.8409e+02 ;     C3 - C4     - H3    
+     9     11     13      1    1.2315e+02    5.3555e+02 ;     C3 - C4     - C5    
+     9     18     16      1    1.1156e+02    5.3053e+02 ;     C3 - C8     - C7    
+     9     18     19      1    1.0956e+02    3.8828e+02 ;     C3 - C8     - H6    
+     9     18     20      1    1.1019e+02    5.6484e+02 ;     C3 - C8     - O3    
+    10      9     11      1    1.0996e+02    3.9413e+02 ;     H2 - C3     - C4    
+    10      9     18      1    1.0956e+02    3.8828e+02 ;     H2 - C3     - C8    
+    11      9     18      1    1.1156e+02    5.3053e+02 ;     C4 - C3     - C8    
+    11     13     14      1    1.2326e+02    5.4727e+02 ;     C4 - C5     - C6    
+    11     13     22      1    1.2042e+02    5.4810e+02 ;     C4 - C5     - C9    
+    12     11     13      1    1.2045e+02    4.1422e+02 ;     H3 - C4     - C5    
+    13     14     15      1    1.1665e+02    3.9497e+02 ;     C5 - C6     - H4    
+    13     14     16      1    1.2326e+02    5.4727e+02 ;     C5 - C6     - C7    
+    13     22     23      1    1.2320e+02    5.7572e+02 ;     C5 - C9     - O4    
+    13     22     24      1    1.2320e+02    5.7572e+02 ;     C5 - C9     - O5    
+    14     13     22      1    1.2098e+02    5.2802e+02 ;     C6 - C5     - C9    
+    14     16     17      1    1.2045e+02    4.1422e+02 ;     C6 - C7     - H5    
+    14     16     18      1    1.2315e+02    5.3555e+02 ;     C6 - C7     - C8    
+    15     14     16      1    1.1994e+02    4.1505e+02 ;     H4 - C6     - C7    
+    16     18     19      1    1.0996e+02    3.9413e+02 ;     C7 - C8     - H6    
+    16     18     20      1    1.1035e+02    5.7070e+02 ;     C7 - C8     - O3    
+    17     16     18      1    1.1568e+02    3.8409e+02 ;     H5 - C7     - C8    
+    18     20     21      1    1.0726e+02    3.9664e+02 ;     C8 - O3     - H7    
+    19     18     20      1    1.1026e+02    4.2593e+02 ;     H6 - C8     - O3    
+    23     22     24      1    1.3025e+02    6.5187e+02 ;     O4 - C9     - O5    
+
+[ dihedrals ] ; propers
+; for gromacs 4.5 or higher, using funct 9
+;    i      j      k      l   func   phase     kd      pn
+     1      4      5      6      9   180.00   9.10020   2 ;      C-    C1-    C2-     O
+     1      4      5      7      9   180.00   9.10020   2 ;      C-    C1-    C2-    O1
+     1      4      8      9      9   180.00   4.39320   2 ;      C-    C1-    O2-    C3
+     2      1      4      5      9   180.00  27.82360   2 ;      H-     C-    C1-    C2
+     2      1      4      8      9   180.00  27.82360   2 ;      H-     C-    C1-    O2
+     3      1      4      5      9   180.00  27.82360   2 ;     H1-     C-    C1-    C2
+     3      1      4      8      9   180.00  27.82360   2 ;     H1-     C-    C1-    O2
+     4      8      9     10      9     0.00   1.60387   3 ;     C1-    O2-    C3-    H2
+     4      8      9     11      9     0.00   1.60387   3 ;     C1-    O2-    C3-    C4
+     4      8      9     18      9     0.00   1.60387   3 ;     C1-    O2-    C3-    C8
+     5      4      8      9      9   180.00   4.39320   2 ;     C2-    C1-    O2-    C3
+     6      5      4      8      9   180.00   9.10020   2 ;      O-    C2-    C1-    O2
+     7      5      4      8      9   180.00   9.10020   2 ;     O1-    C2-    C1-    O2
+     8      9     11     12      9     0.00   0.00000   0 ;     O2-    C3-    C4-    H3
+     8      9     11     13      9     0.00   0.00000   0 ;     O2-    C3-    C4-    C5
+     8      9     18     16      9     0.00   0.65084   3 ;     O2-    C3-    C8-    C7
+     8      9     18     19      9     0.00   0.00000   0 ;     O2-    C3-    C8-    H6
+     8      9     18     19      9     0.00   1.04600   1 ;     O2-    C3-    C8-    H6
+     8      9     18     20      9     0.00   0.60250   3 ;     O2-    C3-    C8-    O3
+     8      9     18     20      9     0.00   4.91620   2 ;     O2-    C3-    C8-    O3
+     9     11     13     14      9   180.00  27.82360   2 ;     C3-    C4-    C5-    C6
+     9     11     13     22      9   180.00  27.82360   2 ;     C3-    C4-    C5-    C9
+     9     18     16     14      9     0.00   0.00000   0 ;     C3-    C8-    C7-    C6
+     9     18     16     17      9     0.00   0.00000   0 ;     C3-    C8-    C7-    H5
+     9     18     20     21      9     0.00   0.66944   3 ;     C3-    C8-    O3-    H7
+     9     18     20     21      9     0.00   1.04600   1 ;     C3-    C8-    O3-    H7
+    10      9     11     12      9     0.00   0.00000   0 ;     H2-    C3-    C4-    H3
+    10      9     11     13      9     0.00   0.00000   0 ;     H2-    C3-    C4-    C5
+    10      9     18     16      9     0.00   0.65084   3 ;     H2-    C3-    C8-    C7
+    10      9     18     19      9     0.00   0.65084   3 ;     H2-    C3-    C8-    H6
+    10      9     18     20      9     0.00   0.00000   0 ;     H2-    C3-    C8-    O3
+    10      9     18     20      9     0.00   1.04600   1 ;     H2-    C3-    C8-    O3
+    11      9     18     16      9     0.00   0.65084   3 ;     C4-    C3-    C8-    C7
+    11      9     18     19      9     0.00   0.65084   3 ;     C4-    C3-    C8-    H6
+    11      9     18     20      9     0.00   0.65084   3 ;     C4-    C3-    C8-    O3
+    11     13     14     15      9   180.00   4.18400   2 ;     C4-    C5-    C6-    H4
+    11     13     14     16      9   180.00   4.18400   2 ;     C4-    C5-    C6-    C7
+    11     13     22     23      9   180.00   9.10020   2 ;     C4-    C5-    C9-    O4
+    11     13     22     24      9   180.00   9.10020   2 ;     C4-    C5-    C9-    O5
+    12     11      9     18      9     0.00   0.00000   0 ;     H3-    C4-    C3-    C8
+    12     11     13     14      9   180.00  27.82360   2 ;     H3-    C4-    C5-    C6
+    12     11     13     22      9   180.00  27.82360   2 ;     H3-    C4-    C5-    C9
+    13     11      9     18      9     0.00   0.00000   0 ;     C5-    C4-    C3-    C8
+    13     14     16     17      9   180.00  27.82360   2 ;     C5-    C6-    C7-    H5
+    13     14     16     18      9   180.00  27.82360   2 ;     C5-    C6-    C7-    C8
+    14     13     22     23      9   180.00   9.10020   2 ;     C6-    C5-    C9-    O4
+    14     13     22     24      9   180.00   9.10020   2 ;     C6-    C5-    C9-    O5
+    14     16     18     19      9     0.00   0.00000   0 ;     C6-    C7-    C8-    H6
+    14     16     18     20      9     0.00   0.00000   0 ;     C6-    C7-    C8-    O3
+    15     14     13     22      9   180.00   4.18400   2 ;     H4-    C6-    C5-    C9
+    15     14     16     17      9   180.00  27.82360   2 ;     H4-    C6-    C7-    H5
+    15     14     16     18      9   180.00  27.82360   2 ;     H4-    C6-    C7-    C8
+    16     14     13     22      9   180.00   4.18400   2 ;     C7-    C6-    C5-    C9
+    16     18     20     21      9     0.00   0.69733   3 ;     C7-    C8-    O3-    H7
+    17     16     18     19      9     0.00   0.00000   0 ;     H5-    C7-    C8-    H6
+    17     16     18     20      9     0.00   0.00000   0 ;     H5-    C7-    C8-    O3
+    19     18     20     21      9     0.00   0.69733   3 ;     H6-    C8-    O3-    H7
+
+[ dihedrals ] ; impropers
+; treated as propers in GROMACS to use correct AMBER analytical function
+;    i      j      k      l   func   phase     kd      pn
+     3      1      2      4      4   180.00   4.60240   2 ;     H1-     C-     H-    C1
+     4      6      5      7      4   180.00   4.60240   2 ;     C1-     O-    C2-    O1
+     5      1      4      8      4   180.00   4.60240   2 ;     C2-     C-    C1-    O2
+     9     13     11     12      4   180.00   4.60240   2 ;     C3-    C5-    C4-    H3
+    13     23     22     24      4   180.00   4.60240   2 ;     C5-    O4-    C9-    O5
+    16     13     14     15      4   180.00   4.60240   2 ;     C7-    C5-    C6-    H4
+    18     14     16     17      4   180.00   4.60240   2 ;     C8-    C6-    C7-    H5
+    22     11     13     14      4   180.00   4.60240   2 ;     C9-    C4-    C5-    C6
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/LigA_output.txt	Thu Jan 27 17:17:54 2022 +0000
@@ -0,0 +1,21 @@
+Remark line goes here
+MASS
+
+BOND
+
+ANGLE
+
+DIHE
+
+IMPROPER
+c2-ha-c2-ha         1.1          180.0         2.0          Using the default value
+c2-c2-c2-os         1.1          180.0         2.0          Using the default value
+c2-o -c2-o          1.1          180.0         2.0          Using the default value
+c2-c3-c2-ha         1.1          180.0         2.0          Using the default value
+c2-c2-c2-c2         1.1          180.0         2.0          Using the default value
+c2-c2-c2-ha         1.1          180.0         2.0          Using the default value
+
+NONBON
+
+
+
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/LigA_prmchk.mol2	Thu Jan 27 17:17:54 2022 +0000
@@ -0,0 +1,59 @@
+@<TRIPOS>MOLECULE
+MOL
+   24    24     1     0     0
+SMALL
+bcc
+
+
+@<TRIPOS>ATOM
+      1 C           49.2110    26.9920    85.5530 c2         1 MOL      -0.412000
+      2 H           49.1050    28.0330    85.7020 ha         1 MOL       0.190500
+      3 H1          48.8320    26.6060    84.6410 ha         1 MOL       0.190500
+      4 C1          49.8460    26.1960    86.4430 c2         1 MOL       0.290000
+      5 C2          50.0590    24.7460    86.2630 c2         1 MOL       0.448000
+      6 O           50.4810    24.0440    87.2160 o          1 MOL      -0.224000
+      7 O1          49.8330    24.2110    85.1490 o          1 MOL      -0.224000
+      8 O2          50.3730    26.8140    87.5890 os         1 MOL      -0.260000
+      9 C3          51.7280    27.3660    87.5930 c3         1 MOL      -0.040000
+     10 H2          51.8840    27.9250    88.5040 h1         1 MOL       0.169000
+     11 C4          51.8170    28.2920    86.3980 c2         1 MOL      -0.190000
+     12 H3          51.3990    29.2560    86.5300 ha         1 MOL       0.188000
+     13 C5          52.1840    27.8630    85.1670 c2         1 MOL       0.171000
+     14 C6          52.8190    26.5610    85.0450 c2         1 MOL      -0.190000
+     15 H4          53.0370    26.2220    84.0630 ha         1 MOL       0.188000
+     16 C7          53.1170    25.8090    86.1190 c2         1 MOL      -0.040000
+     17 H5          53.5700    24.8590    86.0130 ha         1 MOL       0.169000
+     18 C8          52.7610    26.1980    87.5410 c3         1 MOL      -0.003000
+     19 H6          52.3530    25.3480    88.0710 h1         1 MOL       0.221000
+     20 O3          54.0020    26.6280    88.1730 oh         1 MOL      -0.280000
+     21 H7          54.4570    27.1880    87.5220 ho         1 MOL       0.215000
+     22 C9          51.9410    28.6780    83.9640 c2         1 MOL       0.366000
+     23 O4          51.9100    29.9280    84.0860 o          1 MOL      -0.472500
+     24 O5          51.8570    28.1570    82.8230 o          1 MOL      -0.472500
+@<TRIPOS>BOND
+     1     1     2 1   
+     2     1     3 1   
+     3     1     4 1   
+     4     4     5 1   
+     5     4     8 1   
+     6     5     6 1   
+     7     5     7 1   
+     8     8     9 1   
+     9     9    10 1   
+    10     9    11 1   
+    11     9    18 1   
+    12    11    12 1   
+    13    11    13 1   
+    14    13    14 1   
+    15    13    22 1   
+    16    14    15 1   
+    17    14    16 1   
+    18    16    17 1   
+    19    16    18 1   
+    20    18    19 1   
+    21    18    20 1   
+    22    20    21 1   
+    23    22    23 1   
+    24    22    24 1   
+@<TRIPOS>SUBSTRUCTURE
+     1 MOL         1 TEMP              0 ****  ****    0 ROOT
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/ZAFF.frcmod	Thu Jan 27 17:17:54 2022 +0000
@@ -0,0 +1,1332 @@
+ZAFF parameter set created by MTK++/MCPB 
+
+MASS
+ZN  65.400
+S1  32.060
+S2  32.060
+N1  14.010
+S3  32.060
+N2  14.010
+S4  32.060
+N3  14.010
+S5  32.060
+N4  14.010
+N5  14.010
+N6  14.010
+N7  14.010
+O1  16.000
+N8  14.010
+N9  14.010
+N0  14.010
+O2  16.000
+NT  14.010
+O3  16.000
+NY  14.010
+O4  16.000
+E1  14.010
+D1  16.000
+NQ  14.010
+NP  14.010
+E2  14.010
+D2  16.000
+NR  14.010
+
+BOND
+ZN-S1   32.69   2.426
+ZN-S2   51.79   2.355
+ZN-N1   29.24   2.176
+ZN-S3   50.99   2.353
+ZN-N2   35.80   2.145
+ZN-S4   67.39   2.305
+ZN-N3   50.10   2.089
+ZN-S5   88.50   2.262
+ZN-N4   62.61   2.047
+ZN-D1   41.86   2.109
+ZN-E1   36.30   2.133
+ZN-D2   76.81   1.986
+ZN-NQ   70.86   2.028
+ZN-NP   70.85   2.027
+ZN-E2   52.77   2.073
+ZN-NR   78.18   2.011
+ZN-N5   93.97   1.978
+ZN-N6   90.76   1.982
+ZN-N7   90.80   1.984
+ZN-O1   41.32   2.112
+ZN-N8   66.61   2.029
+ZN-N9   66.69   2.040
+ZN-N0   66.11   2.041
+ZN-O2  169.29   1.860
+ZN-NT  113.59   1.947
+ZN-O3   56.37   2.054
+ZN-NY  124.58   1.926
+ZN-O4   71.26   2.011
+CT-S1  237.00   1.810
+HS-S1  274.00   1.336
+CT-S2  237.00   1.810
+HS-S2  274.00   1.336
+CB-N1  414.00   1.391
+CK-N1  529.00   1.304
+CC-N1  410.00   1.394
+CR-N1  488.00   1.335
+CV-N1  410.00   1.394
+CT-S3  237.00   1.810
+HS-S3  274.00   1.336
+CB-N2  414.00   1.391
+CK-N2  529.00   1.304
+CC-N2  410.00   1.394
+CR-N2  488.00   1.335
+CV-N2  410.00   1.394
+CT-S4  237.00   1.810
+HS-S4  274.00   1.336
+CB-N3  414.00   1.391
+CK-N3  529.00   1.304
+CC-N3  410.00   1.394
+CR-N3  488.00   1.335
+CV-N3  410.00   1.394
+CT-S5  237.00   1.810
+HS-S5  274.00   1.336
+CB-N4  414.00   1.391
+CK-N4  529.00   1.304
+CC-N4  410.00   1.394
+CR-N4  488.00   1.335
+CV-N4  410.00   1.394
+CB-N5  414.00   1.391
+CK-N5  529.00   1.304
+CC-N5  410.00   1.394
+CR-N5  488.00   1.335
+CV-N5  410.00   1.394
+CB-N6  414.00   1.391
+CK-N6  529.00   1.304
+CC-N6  410.00   1.394
+CR-N6  488.00   1.335
+CV-N6  410.00   1.394
+CB-N7  414.00   1.391
+CK-N7  529.00   1.304
+CC-N7  410.00   1.394
+CR-N7  488.00   1.335
+CV-N7  410.00   1.394
+O1-HW  553.00   0.957
+CB-N8  414.00   1.391
+CK-N8  529.00   1.304
+CC-N8  410.00   1.394
+CR-N8  488.00   1.335
+CV-N8  410.00   1.394
+CB-N9  414.00   1.391
+CK-N9  529.00   1.304
+CC-N9  410.00   1.394
+CR-N9  488.00   1.335
+CV-N9  410.00   1.394
+CB-N0  414.00   1.391
+CK-N0  529.00   1.304
+CC-N0  410.00   1.394
+CR-N0  488.00   1.335
+CV-N0  410.00   1.394
+O2-HW  553.00   0.957
+O2-HO  566.02   0.967
+CB-NT  414.00   1.391
+CK-NT  529.00   1.304
+CC-NT  410.00   1.394
+CR-NT  488.00   1.335
+CV-NT  410.00   1.394
+O3-HW  553.00   0.957
+CB-NY  414.00   1.391
+CK-NY  529.00   1.304
+CC-NY  410.00   1.394
+CR-NY  488.00   1.335
+CV-NY  410.00   1.394
+O4-HW  553.00   0.957
+CB-E1  414.00   1.391
+CK-E1  529.00   1.304
+CC-E1  410.00   1.394
+CR-E1  488.00   1.335
+CV-E1  410.00   1.394
+C -D1  656.00   1.250
+D1-P   525.00   1.480
+CB-NQ  414.00   1.391
+CK-NQ  529.00   1.304
+CC-NQ  410.00   1.394
+CR-NQ  488.00   1.335
+CV-NQ  410.00   1.394
+CB-NP  414.00   1.391
+CK-NP  529.00   1.304
+CC-NP  410.00   1.394
+CR-NP  488.00   1.335
+CV-NP  410.00   1.394
+CB-E2  414.00   1.391
+CK-E2  529.00   1.304
+CC-E2  410.00   1.394
+CR-E2  488.00   1.335
+CV-E2  410.00   1.394
+C -D2  656.00   1.250
+D2-P   525.00   1.480
+CB-NR  414.00   1.391
+CK-NR  529.00   1.304
+CC-NR  410.00   1.394
+CR-NR  488.00   1.335
+CV-NR  410.00   1.394
+
+ANGL
+CT-S1-ZN   64.397     101.733
+S1-ZN-S1   35.729     109.472
+CT-S2-ZN   61.944     102.595
+CR-N1-ZN   56.635     118.830
+CC-N1-ZN   57.308     133.971
+S2-ZN-S2   35.018     115.180
+S2-ZN-N1   31.195     102.917
+CT-S3-ZN   61.716     101.845
+CR-N2-ZN   57.361     124.866
+S3-ZN-S3   33.795     116.417
+S3-ZN-N2   29.241     101.219
+CV-N2-ZN   59.513     128.392
+CT-S4-ZN   76.591     104.861
+CV-N3-ZN   47.416     129.669
+N3-ZN-N3   31.653     106.850
+S4-ZN-S4   22.852     135.466
+S4-ZN-N3   29.089     103.036
+CR-N3-ZN   48.496     123.515
+CT-S5-ZN   75.153     104.327
+CR-N4-ZN   54.251     126.180
+CV-N4-ZN   52.632     127.159
+S5-ZN-N4   33.446     112.979
+N4-ZN-N4   33.462     105.809
+CR-E1-ZN   53.751     119.546
+CC-E1-ZN   53.250     131.745
+C -D1-ZN   84.000      91.300
+E1-ZN-E1   23.827      96.990
+D1-ZN-E1   38.492      97.446
+D1-ZN-D1   79.308     155.527
+NP-ZN-E2   33.795     105.438
+CR-NQ-ZN   48.072     123.299
+C -D2-ZN   60.213     100.499
+CR-E2-ZN   52.444     115.956
+CC-E2-ZN   53.580     136.979
+CV-NP-ZN   49.953     130.128
+NQ-ZN-NP   38.170     120.039
+NQ-ZN-E2   36.052     105.366
+CR-NP-ZN   47.867     123.274
+CV-NQ-ZN   50.352     130.170
+D2-ZN-NQ   42.691     113.189
+D2-ZN-NP   40.339     113.247
+D2-ZN-E2   46.987      95.808
+CR-NR-ZN   54.533     127.273
+CV-NR-ZN   54.756     126.452
+NR-ZN-NR   34.279     109.482
+HW-O1-ZN   43.950     125.345
+N6-ZN-N7   35.185     113.479
+N6-ZN-O1   37.378     109.534
+CR-N5-ZN   57.485     128.302
+CR-N7-ZN   56.532     125.145
+CC-N7-ZN   58.174     127.730
+CV-N6-ZN   50.378     126.100
+N5-ZN-N6   28.483     109.645
+N5-ZN-N7   39.187     123.191
+N5-ZN-O1   28.218     100.449
+N7-ZN-O1   42.312      98.193
+CR-N6-ZN   49.810     127.604
+CV-N5-ZN   59.837     125.323
+HO-O2-ZN    4.382     116.648
+N9-ZN-N0   38.347     116.017
+N9-ZN-O2   40.020     102.656
+CR-N8-ZN   50.358     126.720
+CR-N0-ZN   48.113     113.620
+CC-N0-ZN   49.303     138.859
+CV-N9-ZN   47.210     139.179
+N8-ZN-N9   34.293     106.050
+N8-ZN-N0   30.984     107.502
+N8-ZN-O2   55.162     124.853
+N0-ZN-O2   47.934     100.380
+CR-N9-ZN   46.456     114.165
+CV-N8-ZN   47.761     126.592
+O3-ZN-O3   34.034      98.034
+NT-ZN-O3   34.930     108.521
+CR-NT-ZN   48.679     129.160
+HW-O3-ZN   43.666     124.703
+CV-NT-ZN   49.844     124.358
+NT-ZN-NT   37.220     121.973
+HW-O4-ZN   44.946     125.105
+CR-NY-ZN   49.584     125.908
+CC-NY-ZN   49.889     126.608
+O4-ZN-O4   34.202     100.669
+NY-ZN-O4   36.615     117.231
+H1-CT-S1   50.000     109.500
+CT-CT-S1   50.000     108.600
+CT-S1-HS   43.000      96.000
+HS-S1-HS   35.000      92.070
+H1-CT-S2   50.000     109.500
+CT-CT-S2   50.000     108.600
+CT-S2-HS   43.000      96.000
+HS-S2-HS   35.000      92.070
+C -CB-N1   70.000     130.000
+CA-CB-N1   70.000     132.400
+CB-CB-N1   70.000     110.400
+H5-CK-N1   35.000     123.050
+N*-CK-N1   70.000     113.900
+CT-CC-N1   70.000     120.000
+CW-CC-N1   70.000     120.000
+H5-CR-N1   35.000     120.000
+NA-CR-N1   70.000     120.000
+CC-CV-N1   70.000     120.000
+H4-CV-N1   35.000     120.000
+CB-N1-CK   70.000     103.800
+CC-N1-CR   70.000     117.000
+CR-N1-CV   70.000     117.000
+H1-CT-S3   50.000     109.500
+CT-CT-S3   50.000     108.600
+CT-S3-HS   43.000      96.000
+HS-S3-HS   35.000      92.070
+C -CB-N2   70.000     130.000
+CA-CB-N2   70.000     132.400
+CB-CB-N2   70.000     110.400
+H5-CK-N2   35.000     123.050
+N*-CK-N2   70.000     113.900
+CT-CC-N2   70.000     120.000
+CW-CC-N2   70.000     120.000
+H5-CR-N2   35.000     120.000
+NA-CR-N2   70.000     120.000
+CC-CV-N2   70.000     120.000
+H4-CV-N2   35.000     120.000
+CB-N2-CK   70.000     103.800
+CC-N2-CR   70.000     117.000
+CR-N2-CV   70.000     117.000
+H1-CT-S4   50.000     109.500
+CT-CT-S4   50.000     108.600
+CT-S4-HS   43.000      96.000
+HS-S4-HS   35.000      92.070
+C -CB-N3   70.000     130.000
+CA-CB-N3   70.000     132.400
+CB-CB-N3   70.000     110.400
+H5-CK-N3   35.000     123.050
+N*-CK-N3   70.000     113.900
+CT-CC-N3   70.000     120.000
+CW-CC-N3   70.000     120.000
+H5-CR-N3   35.000     120.000
+NA-CR-N3   70.000     120.000
+CC-CV-N3   70.000     120.000
+H4-CV-N3   35.000     120.000
+CB-N3-CK   70.000     103.800
+CC-N3-CR   70.000     117.000
+CR-N3-CV   70.000     117.000
+H1-CT-S5   50.000     109.500
+CT-CT-S5   50.000     108.600
+CT-S5-HS   43.000      96.000
+HS-S5-HS   35.000      92.070
+C -CB-N4   70.000     130.000
+CA-CB-N4   70.000     132.400
+CB-CB-N4   70.000     110.400
+H5-CK-N4   35.000     123.050
+N*-CK-N4   70.000     113.900
+CT-CC-N4   70.000     120.000
+CW-CC-N4   70.000     120.000
+H5-CR-N4   35.000     120.000
+NA-CR-N4   70.000     120.000
+CC-CV-N4   70.000     120.000
+H4-CV-N4   35.000     120.000
+CB-N4-CK   70.000     103.800
+CC-N4-CR   70.000     117.000
+CR-N4-CV   70.000     117.000
+C -CB-N5   70.000     130.000
+CA-CB-N5   70.000     132.400
+CB-CB-N5   70.000     110.400
+H5-CK-N5   35.000     123.050
+N*-CK-N5   70.000     113.900
+CT-CC-N5   70.000     120.000
+CW-CC-N5   70.000     120.000
+H5-CR-N5   35.000     120.000
+NA-CR-N5   70.000     120.000
+CC-CV-N5   70.000     120.000
+H4-CV-N5   35.000     120.000
+CB-N5-CK   70.000     103.800
+CC-N5-CR   70.000     117.000
+CR-N5-CV   70.000     117.000
+C -CB-N6   70.000     130.000
+CA-CB-N6   70.000     132.400
+CB-CB-N6   70.000     110.400
+H5-CK-N6   35.000     123.050
+N*-CK-N6   70.000     113.900
+CT-CC-N6   70.000     120.000
+CW-CC-N6   70.000     120.000
+H5-CR-N6   35.000     120.000
+NA-CR-N6   70.000     120.000
+CC-CV-N6   70.000     120.000
+H4-CV-N6   35.000     120.000
+CB-N6-CK   70.000     103.800
+CC-N6-CR   70.000     117.000
+CR-N6-CV   70.000     117.000
+C -CB-N7   70.000     130.000
+CA-CB-N7   70.000     132.400
+CB-CB-N7   70.000     110.400
+H5-CK-N7   35.000     123.050
+N*-CK-N7   70.000     113.900
+CT-CC-N7   70.000     120.000
+CW-CC-N7   70.000     120.000
+H5-CR-N7   35.000     120.000
+NA-CR-N7   70.000     120.000
+CC-CV-N7   70.000     120.000
+H4-CV-N7   35.000     120.000
+CB-N7-CK   70.000     103.800
+CC-N7-CR   70.000     117.000
+CR-N7-CV   70.000     117.000
+HW-O1-HW  100.000     104.520
+HW-HW-O1    0.000     127.740
+C -CB-N8   70.000     130.000
+CA-CB-N8   70.000     132.400
+CB-CB-N8   70.000     110.400
+H5-CK-N8   35.000     123.050
+N*-CK-N8   70.000     113.900
+CT-CC-N8   70.000     120.000
+CW-CC-N8   70.000     120.000
+H5-CR-N8   35.000     120.000
+NA-CR-N8   70.000     120.000
+CC-CV-N8   70.000     120.000
+H4-CV-N8   35.000     120.000
+CB-N8-CK   70.000     103.800
+CC-N8-CR   70.000     117.000
+CR-N8-CV   70.000     117.000
+C -CB-N9   70.000     130.000
+CA-CB-N9   70.000     132.400
+CB-CB-N9   70.000     110.400
+H5-CK-N9   35.000     123.050
+N*-CK-N9   70.000     113.900
+CT-CC-N9   70.000     120.000
+CW-CC-N9   70.000     120.000
+H5-CR-N9   35.000     120.000
+NA-CR-N9   70.000     120.000
+CC-CV-N9   70.000     120.000
+H4-CV-N9   35.000     120.000
+CB-N9-CK   70.000     103.800
+CC-N9-CR   70.000     117.000
+CR-N9-CV   70.000     117.000
+C -CB-N0   70.000     130.000
+CA-CB-N0   70.000     132.400
+CB-CB-N0   70.000     110.400
+H5-CK-N0   35.000     123.050
+N*-CK-N0   70.000     113.900
+CT-CC-N0   70.000     120.000
+CW-CC-N0   70.000     120.000
+H5-CR-N0   35.000     120.000
+NA-CR-N0   70.000     120.000
+CC-CV-N0   70.000     120.000
+H4-CV-N0   35.000     120.000
+CB-N0-CK   70.000     103.800
+CC-N0-CR   70.000     117.000
+CR-N0-CV   70.000     117.000
+O2-C -D1  126.557     121.174
+HW-O2-HW  100.000     104.520
+HW-HW-O2    0.000     127.740
+C -CB-NT   70.000     130.000
+CA-CB-NT   70.000     132.400
+CB-CB-NT   70.000     110.400
+H5-CK-NT   35.000     123.050
+N*-CK-NT   70.000     113.900
+CT-CC-NT   70.000     120.000
+CW-CC-NT   70.000     120.000
+H5-CR-NT   35.000     120.000
+NA-CR-NT   70.000     120.000
+CC-CV-NT   70.000     120.000
+H4-CV-NT   35.000     120.000
+CB-NT-CK   70.000     103.800
+CC-NT-CR   70.000     117.000
+CR-NT-CV   70.000     117.000
+HW-O3-HW  100.000     104.520
+HW-HW-O3    0.000     127.740
+C -CB-NY   70.000     130.000
+CA-CB-NY   70.000     132.400
+CB-CB-NY   70.000     110.400
+H5-CK-NY   35.000     123.050
+N*-CK-NY   70.000     113.900
+CT-CC-NY   70.000     120.000
+CW-CC-NY   70.000     120.000
+H5-CR-NY   35.000     120.000
+NA-CR-NY   70.000     120.000
+CC-CV-NY   70.000     120.000
+H4-CV-NY   35.000     120.000
+CB-NY-CK   70.000     103.800
+CC-NY-CR   70.000     117.000
+CR-NY-CV   70.000     117.000
+HW-O4-HW  100.000     104.520
+HW-HW-O4    0.000     127.740
+C -CB-E1   70.000     130.000
+CA-CB-E1   70.000     132.400
+CB-CB-E1   70.000     110.400
+H5-CK-E1   35.000     123.050
+N*-CK-E1   70.000     113.900
+CT-CC-E1   70.000     120.000
+CW-CC-E1   70.000     120.000
+H5-CR-E1   35.000     120.000
+NA-CR-E1   70.000     120.000
+CC-CV-E1   70.000     120.000
+H4-CV-E1   35.000     120.000
+CB-E1-CK   70.000     103.800
+CC-E1-CR   70.000     117.000
+CR-E1-CV   70.000     117.000
+CT-C -D1   70.000     117.000
+D1-C -D1   80.000     126.000
+D1-P -OH   45.000     108.230
+D1-P -D1   40.000     119.900
+D1-P -OS    0.000     108.230
+C -CB-NQ   70.000     130.000
+CA-CB-NQ   70.000     132.400
+CB-CB-NQ   70.000     110.400
+H5-CK-NQ   35.000     123.050
+N*-CK-NQ   70.000     113.900
+CT-CC-NQ   70.000     120.000
+CW-CC-NQ   70.000     120.000
+H5-CR-NQ   35.000     120.000
+NA-CR-NQ   70.000     120.000
+CC-CV-NQ   70.000     120.000
+H4-CV-NQ   35.000     120.000
+CB-NQ-CK   70.000     103.800
+CC-NQ-CR   70.000     117.000
+CR-NQ-CV   70.000     117.000
+C -CB-NP   70.000     130.000
+CA-CB-NP   70.000     132.400
+CB-CB-NP   70.000     110.400
+H5-CK-NP   35.000     123.050
+N*-CK-NP   70.000     113.900
+CT-CC-NP   70.000     120.000
+CW-CC-NP   70.000     120.000
+H5-CR-NP   35.000     120.000
+NA-CR-NP   70.000     120.000
+CC-CV-NP   70.000     120.000
+H4-CV-NP   35.000     120.000
+CB-NP-CK   70.000     103.800
+CC-NP-CR   70.000     117.000
+CR-NP-CV   70.000     117.000
+C -CB-E2   70.000     130.000
+CA-CB-E2   70.000     132.400
+CB-CB-E2   70.000     110.400
+H5-CK-E2   35.000     123.050
+N*-CK-E2   70.000     113.900
+CT-CC-E2   70.000     120.000
+CW-CC-E2   70.000     120.000
+H5-CR-E2   35.000     120.000
+NA-CR-E2   70.000     120.000
+CC-CV-E2   70.000     120.000
+H4-CV-E2   35.000     120.000
+CB-E2-CK   70.000     103.800
+CC-E2-CR   70.000     117.000
+CR-E2-CV   70.000     117.000
+CT-C -D2   70.000     117.000
+D2-C -D2   80.000     126.000
+D2-P -OH   45.000     108.230
+D2-P -D2   40.000     119.900
+D2-P -OS    0.000     108.230
+C -CB-NR   70.000     130.000
+CA-CB-NR   70.000     132.400
+CB-CB-NR   70.000     110.400
+H5-CK-NR   35.000     123.050
+N*-CK-NR   70.000     113.900
+CT-CC-NR   70.000     120.000
+CW-CC-NR   70.000     120.000
+H5-CR-NR   35.000     120.000
+NA-CR-NR   70.000     120.000
+CC-CV-NR   70.000     120.000
+H4-CV-NR   35.000     120.000
+CB-NR-CK   70.000     103.800
+CC-NR-CR   70.000     117.000
+CR-NR-CV   70.000     117.000
+
+DIHE
+S1-ZN-S1-CT   3    0.000         0.000           3.000
+CT-S2-ZN-N1   3    0.000         0.000           3.000
+S2-ZN-S2-CT   3    0.000         0.000           3.000
+S2-ZN-N1-CC   3    0.000         0.000           3.000
+S2-ZN-N1-CR   3    0.000         0.000           3.000
+CT-S3-ZN-N2   3    0.000         0.000           3.000
+S3-ZN-S3-CT   3    0.000         0.000           3.000
+S3-ZN-N2-CV   3    0.000         0.000           3.000
+S3-ZN-N2-CR   3    0.000         0.000           3.000
+S4-ZN-N3-CV   3    0.000         0.000           3.000
+S4-ZN-N3-CR   3    0.000         0.000           3.000
+CT-S4-ZN-N3   3    0.000         0.000           3.000
+N3-ZN-N3-CV   3    0.000         0.000           3.000
+N3-ZN-N3-CR   3    0.000         0.000           3.000
+CT-S4-ZN-S4   3    0.000         0.000           3.000
+N4-ZN-N4-CV   3    0.000         0.000           3.000
+N4-ZN-N4-CR   3    0.000         0.000           3.000
+CT-S5-ZN-N4   3    0.000         0.000           3.000
+S5-ZN-N4-CV   3    0.000         0.000           3.000
+S5-ZN-N4-CR   3    0.000         0.000           3.000
+D1-ZN-D1-C    3    0.000         0.000           3.000
+D1-ZN-E1-CC   3    0.000         0.000           3.000
+D1-ZN-E1-CR   3    0.000         0.000           3.000
+CT-C -D1-ZN   3    0.000         0.000           3.000
+E1-ZN-E1-CC   3    0.000         0.000           3.000
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+C -D2-ZN-NQ   3    0.000         0.000           3.000
+C -D2-ZN-NP   3    0.000         0.000           3.000
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+NY-ZN-O4-HW   3    0.000         0.000           3.000
+CR-NY-ZN-O4   3    0.000         0.000           3.000
+CC-NY-ZN-O4   3    0.000         0.000           3.000
+NY-ZN-O4-HW   3    0.000         0.000           3.000
+CR-NY-ZN-O4   3    0.000         0.000           3.000
+CC-NY-ZN-O4   3    0.000         0.000           3.000
+NY-ZN-O4-HW   3    0.000         0.000           3.000
+X -CB-E1-X    2    5.100       180.000           2.000
+X -CK-E1-X    2   20.000       180.000           2.000
+X -CC-E1-X    2    4.800       180.000           2.000
+X -CR-E1-X    2   10.000       180.000           2.000
+X -CV-E1-X    2    4.800       180.000           2.000
+D1-ZN-E1-CC   3    0.000         0.000           3.000
+D1-ZN-E1-CR   3    0.000         0.000           3.000
+E1-ZN-E1-CC   3    0.000         0.000           3.000
+E1-ZN-E1-CR   3    0.000         0.000           3.000
+C -D1-ZN-E1   3    0.000         0.000           3.000
+D1-ZN-E1-CC   3    0.000         0.000           3.000
+D1-ZN-E1-CR   3    0.000         0.000           3.000
+E1-ZN-E1-CC   3    0.000         0.000           3.000
+E1-ZN-E1-CR   3    0.000         0.000           3.000
+C -D1-ZN-E1   3    0.000         0.000           3.000
+D1-ZN-D1-C    3    0.000         0.000           3.000
+D1-ZN-E1-CC   3    0.000         0.000           3.000
+D1-ZN-E1-CR   3    0.000         0.000           3.000
+CT-C -D1-ZN   3    0.000         0.000           3.000
+O2-C -D1-ZN   3    0.000         0.000           3.000
+C -D1-ZN-E1   3    0.000         0.000           3.000
+D1-ZN-D1-C    3    0.000         0.000           3.000
+D1-ZN-E1-CC   3    0.000         0.000           3.000
+D1-ZN-E1-CR   3    0.000         0.000           3.000
+CT-C -D1-ZN   3    0.000         0.000           3.000
+O2-C -D1-ZN   3    0.000         0.000           3.000
+C -D1-ZN-E1   3    0.000         0.000           3.000
+O2-C -D1-ZN   3    0.000         0.000           3.000
+O2-C -D1-ZN   3    0.000         0.000           3.000
+D1-ZN-E1-CC   3    0.000         0.000           3.000
+D1-ZN-E1-CR   3    0.000         0.000           3.000
+C -D1-ZN-E1   3    0.000         0.000           3.000
+D1-ZN-E1-CC   3    0.000         0.000           3.000
+D1-ZN-E1-CR   3    0.000         0.000           3.000
+C -D1-ZN-E1   3    0.000         0.000           3.000
+X -CB-NQ-X    2    5.100       180.000           2.000
+X -CK-NQ-X    2   20.000       180.000           2.000
+X -CC-NQ-X    2    4.800       180.000           2.000
+X -CR-NQ-X    2   10.000       180.000           2.000
+X -CV-NQ-X    2    4.800       180.000           2.000
+CR-NQ-ZN-NP   3    0.000         0.000           3.000
+CR-NQ-ZN-E2   3    0.000         0.000           3.000
+CV-NQ-ZN-NP   3    0.000         0.000           3.000
+CV-NQ-ZN-E2   3    0.000         0.000           3.000
+C -D2-ZN-NQ   3    0.000         0.000           3.000
+D2-ZN-NQ-CV   3    0.000         0.000           3.000
+D2-ZN-NQ-CR   3    0.000         0.000           3.000
+NQ-ZN-NP-CV   3    0.000         0.000           3.000
+NQ-ZN-NP-CR   3    0.000         0.000           3.000
+NQ-ZN-E2-CC   3    0.000         0.000           3.000
+NQ-ZN-E2-CR   3    0.000         0.000           3.000
+CR-NQ-ZN-NP   3    0.000         0.000           3.000
+CR-NQ-ZN-E2   3    0.000         0.000           3.000
+CV-NQ-ZN-NP   3    0.000         0.000           3.000
+CV-NQ-ZN-E2   3    0.000         0.000           3.000
+C -D2-ZN-NQ   3    0.000         0.000           3.000
+D2-ZN-NQ-CV   3    0.000         0.000           3.000
+D2-ZN-NQ-CR   3    0.000         0.000           3.000
+NQ-ZN-NP-CV   3    0.000         0.000           3.000
+NQ-ZN-NP-CR   3    0.000         0.000           3.000
+NQ-ZN-E2-CC   3    0.000         0.000           3.000
+NQ-ZN-E2-CR   3    0.000         0.000           3.000
+X -CB-NP-X    2    5.100       180.000           2.000
+X -CK-NP-X    2   20.000       180.000           2.000
+X -CC-NP-X    2    4.800       180.000           2.000
+X -CR-NP-X    2   10.000       180.000           2.000
+X -CV-NP-X    2    4.800       180.000           2.000
+CR-NQ-ZN-NP   3    0.000         0.000           3.000
+CV-NP-ZN-E2   3    0.000         0.000           3.000
+CV-NQ-ZN-NP   3    0.000         0.000           3.000
+C -D2-ZN-NP   3    0.000         0.000           3.000
+D2-ZN-NP-CV   3    0.000         0.000           3.000
+D2-ZN-NP-CR   3    0.000         0.000           3.000
+CR-NP-ZN-E2   3    0.000         0.000           3.000
+NQ-ZN-NP-CV   3    0.000         0.000           3.000
+NQ-ZN-NP-CR   3    0.000         0.000           3.000
+NP-ZN-E2-CC   3    0.000         0.000           3.000
+NP-ZN-E2-CR   3    0.000         0.000           3.000
+CR-NQ-ZN-NP   3    0.000         0.000           3.000
+CV-NP-ZN-E2   3    0.000         0.000           3.000
+CV-NQ-ZN-NP   3    0.000         0.000           3.000
+C -D2-ZN-NP   3    0.000         0.000           3.000
+D2-ZN-NP-CV   3    0.000         0.000           3.000
+D2-ZN-NP-CR   3    0.000         0.000           3.000
+CR-NP-ZN-E2   3    0.000         0.000           3.000
+NQ-ZN-NP-CV   3    0.000         0.000           3.000
+NQ-ZN-NP-CR   3    0.000         0.000           3.000
+NP-ZN-E2-CC   3    0.000         0.000           3.000
+NP-ZN-E2-CR   3    0.000         0.000           3.000
+CR-NQ-ZN-NP   3    0.000         0.000           3.000
+CV-NQ-ZN-NP   3    0.000         0.000           3.000
+NQ-ZN-NP-CV   3    0.000         0.000           3.000
+NQ-ZN-NP-CR   3    0.000         0.000           3.000
+CR-NQ-ZN-NP   3    0.000         0.000           3.000
+CV-NQ-ZN-NP   3    0.000         0.000           3.000
+NQ-ZN-NP-CV   3    0.000         0.000           3.000
+NQ-ZN-NP-CR   3    0.000         0.000           3.000
+X -CB-E2-X    2    5.100       180.000           2.000
+X -CK-E2-X    2   20.000       180.000           2.000
+X -CC-E2-X    2    4.800       180.000           2.000
+X -CR-E2-X    2   10.000       180.000           2.000
+X -CV-E2-X    2    4.800       180.000           2.000
+CR-NQ-ZN-E2   3    0.000         0.000           3.000
+CV-NP-ZN-E2   3    0.000         0.000           3.000
+CV-NQ-ZN-E2   3    0.000         0.000           3.000
+C -D2-ZN-E2   3    0.000         0.000           3.000
+D2-ZN-E2-CC   3    0.000         0.000           3.000
+D2-ZN-E2-CR   3    0.000         0.000           3.000
+CR-NP-ZN-E2   3    0.000         0.000           3.000
+NQ-ZN-E2-CC   3    0.000         0.000           3.000
+NQ-ZN-E2-CR   3    0.000         0.000           3.000
+NP-ZN-E2-CC   3    0.000         0.000           3.000
+NP-ZN-E2-CR   3    0.000         0.000           3.000
+CR-NQ-ZN-E2   3    0.000         0.000           3.000
+CV-NP-ZN-E2   3    0.000         0.000           3.000
+CV-NQ-ZN-E2   3    0.000         0.000           3.000
+C -D2-ZN-E2   3    0.000         0.000           3.000
+D2-ZN-E2-CC   3    0.000         0.000           3.000
+D2-ZN-E2-CR   3    0.000         0.000           3.000
+CR-NP-ZN-E2   3    0.000         0.000           3.000
+NQ-ZN-E2-CC   3    0.000         0.000           3.000
+NQ-ZN-E2-CR   3    0.000         0.000           3.000
+NP-ZN-E2-CC   3    0.000         0.000           3.000
+NP-ZN-E2-CR   3    0.000         0.000           3.000
+CR-NQ-ZN-E2   3    0.000         0.000           3.000
+CV-NQ-ZN-E2   3    0.000         0.000           3.000
+NQ-ZN-E2-CC   3    0.000         0.000           3.000
+NQ-ZN-E2-CR   3    0.000         0.000           3.000
+CR-NQ-ZN-E2   3    0.000         0.000           3.000
+CV-NQ-ZN-E2   3    0.000         0.000           3.000
+NQ-ZN-E2-CC   3    0.000         0.000           3.000
+NQ-ZN-E2-CR   3    0.000         0.000           3.000
+CV-NP-ZN-E2   3    0.000         0.000           3.000
+CR-NP-ZN-E2   3    0.000         0.000           3.000
+NP-ZN-E2-CC   3    0.000         0.000           3.000
+NP-ZN-E2-CR   3    0.000         0.000           3.000
+CV-NP-ZN-E2   3    0.000         0.000           3.000
+CR-NP-ZN-E2   3    0.000         0.000           3.000
+NP-ZN-E2-CC   3    0.000         0.000           3.000
+NP-ZN-E2-CR   3    0.000         0.000           3.000
+CT-C -D2-ZN   3    0.000         0.000           3.000
+D2-C -D2-ZN   3    0.000         0.000           3.000
+C -D2-ZN-NQ   3    0.000         0.000           3.000
+C -D2-ZN-NP   3    0.000         0.000           3.000
+C -D2-ZN-E2   3    0.000         0.000           3.000
+D2-ZN-NQ-CV   3    0.000         0.000           3.000
+D2-ZN-NQ-CR   3    0.000         0.000           3.000
+D2-ZN-NP-CV   3    0.000         0.000           3.000
+D2-ZN-NP-CR   3    0.000         0.000           3.000
+D2-ZN-E2-CC   3    0.000         0.000           3.000
+D2-ZN-E2-CR   3    0.000         0.000           3.000
+CT-C -D2-ZN   3    0.000         0.000           3.000
+D2-C -D2-ZN   3    0.000         0.000           3.000
+C -D2-ZN-NQ   3    0.000         0.000           3.000
+C -D2-ZN-NP   3    0.000         0.000           3.000
+C -D2-ZN-E2   3    0.000         0.000           3.000
+D2-ZN-NQ-CV   3    0.000         0.000           3.000
+D2-ZN-NQ-CR   3    0.000         0.000           3.000
+D2-ZN-NP-CV   3    0.000         0.000           3.000
+D2-ZN-NP-CR   3    0.000         0.000           3.000
+D2-ZN-E2-CC   3    0.000         0.000           3.000
+D2-ZN-E2-CR   3    0.000         0.000           3.000
+C -D2-ZN-NQ   3    0.000         0.000           3.000
+D2-ZN-NQ-CV   3    0.000         0.000           3.000
+D2-ZN-NQ-CR   3    0.000         0.000           3.000
+C -D2-ZN-NQ   3    0.000         0.000           3.000
+D2-ZN-NQ-CV   3    0.000         0.000           3.000
+D2-ZN-NQ-CR   3    0.000         0.000           3.000
+C -D2-ZN-NP   3    0.000         0.000           3.000
+D2-ZN-NP-CV   3    0.000         0.000           3.000
+D2-ZN-NP-CR   3    0.000         0.000           3.000
+C -D2-ZN-NP   3    0.000         0.000           3.000
+D2-ZN-NP-CV   3    0.000         0.000           3.000
+D2-ZN-NP-CR   3    0.000         0.000           3.000
+C -D2-ZN-E2   3    0.000         0.000           3.000
+D2-ZN-E2-CC   3    0.000         0.000           3.000
+D2-ZN-E2-CR   3    0.000         0.000           3.000
+C -D2-ZN-E2   3    0.000         0.000           3.000
+D2-ZN-E2-CC   3    0.000         0.000           3.000
+D2-ZN-E2-CR   3    0.000         0.000           3.000
+X -CB-NR-X    2    5.100       180.000           2.000
+X -CK-NR-X    2   20.000       180.000           2.000
+X -CC-NR-X    2    4.800       180.000           2.000
+X -CR-NR-X    2   10.000       180.000           2.000
+X -CV-NR-X    2    4.800       180.000           2.000
+CR-NR-ZN-NR   3    0.000         0.000           3.000
+CV-NR-ZN-NR   3    0.000         0.000           3.000
+CR-NR-ZN-NR   3    0.000         0.000           3.000
+CV-NR-ZN-NR   3    0.000         0.000           3.000
+
+IMPR
+N1-CW-CC-CT       1.100        180.000       2.000
+N2-CW-CC-CT       1.100        180.000       2.000
+N3-CW-CC-CT       1.100        180.000       2.000
+N4-CW-CC-CT       1.100        180.000       2.000
+N5-CW-CC-CT       1.100        180.000       2.000
+N6-CW-CC-CT       1.100        180.000       2.000
+N7-CW-CC-CT       1.100        180.000       2.000
+N8-CW-CC-CT       1.100        180.000       2.000
+N9-CW-CC-CT       1.100        180.000       2.000
+N0-CW-CC-CT       1.100        180.000       2.000
+NT-CW-CC-CT       1.100        180.000       2.000
+NY-CW-CC-CT       1.100        180.000       2.000
+E1-CW-CC-CT       1.100        180.000       2.000
+X -D1-C -D1      10.500        180.000       2.000
+NQ-CW-CC-CT       1.100        180.000       2.000
+NP-CW-CC-CT       1.100        180.000       2.000
+E2-CW-CC-CT       1.100        180.000       2.000
+X -D2-C -D2      10.500        180.000       2.000
+NR-CW-CC-CT       1.100        180.000       2.000
+
+NONB
+ZN     1.10    0.013
+S1     2.00    0.250
+S2     2.00    0.250
+N1     1.82    0.170
+S3     2.00    0.250
+N2     1.82    0.170
+S4     2.00    0.250
+N3     1.82    0.170
+S5     2.00    0.250
+N4     1.82    0.170
+N5     1.82    0.170
+N6     1.82    0.170
+N7     1.82    0.170
+O1     1.77    0.152
+N8     1.82    0.170
+N9     1.82    0.170
+N0     1.82    0.170
+O2     1.77    0.152
+NT     1.82    0.170
+O3     1.77    0.152
+NY     1.82    0.170
+O4     1.77    0.152
+E1     1.82    0.170
+D1     1.66    0.210
+NQ     1.82    0.170
+NP     1.82    0.170
+E2     1.82    0.170
+D2     1.66    0.210
+NR     1.82    0.170
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/ZAFF.prep	Thu Jan 27 17:17:54 2022 +0000
@@ -0,0 +1,1015 @@
+    1    1    2
+ZAFF_201108 set created by MTK++/MCPB
+CYSTEINE with negative charge
+
+ CY1 INT 1
+ CORR OMIT DU   BEG 
+0.00000
+   1  DUMM  DU    M    0  -1  -2     0.000      .0        .0      .00000
+   2  DUMM  DU    M    1   0  -1     1.449      .0        .0      .00000
+   3  DUMM  DU    M    2   1   0     1.522   111.1        .0      .00000
+   4  N     N     M    3   2   1     1.335   116.600   180.000  -0.46300
+   5  HN    H     E    4   3   2     1.010   119.800     0.000   0.25200
+   6  CA    CT    M    4   3   2     1.449   121.900   180.000   0.03500
+   7  HA    H1    E    6   4   3     1.090   109.500   300.000   0.04800
+   8  CB    CT    3    6   4   3     1.525   111.100    60.000  -0.54300
+   9  HB3   H1    E    8   6   4     1.090   109.500    60.000   0.18377
+  10  HB2   H1    E    8   6   4     1.090   109.500   300.000   0.18377
+  11  SG    S1    E    8   6   4     1.810   116.000   180.000  -0.43963
+  12  C     C     M    6   4   3     1.522   111.100   180.000   0.61600
+  13  O     O     E   12   6   4     1.229   120.500     0.000  -0.50400
+ 
+IMPROPER
+ -M   CA   N    HN 
+ CA   +M   C    O  
+ 
+DONE
+Zinc(II) Ion
+
+ ZN1 INT 1
+ CORR OMIT DU   BEG 
+0.00000
+   1  DUMM  DU    M    0  -1  -2     0.000      .0        .0      .00000
+   2  DUMM  DU    M    1   0  -1     1.449      .0        .0      .00000
+   3  DUMM  DU    M    2   1   0     1.522   111.1        .0      .00000
+   4 ZN     ZN    M    3   2   1     1.000    90.000   180.000   0.52437
+ 
+DONE
+CYSTEINE with negative charge
+
+ CY2 INT 1
+ CORR OMIT DU   BEG 
+0.00000
+   1  DUMM  DU    M    0  -1  -2     0.000      .0        .0      .00000
+   2  DUMM  DU    M    1   0  -1     1.449      .0        .0      .00000
+   3  DUMM  DU    M    2   1   0     1.522   111.1        .0      .00000
+   4  N     N     M    3   2   1     1.335   116.600   180.000  -0.46300
+   5  HN    H     E    4   3   2     1.010   119.800     0.000   0.25200
+   6  CA    CT    M    4   3   2     1.449   121.900   180.000   0.03500
+   7  HA    H1    E    6   4   3     1.090   109.500   300.000   0.04800
+   8  CB    CT    3    6   4   3     1.525   111.100    60.000  -0.42561
+   9  HB3   H1    E    8   6   4     1.090   109.500    60.000   0.17337
+  10  HB2   H1    E    8   6   4     1.090   109.500   300.000   0.17337
+  11  SG    S2    E    8   6   4     1.810   116.000   180.000  -0.44155
+  12  C     C     M    6   4   3     1.522   111.100   180.000   0.61600
+  13  O     O     E   12   6   4     1.229   120.500     0.000  -0.50400
+ 
+IMPROPER
+ -M   CA   N    HN 
+ CA   +M   C    O  
+ 
+DONE
+HISTIDINE EPSILONH
+
+ HE1 INT 1
+ CORR OMIT DU   BEG 
+0.00000
+   1  DUMM  DU    M    0  -1  -2     0.000      .0        .0      .00000
+   2  DUMM  DU    M    1   0  -1     1.449      .0        .0      .00000
+   3  DUMM  DU    M    2   1   0     1.522   111.1        .0      .00000
+   4  N     N     M    3   2   1     1.335   116.600   180.000  -0.41570
+   5  H     H     E    4   3   2     1.010   119.800     0.000   0.27190
+   6  CA    CT    M    4   3   2     1.449   121.900   180.000  -0.05810
+   7  HA    H1    E    6   4   3     1.090   109.500   300.000   0.13600
+   8  CB    CT    3    6   4   3     1.525   111.100    60.000   0.04092
+   9  HB2   HC    E    8   6   4     1.090   109.500   300.000   0.06506
+  10  HB3   HC    E    8   6   4     1.090   109.500    60.000   0.06506
+  11  CG    CC    S    8   6   4     1.510   115.000   180.000  -0.11300
+  12  ND1   N1    S   11   8   6     1.390   122.000   180.000  -0.08206
+  13  CE1   CR    B   12  11   8     1.320   108.000   180.000  -0.14656
+  14  HE1   H5    E   13  12  11     1.090   120.000   180.000   0.19871
+  15  NE2   NA    B   13  12  11     1.310   109.000     0.000  -0.01782
+  16  HE2   H     E   15  13  12     1.010   125.000   180.000   0.27163
+  17  CD2   CW    S   15  13  12     1.360   110.000     0.000  -0.19685
+  18  HD2   H4    E   17  15  13     1.090   120.000   180.000   0.12407
+  19  C     C     M    6   4   3     1.522   111.100   180.000   0.59730
+  20  O     O     E   19   6   4     1.229   120.500     0.000  -0.56790
+ 
+LOOP
+ CG   CD2
+ 
+IMPROPER
+ -M   CA   N    H  
+ CA   +M   C    O  
+ CE1  CD2  NE2  HE2
+ CG   NE2  CD2  HD2
+ ND1  NE2  CE1  HE1
+ ND1  CD2  CG   CB 
+ 
+DONE
+Zinc(II) Ion
+
+ ZN2 INT 1
+ CORR OMIT DU   BEG 
+0.00000
+   1  DUMM  DU    M    0  -1  -2     0.000      .0        .0      .00000
+   2  DUMM  DU    M    1   0  -1     1.449      .0        .0      .00000
+   3  DUMM  DU    M    2   1   0     1.522   111.1        .0      .00000
+   4 ZN     ZN    M    3   2   1     1.000    90.000   180.000   0.43655
+ 
+DONE
+CYSTEINE with negative charge
+
+ CY3 INT 1
+ CORR OMIT DU   BEG 
+0.00000
+   1  DUMM  DU    M    0  -1  -2     0.000      .0        .0      .00000
+   2  DUMM  DU    M    1   0  -1     1.449      .0        .0      .00000
+   3  DUMM  DU    M    2   1   0     1.522   111.1        .0      .00000
+   4  N     N     M    3   2   1     1.335   116.600   180.000  -0.46300
+   5  HN    H     E    4   3   2     1.010   119.800     0.000   0.25200
+   6  CA    CT    M    4   3   2     1.449   121.900   180.000   0.03500
+   7  HA    H1    E    6   4   3     1.090   109.500   300.000   0.04800
+   8  CB    CT    3    6   4   3     1.525   111.100    60.000  -0.54858
+   9  HB3   H1    E    8   6   4     1.090   109.500    60.000   0.23928
+  10  HB2   H1    E    8   6   4     1.090   109.500   300.000   0.23928
+  11  SG    S3    E    8   6   4     1.810   116.000   180.000  -0.57501
+  12  C     C     M    6   4   3     1.522   111.100   180.000   0.61600
+  13  O     O     E   12   6   4     1.229   120.500     0.000  -0.50400
+ 
+IMPROPER
+ -M   CA   N    HN 
+ CA   +M   C    O  
+ 
+DONE
+HISTIDINE DELTAH
+
+ HD1 INT 1
+ CORR OMIT DU   BEG 
+0.00000
+   1  DUMM  DU    M    0  -1  -2     0.000      .0        .0      .00000
+   2  DUMM  DU    M    1   0  -1     1.449      .0        .0      .00000
+   3  DUMM  DU    M    2   1   0     1.522   111.1        .0      .00000
+   4  N     N     M    3   2   1     1.335   116.600   180.000  -0.41570
+   5  H     H     E    4   3   2     1.010   119.800     0.000   0.27190
+   6  CA    CT    M    4   3   2     1.449   121.900   180.000   0.01880
+   7  HA    H1    E    6   4   3     1.090   109.500   300.000   0.08810
+   8  CB    CT    3    6   4   3     1.525   111.100    60.000   0.28625
+   9  HB2   HC    E    8   6   4     1.090   109.500   300.000  -0.10029
+  10  HB3   HC    E    8   6   4     1.090   109.500    60.000  -0.10029
+  11  CG    CC    S    8   6   4     1.510   115.000   180.000  -0.19057
+  12  ND1   NA    B   11   8   6     1.390   122.000   180.000  -0.04145
+  13  HD1   H     E   12  11   8     1.010   126.000     0.000   0.25478
+  14  CE1   CR    B   12  11   8     1.320   108.000   180.000   0.12120
+  15  HE1   H5    E   14  12  11     1.090   120.000   180.000   0.07902
+  16  NE2   N2    S   14  12  11     1.310   109.000     0.000  -0.53575
+  17  CD2   CV    S   16  14  12     1.360   110.000     0.000   0.20757
+  18  HD2   H4    E   17  16  14     1.090   120.000   180.000   0.16660
+  19  C     C     M    6   4   3     1.522   111.100   180.000   0.59730
+  20  O     O     E   19   6   4     1.229   120.500     0.000  -0.56790
+ 
+LOOP
+ CG   CD2
+ 
+IMPROPER
+ -M   CA   N    H  
+ CA   +M   C    O  
+ CG   CE1  ND1  HD1
+ CG   NE2  CD2  HD2
+ ND1  NE2  CE1  HE1
+ ND1  CD2  CG   CB 
+ 
+DONE
+Zinc(II) Ion
+
+ ZN3 INT 1
+ CORR OMIT DU   BEG 
+0.00000
+   1  DUMM  DU    M    0  -1  -2     0.000      .0        .0      .00000
+   2  DUMM  DU    M    1   0  -1     1.449      .0        .0      .00000
+   3  DUMM  DU    M    2   1   0     1.522   111.1        .0      .00000
+   4 ZN     ZN    M    3   2   1     1.000    90.000   180.000   0.84354
+ 
+DONE
+CYSTEINE with negative charge
+
+ CY4 INT 1
+ CORR OMIT DU   BEG 
+0.00000
+   1  DUMM  DU    M    0  -1  -2     0.000      .0        .0      .00000
+   2  DUMM  DU    M    1   0  -1     1.449      .0        .0      .00000
+   3  DUMM  DU    M    2   1   0     1.522   111.1        .0      .00000
+   4  N     N     M    3   2   1     1.335   116.600   180.000  -0.46300
+   5  HN    H     E    4   3   2     1.010   119.800     0.000   0.25200
+   6  CA    CT    M    4   3   2     1.449   121.900   180.000   0.03500
+   7  HA    H1    E    6   4   3     1.090   109.500   300.000   0.04800
+   8  CB    CT    3    6   4   3     1.525   111.100    60.000  -0.17661
+   9  HB3   H1    E    8   6   4     1.090   109.500    60.000   0.13861
+  10  HB2   H1    E    8   6   4     1.090   109.500   300.000   0.13861
+  11  SG    S4    E    8   6   4     1.810   116.000   180.000  -0.61293
+  12  C     C     M    6   4   3     1.522   111.100   180.000   0.61600
+  13  O     O     E   12   6   4     1.229   120.500     0.000  -0.50400
+ 
+IMPROPER
+ -M   CA   N    HN 
+ CA   +M   C    O  
+ 
+DONE
+HISTIDINE DELTAH
+
+ HD2 INT 1
+ CORR OMIT DU   BEG 
+0.00000
+   1  DUMM  DU    M    0  -1  -2     0.000      .0        .0      .00000
+   2  DUMM  DU    M    1   0  -1     1.449      .0        .0      .00000
+   3  DUMM  DU    M    2   1   0     1.522   111.1        .0      .00000
+   4  N     N     M    3   2   1     1.335   116.600   180.000  -0.41570
+   5  H     H     E    4   3   2     1.010   119.800     0.000   0.27190
+   6  CA    CT    M    4   3   2     1.449   121.900   180.000   0.01880
+   7  HA    H1    E    6   4   3     1.090   109.500   300.000   0.08810
+   8  CB    CT    3    6   4   3     1.525   111.100    60.000   0.02247
+   9  HB2   HC    E    8   6   4     1.090   109.500   300.000   0.03771
+  10  HB3   HC    E    8   6   4     1.090   109.500    60.000   0.03771
+  11  CG    CC    S    8   6   4     1.510   115.000   180.000  -0.05567
+  12  ND1   NA    B   11   8   6     1.390   122.000   180.000  -0.09621
+  13  HD1   H     E   12  11   8     1.010   126.000     0.000   0.31291
+  14  CE1   CR    B   12  11   8     1.320   108.000   180.000  -0.10816
+  15  HE1   H5    E   14  12  11     1.090   120.000   180.000   0.16876
+  16  NE2   N3    S   14  12  11     1.310   109.000     0.000  -0.04270
+  17  CD2   CV    S   16  14  12     1.360   110.000     0.000  -0.10253
+  18  HD2   H4    E   17  16  14     1.090   120.000   180.000   0.13565
+  19  C     C     M    6   4   3     1.522   111.100   180.000   0.59730
+  20  O     O     E   19   6   4     1.229   120.500     0.000  -0.56790
+ 
+LOOP
+ CG   CD2
+ 
+IMPROPER
+ -M   CA   N    H  
+ CA   +M   C    O  
+ CG   CE1  ND1  HD1
+ CG   NE2  CD2  HD2
+ ND1  NE2  CE1  HE1
+ ND1  CD2  CG   CB 
+ 
+DONE
+Zinc(II) Ion
+
+ ZN4 INT 1
+ CORR OMIT DU   BEG 
+0.00000
+   1  DUMM  DU    M    0  -1  -2     0.000      .0        .0      .00000
+   2  DUMM  DU    M    1   0  -1     1.449      .0        .0      .00000
+   3  DUMM  DU    M    2   1   0     1.522   111.1        .0      .00000
+   4 ZN     ZN    M    3   2   1     1.000    90.000   180.000   0.45174
+ 
+DONE
+CYSTEINE with negative charge
+
+ CY5 INT 1
+ CORR OMIT DU   BEG 
+0.00000
+   1  DUMM  DU    M    0  -1  -2     0.000      .0        .0      .00000
+   2  DUMM  DU    M    1   0  -1     1.449      .0        .0      .00000
+   3  DUMM  DU    M    2   1   0     1.522   111.1        .0      .00000
+   4  N     N     M    3   2   1     1.335   116.600   180.000  -0.46300
+   5  HN    H     E    4   3   2     1.010   119.800     0.000   0.25200
+   6  CA    CT    M    4   3   2     1.449   121.900   180.000   0.03500
+   7  HA    H1    E    6   4   3     1.090   109.500   300.000   0.04800
+   8  CB    CT    3    6   4   3     1.525   111.100    60.000   0.09333
+   9  HB3   H1    E    8   6   4     1.090   109.500    60.000   0.02717
+  10  HB2   H1    E    8   6   4     1.090   109.500   300.000   0.02717
+  11  SG    S5    E    8   6   4     1.810   116.000   180.000  -0.51567
+  12  C     C     M    6   4   3     1.522   111.100   180.000   0.61600
+  13  O     O     E   12   6   4     1.229   120.500     0.000  -0.50400
+ 
+IMPROPER
+ -M   CA   N    HN 
+ CA   +M   C    O  
+ 
+DONE
+HISTIDINE DELTAH
+
+ HD3 INT 1
+ CORR OMIT DU   BEG 
+0.00000
+   1  DUMM  DU    M    0  -1  -2     0.000      .0        .0      .00000
+   2  DUMM  DU    M    1   0  -1     1.449      .0        .0      .00000
+   3  DUMM  DU    M    2   1   0     1.522   111.1        .0      .00000
+   4  N     N     M    3   2   1     1.335   116.600   180.000  -0.41570
+   5  H     H     E    4   3   2     1.010   119.800     0.000   0.27190
+   6  CA    CT    M    4   3   2     1.449   121.900   180.000   0.01880
+   7  HA    H1    E    6   4   3     1.090   109.500   300.000   0.08810
+   8  CB    CT    3    6   4   3     1.525   111.100    60.000   0.19087
+   9  HB2   HC    E    8   6   4     1.090   109.500   300.000   0.02593
+  10  HB3   HC    E    8   6   4     1.090   109.500    60.000   0.02593
+  11  CG    CC    S    8   6   4     1.510   115.000   180.000  -0.23217
+  12  ND1   NA    B   11   8   6     1.390   122.000   180.000  -0.00378
+  13  HD1   H     E   12  11   8     1.010   126.000     0.000   0.27721
+  14  CE1   CR    B   12  11   8     1.320   108.000   180.000  -0.07313
+  15  HE1   H5    E   14  12  11     1.090   120.000   180.000   0.15761
+  16  NE2   N4    S   14  12  11     1.310   109.000     0.000  -0.20593
+  17  CD2   CV    S   16  14  12     1.360   110.000     0.000   0.04659
+  18  HD2   H4    E   17  16  14     1.090   120.000   180.000   0.10306
+  19  C     C     M    6   4   3     1.522   111.100   180.000   0.59730
+  20  O     O     E   19   6   4     1.229   120.500     0.000  -0.56790
+ 
+LOOP
+ CG   CD2
+ 
+IMPROPER
+ -M   CA   N    H  
+ CA   +M   C    O  
+ CG   CE1  ND1  HD1
+ CG   NE2  CD2  HD2
+ ND1  NE2  CE1  HE1
+ ND1  CD2  CG   CB 
+ 
+DONE
+Zinc(II) Ion
+
+ ZN5 INT 1
+ CORR OMIT DU   BEG 
+0.00000
+   1  DUMM  DU    M    0  -1  -2     0.000      .0        .0      .00000
+   2  DUMM  DU    M    1   0  -1     1.449      .0        .0      .00000
+   3  DUMM  DU    M    2   1   0     1.522   111.1        .0      .00000
+   4 ZN     ZN    M    3   2   1     1.000    90.000   180.000   0.46992
+ 
+DONE
+ASPARTIC ACID
+
+ AP1 INT 1
+ CORR OMIT DU   BEG 
+0.00000
+   1  DUMM  DU    M    0  -1  -2     0.000      .0        .0      .00000
+   2  DUMM  DU    M    1   0  -1     1.449      .0        .0      .00000
+   3  DUMM  DU    M    2   1   0     1.522   111.1        .0      .00000
+   4  N     N     M    3   2   1     1.335   116.600   180.000  -0.51630
+   5  H     H     E    4   3   2     1.010   119.800     0.000   0.29360
+   6  CA    CT    M    4   3   2     1.449   121.900   180.000   0.03810
+   7  HA    H1    E    6   4   3     1.090   109.500   300.000   0.08800
+   8  CB    CT    3    6   4   3     1.525   111.100    60.000   0.24878
+   9  HB2   HC    E    8   6   4     1.090   109.500   300.000   0.00516
+  10  HB3   HC    E    8   6   4     1.090   109.500    60.000   0.00516
+  11  CG    C     B    8   6   4     1.527   109.470   180.000   0.55272
+  12  OD1   O2    E   11   8   6     1.260   117.200    90.000  -0.65184
+  13  OD2   D1    E   11   8   6     1.260   117.200   270.000  -0.69157
+  14  C     C     M    6   4   3     1.522   111.100   180.000   0.53660
+  15  O     O     E   14   6   4     1.229   120.500     0.000  -0.58190
+ 
+IMPROPER
+ -M   CA   N    H  
+ CA   +M   C    O  
+ CB   OD1  CG   OD2
+ 
+DONE
+HISTIDINE EPSILONH
+
+ HE4 INT 1
+ CORR OMIT DU   BEG 
+0.00000
+   1  DUMM  DU    M    0  -1  -2     0.000      .0        .0      .00000
+   2  DUMM  DU    M    1   0  -1     1.449      .0        .0      .00000
+   3  DUMM  DU    M    2   1   0     1.522   111.1        .0      .00000
+   4  N     N     M    3   2   1     1.335   116.600   180.000  -0.41570
+   5  H     H     E    4   3   2     1.010   119.800     0.000   0.27190
+   6  CA    CT    M    4   3   2     1.449   121.900   180.000  -0.05810
+   7  HA    H1    E    6   4   3     1.090   109.500   300.000   0.13600
+   8  CB    CT    3    6   4   3     1.525   111.100    60.000   0.08504
+   9  HB2   HC    E    8   6   4     1.090   109.500   300.000   0.01528
+  10  HB3   HC    E    8   6   4     1.090   109.500    60.000   0.01528
+  11  CG    CC    S    8   6   4     1.510   115.000   180.000   0.11815
+  12  ND1   E1    S   11   8   6     1.390   122.000   180.000  -0.34192
+  13  CE1   CR    B   12  11   8     1.320   108.000   180.000  -0.00828
+  14  HE1   H5    E   13  12  11     1.090   120.000   180.000   0.14511
+  15  NE2   NA    B   13  12  11     1.310   109.000     0.000  -0.13423
+  16  HE2   H     E   15  13  12     1.010   125.000   180.000   0.31756
+  17  CD2   CW    S   15  13  12     1.360   110.000     0.000  -0.19050
+  18  HD2   H4    E   17  15  13     1.090   120.000   180.000   0.16305
+  19  C     C     M    6   4   3     1.522   111.100   180.000   0.59730
+  20  O     O     E   19   6   4     1.229   120.500     0.000  -0.56790
+ 
+LOOP
+ CG   CD2
+ 
+IMPROPER
+ -M   CA   N    H  
+ CA   +M   C    O  
+ CE1  CD2  NE2  HE2
+ CG   NE2  CD2  HD2
+ ND1  NE2  CE1  HE1
+ ND1  CD2  CG   CB 
+ 
+DONE
+Zinc(II) Ion
+
+ ZN8 INT 1
+ CORR OMIT DU   BEG 
+0.00000
+   1  DUMM  DU    M    0  -1  -2     0.000      .0        .0      .00000
+   2  DUMM  DU    M    1   0  -1     1.449      .0        .0      .00000
+   3  DUMM  DU    M    2   1   0     1.522   111.1        .0      .00000
+   4 ZN     ZN    M    3   2   1     1.000    90.000   180.000   1.05092
+ 
+DONE
+ASPARTIC ACID
+
+ AP2 INT 1
+ CORR OMIT DU   BEG 
+0.00000
+   1  DUMM  DU    M    0  -1  -2     0.000      .0        .0      .00000
+   2  DUMM  DU    M    1   0  -1     1.449      .0        .0      .00000
+   3  DUMM  DU    M    2   1   0     1.522   111.1        .0      .00000
+   4  N     N     M    3   2   1     1.335   116.600   180.000  -0.51630
+   5  H     H     E    4   3   2     1.010   119.800     0.000   0.29360
+   6  CA    CT    M    4   3   2     1.449   121.900   180.000   0.03810
+   7  HA    H1    E    6   4   3     1.090   109.500   300.000   0.08800
+   8  CB    CT    3    6   4   3     1.525   111.100    60.000   0.33519
+   9  HB2   HC    E    8   6   4     1.090   109.500   300.000  -0.07433
+  10  HB3   HC    E    8   6   4     1.090   109.500    60.000  -0.07433
+  11  CG    C     B    8   6   4     1.527   109.470   180.000   0.52189
+  12  OD1   D2    E   11   8   6     1.260   117.200    90.000  -0.52163
+  13  OD2   D2    E   11   8   6     1.260   117.200   270.000  -0.66205
+  14  C     C     M    6   4   3     1.522   111.100   180.000   0.53660
+  15  O     O     E   14   6   4     1.229   120.500     0.000  -0.58190
+ 
+IMPROPER
+ -M   CA   N    H  
+ CA   +M   C    O  
+ CB   OD1  CG   OD2
+ 
+DONE
+HISTIDINE DELTAH
+
+ HD8 INT 1
+ CORR OMIT DU   BEG 
+0.00000
+   1  DUMM  DU    M    0  -1  -2     0.000      .0        .0      .00000
+   2  DUMM  DU    M    1   0  -1     1.449      .0        .0      .00000
+   3  DUMM  DU    M    2   1   0     1.522   111.1        .0      .00000
+   4  N     N     M    3   2   1     1.335   116.600   180.000  -0.41570
+   5  H     H     E    4   3   2     1.010   119.800     0.000   0.27190
+   6  CA    CT    M    4   3   2     1.449   121.900   180.000   0.01880
+   7  HA    H1    E    6   4   3     1.090   109.500   300.000   0.08810
+   8  CB    CT    3    6   4   3     1.525   111.100    60.000   0.16974
+   9  HB2   HC    E    8   6   4     1.090   109.500   300.000   0.01796
+  10  HB3   HC    E    8   6   4     1.090   109.500    60.000   0.01796
+  11  CG    CC    S    8   6   4     1.510   115.000   180.000  -0.05470
+  12  ND1   NA    B   11   8   6     1.390   122.000   180.000  -0.07381
+  13  HD1   H     E   12  11   8     1.010   126.000     0.000   0.28312
+  14  CE1   CR    B   12  11   8     1.320   108.000   180.000  -0.09436
+  15  HE1   H5    E   14  12  11     1.090   120.000   180.000   0.17880
+  16  NE2   NQ    S   14  12  11     1.310   109.000     0.000  -0.21845
+  17  CD2   CV    S   16  14  12     1.360   110.000     0.000  -0.14309
+  18  HD2   H4    E   17  16  14     1.090   120.000   180.000   0.20161
+  19  C     C     M    6   4   3     1.522   111.100   180.000   0.59730
+  20  O     O     E   19   6   4     1.229   120.500     0.000  -0.56790
+ 
+LOOP
+ CG   CD2
+ 
+IMPROPER
+ -M   CA   N    H  
+ CA   +M   C    O  
+ CG   CE1  ND1  HD1
+ CG   NE2  CD2  HD2
+ ND1  NE2  CE1  HE1
+ ND1  CD2  CG   CB 
+ 
+DONE
+HISTIDINE DELTAH
+
+ HD9 INT 1
+ CORR OMIT DU   BEG 
+0.00000
+   1  DUMM  DU    M    0  -1  -2     0.000      .0        .0      .00000
+   2  DUMM  DU    M    1   0  -1     1.449      .0        .0      .00000
+   3  DUMM  DU    M    2   1   0     1.522   111.1        .0      .00000
+   4  N     N     M    3   2   1     1.335   116.600   180.000  -0.41570
+   5  H     H     E    4   3   2     1.010   119.800     0.000   0.27190
+   6  CA    CT    M    4   3   2     1.449   121.900   180.000   0.01880
+   7  HA    H1    E    6   4   3     1.090   109.500   300.000   0.08810
+   8  CB    CT    3    6   4   3     1.525   111.100    60.000   0.24934
+   9  HB2   HC    E    8   6   4     1.090   109.500   300.000  -0.01611
+  10  HB3   HC    E    8   6   4     1.090   109.500    60.000  -0.01611
+  11  CG    CC    S    8   6   4     1.510   115.000   180.000  -0.01350
+  12  ND1   NA    B   11   8   6     1.390   122.000   180.000  -0.23979
+  13  HD1   H     E   12  11   8     1.010   126.000     0.000   0.36104
+  14  CE1   CR    B   12  11   8     1.320   108.000   180.000  -0.02222
+  15  HE1   H5    E   14  12  11     1.090   120.000   180.000   0.18280
+  16  NE2   NP    S   14  12  11     1.310   109.000     0.000  -0.11848
+  17  CD2   CV    S   16  14  12     1.360   110.000     0.000  -0.13507
+  18  HD2   H4    E   17  16  14     1.090   120.000   180.000   0.13944
+  19  C     C     M    6   4   3     1.522   111.100   180.000   0.59730
+  20  O     O     E   19   6   4     1.229   120.500     0.000  -0.56790
+ 
+LOOP
+ CG   CD2
+ 
+IMPROPER
+ -M   CA   N    H  
+ CA   +M   C    O  
+ CG   CE1  ND1  HD1
+ CG   NE2  CD2  HD2
+ ND1  NE2  CE1  HE1
+ ND1  CD2  CG   CB 
+ 
+DONE
+HISTIDINE EPSILONH
+
+ HE5 INT 1
+ CORR OMIT DU   BEG 
+0.00000
+   1  DUMM  DU    M    0  -1  -2     0.000      .0        .0      .00000
+   2  DUMM  DU    M    1   0  -1     1.449      .0        .0      .00000
+   3  DUMM  DU    M    2   1   0     1.522   111.1        .0      .00000
+   4  N     N     M    3   2   1     1.335   116.600   180.000  -0.41570
+   5  H     H     E    4   3   2     1.010   119.800     0.000   0.27190
+   6  CA    CT    M    4   3   2     1.449   121.900   180.000  -0.05810
+   7  HA    H1    E    6   4   3     1.090   109.500   300.000   0.13600
+   8  CB    CT    3    6   4   3     1.525   111.100    60.000   0.46072
+   9  HB2   HC    E    8   6   4     1.090   109.500   300.000  -0.09078
+  10  HB3   HC    E    8   6   4     1.090   109.500    60.000  -0.09078
+  11  CG    CC    S    8   6   4     1.510   115.000   180.000  -0.10770
+  12  ND1   E2    S   11   8   6     1.390   122.000   180.000  -0.06184
+  13  CE1   CR    B   12  11   8     1.320   108.000   180.000  -0.11534
+  14  HE1   H5    E   13  12  11     1.090   120.000   180.000   0.19061
+  15  NE2   NA    B   13  12  11     1.310   109.000     0.000  -0.03558
+  16  HE2   H     E   15  13  12     1.010   125.000   180.000   0.33152
+  17  CD2   CW    S   15  13  12     1.360   110.000     0.000  -0.19902
+  18  HD2   H4    E   17  15  13     1.090   120.000   180.000   0.15190
+  19  C     C     M    6   4   3     1.522   111.100   180.000   0.59730
+  20  O     O     E   19   6   4     1.229   120.500     0.000  -0.56790
+ 
+LOOP
+ CG   CD2
+ 
+IMPROPER
+ -M   CA   N    H  
+ CA   +M   C    O  
+ CE1  CD2  NE2  HE2
+ CG   NE2  CD2  HD2
+ ND1  NE2  CE1  HE1
+ ND1  CD2  CG   CB 
+ 
+DONE
+Zinc(II) Ion
+
+ ZN9 INT 1
+ CORR OMIT DU   BEG 
+0.00000
+   1  DUMM  DU    M    0  -1  -2     0.000      .0        .0      .00000
+   2  DUMM  DU    M    1   0  -1     1.449      .0        .0      .00000
+   3  DUMM  DU    M    2   1   0     1.522   111.1        .0      .00000
+   4 ZN     ZN    M    3   2   1     1.000    90.000   180.000   0.57880
+ 
+DONE
+HISTIDINE DELTAH
+
+ HDD INT 1
+ CORR OMIT DU   BEG 
+0.00000
+   1  DUMM  DU    M    0  -1  -2     0.000      .0        .0      .00000
+   2  DUMM  DU    M    1   0  -1     1.449      .0        .0      .00000
+   3  DUMM  DU    M    2   1   0     1.522   111.1        .0      .00000
+   4  N     N     M    3   2   1     1.335   116.600   180.000  -0.41570
+   5  H     H     E    4   3   2     1.010   119.800     0.000   0.27190
+   6  CA    CT    M    4   3   2     1.449   121.900   180.000   0.01880
+   7  HA    H1    E    6   4   3     1.090   109.500   300.000   0.08810
+   8  CB    CT    3    6   4   3     1.525   111.100    60.000   0.40554
+   9  HB2   HC    E    8   6   4     1.090   109.500   300.000  -0.02653
+  10  HB3   HC    E    8   6   4     1.090   109.500    60.000  -0.02653
+  11  CG    CC    S    8   6   4     1.510   115.000   180.000  -0.22905
+  12  ND1   NA    B   11   8   6     1.390   122.000   180.000  -0.08710
+  13  HD1   H     E   12  11   8     1.010   126.000     0.000   0.29391
+  14  CE1   CR    B   12  11   8     1.320   108.000   180.000  -0.03989
+  15  HE1   H5    E   14  12  11     1.090   120.000   180.000   0.17207
+  16  NE2   NR    S   14  12  11     1.310   109.000     0.000  -0.09616
+  17  CD2   CV    S   16  14  12     1.360   110.000     0.000  -0.09905
+  18  HD2   H4    E   17  16  14     1.090   120.000   180.000   0.16357
+  19  C     C     M    6   4   3     1.522   111.100   180.000   0.59730
+  20  O     O     E   19   6   4     1.229   120.500     0.000  -0.56790
+ 
+LOOP
+ CG   CD2
+ 
+IMPROPER
+ -M   CA   N    H  
+ CA   +M   C    O  
+ CG   CE1  ND1  HD1
+ CG   NE2  CD2  HD2
+ ND1  NE2  CE1  HE1
+ ND1  CD2  CG   CB 
+ 
+DONE
+Zinc(II) Ion
+
+ Z10 INT 1
+ CORR OMIT DU   BEG 
+0.00000
+   1  DUMM  DU    M    0  -1  -2     0.000      .0        .0      .00000
+   2  DUMM  DU    M    1   0  -1     1.449      .0        .0      .00000
+   3  DUMM  DU    M    2   1   0     1.522   111.1        .0      .00000
+   4 ZN     ZN    M    3   2   1     1.000    90.000   180.000   0.30693
+ 
+DONE
+HISTIDINE DELTAH
+
+ HD4 INT 1
+ CORR OMIT DU   BEG 
+0.00000
+   1  DUMM  DU    M    0  -1  -2     0.000      .0        .0      .00000
+   2  DUMM  DU    M    1   0  -1     1.449      .0        .0      .00000
+   3  DUMM  DU    M    2   1   0     1.522   111.1        .0      .00000
+   4  N     N     M    3   2   1     1.335   116.600   180.000  -0.41570
+   5  H     H     E    4   3   2     1.010   119.800     0.000   0.27190
+   6  CA    CT    M    4   3   2     1.449   121.900   180.000   0.01880
+   7  HA    H1    E    6   4   3     1.090   109.500   300.000   0.08810
+   8  CB    CT    3    6   4   3     1.525   111.100    60.000   0.22851
+   9  HB2   HC    E    8   6   4     1.090   109.500   300.000  -0.00852
+  10  HB3   HC    E    8   6   4     1.090   109.500    60.000  -0.00852
+  11  CG    CC    S    8   6   4     1.510   115.000   180.000  -0.00477
+  12  ND1   NA    B   11   8   6     1.390   122.000   180.000  -0.03294
+  13  HD1   H     E   12  11   8     1.010   126.000     0.000   0.30707
+  14  CE1   CR    B   12  11   8     1.320   108.000   180.000  -0.16957
+  15  HE1   H5    E   14  12  11     1.090   120.000   180.000   0.19403
+  16  NE2   N5    S   14  12  11     1.310   109.000     0.000  -0.13847
+  17  CD2   CV    S   16  14  12     1.360   110.000     0.000  -0.14780
+  18  HD2   H4    E   17  16  14     1.090   120.000   180.000   0.10770
+  19  C     C     M    6   4   3     1.522   111.100   180.000   0.59730
+  20  O     O     E   19   6   4     1.229   120.500     0.000  -0.56790
+ 
+LOOP
+ CG   CD2
+ 
+IMPROPER
+ -M   CA   N    H  
+ CA   +M   C    O  
+ CG   CE1  ND1  HD1
+ CG   NE2  CD2  HD2
+ ND1  NE2  CE1  HE1
+ ND1  CD2  CG   CB 
+ 
+DONE
+HISTIDINE DELTAH
+
+ HD5 INT 1
+ CORR OMIT DU   BEG 
+0.00000
+   1  DUMM  DU    M    0  -1  -2     0.000      .0        .0      .00000
+   2  DUMM  DU    M    1   0  -1     1.449      .0        .0      .00000
+   3  DUMM  DU    M    2   1   0     1.522   111.1        .0      .00000
+   4  N     N     M    3   2   1     1.335   116.600   180.000  -0.41570
+   5  H     H     E    4   3   2     1.010   119.800     0.000   0.27190
+   6  CA    CT    M    4   3   2     1.449   121.900   180.000   0.01880
+   7  HA    H1    E    6   4   3     1.090   109.500   300.000   0.08810
+   8  CB    CT    3    6   4   3     1.525   111.100    60.000   0.68544
+   9  HB2   HC    E    8   6   4     1.090   109.500   300.000  -0.11820
+  10  HB3   HC    E    8   6   4     1.090   109.500    60.000  -0.11820
+  11  CG    CC    S    8   6   4     1.510   115.000   180.000  -0.27760
+  12  ND1   NA    B   11   8   6     1.390   122.000   180.000  -0.19557
+  13  HD1   H     E   12  11   8     1.010   126.000     0.000   0.33482
+  14  CE1   CR    B   12  11   8     1.320   108.000   180.000  -0.01077
+  15  HE1   H5    E   14  12  11     1.090   120.000   180.000   0.20873
+  16  NE2   N6    S   14  12  11     1.310   109.000     0.000  -0.14199
+  17  CD2   CV    S   16  14  12     1.360   110.000     0.000   0.03137
+  18  HD2   H4    E   17  16  14     1.090   120.000   180.000   0.04768
+  19  C     C     M    6   4   3     1.522   111.100   180.000   0.59730
+  20  O     O     E   19   6   4     1.229   120.500     0.000  -0.56790
+ 
+LOOP
+ CG   CD2
+ 
+IMPROPER
+ -M   CA   N    H  
+ CA   +M   C    O  
+ CG   CE1  ND1  HD1
+ CG   NE2  CD2  HD2
+ ND1  NE2  CE1  HE1
+ ND1  CD2  CG   CB 
+ 
+DONE
+HISTIDINE EPSILONH
+
+ HE2 INT 1
+ CORR OMIT DU   BEG 
+0.00000
+   1  DUMM  DU    M    0  -1  -2     0.000      .0        .0      .00000
+   2  DUMM  DU    M    1   0  -1     1.449      .0        .0      .00000
+   3  DUMM  DU    M    2   1   0     1.522   111.1        .0      .00000
+   4  N     N     M    3   2   1     1.335   116.600   180.000  -0.41570
+   5  H     H     E    4   3   2     1.010   119.800     0.000   0.27190
+   6  CA    CT    M    4   3   2     1.449   121.900   180.000  -0.05810
+   7  HA    H1    E    6   4   3     1.090   109.500   300.000   0.13600
+   8  CB    CT    3    6   4   3     1.525   111.100    60.000   0.88299
+   9  HB2   HC    E    8   6   4     1.090   109.500   300.000  -0.21629
+  10  HB3   HC    E    8   6   4     1.090   109.500    60.000  -0.21629
+  11  CG    CC    S    8   6   4     1.510   115.000   180.000  -0.25909
+  12  ND1   N7    S   11   8   6     1.390   122.000   180.000  -0.15265
+  13  CE1   CR    B   12  11   8     1.320   108.000   180.000  -0.10122
+  14  HE1   H5    E   13  12  11     1.090   120.000   180.000   0.15727
+  15  NE2   NA    B   13  12  11     1.310   109.000     0.000  -0.02146
+  16  HE2   H     E   15  13  12     1.010   125.000   180.000   0.33268
+  17  CD2   CW    S   15  13  12     1.360   110.000     0.000  -0.14773
+  18  HD2   H4    E   17  15  13     1.090   120.000   180.000   0.15855
+  19  C     C     M    6   4   3     1.522   111.100   180.000   0.59730
+  20  O     O     E   19   6   4     1.229   120.500     0.000  -0.56790
+ 
+LOOP
+ CG   CD2
+ 
+IMPROPER
+ -M   CA   N    H  
+ CA   +M   C    O  
+ CE1  CD2  NE2  HE2
+ CG   NE2  CD2  HD2
+ ND1  NE2  CE1  HE1
+ ND1  CD2  CG   CB 
+ 
+DONE
+WATER, TIP3P MODEL
+
+ WT1 INT 1
+ CORR OMIT DU   BEG 
+0.00000
+   1  DUMM  DU    M    0  -1  -2     0.000      .0        .0      .00000
+   2  DUMM  DU    M    1   0  -1     1.449      .0        .0      .00000
+   3  DUMM  DU    M    2   1   0     1.522   111.1        .0      .00000
+   4  H1    HW    M    3   2   1     1.000   101.430   -98.890   0.47355
+   5  O     O1    M    4   3   2     0.957   104.520   -39.220  -0.77719
+   6  H2    HW    E    5   4   3     0.957   104.520  -151.000   0.47355
+ 
+LOOP
+ H1   H2 
+ 
+DONE
+Zinc(II) Ion
+
+ ZN6 INT 1
+ CORR OMIT DU   BEG 
+0.00000
+   1  DUMM  DU    M    0  -1  -2     0.000      .0        .0      .00000
+   2  DUMM  DU    M    1   0  -1     1.449      .0        .0      .00000
+   3  DUMM  DU    M    2   1   0     1.522   111.1        .0      .00000
+   4 ZN     ZN    M    3   2   1     1.000    90.000   180.000   0.69239
+ 
+DONE
+HISTIDINE DELTAH
+
+ HD6 INT 1
+ CORR OMIT DU   BEG 
+0.00000
+   1  DUMM  DU    M    0  -1  -2     0.000      .0        .0      .00000
+   2  DUMM  DU    M    1   0  -1     1.449      .0        .0      .00000
+   3  DUMM  DU    M    2   1   0     1.522   111.1        .0      .00000
+   4  N     N     M    3   2   1     1.335   116.600   180.000  -0.41570
+   5  H     H     E    4   3   2     1.010   119.800     0.000   0.27190
+   6  CA    CT    M    4   3   2     1.449   121.900   180.000   0.01880
+   7  HA    H1    E    6   4   3     1.090   109.500   300.000   0.08810
+   8  CB    CT    3    6   4   3     1.525   111.100    60.000   0.00991
+   9  HB2   HC    E    8   6   4     1.090   109.500   300.000   0.04604
+  10  HB3   HC    E    8   6   4     1.090   109.500    60.000   0.04604
+  11  CG    CC    S    8   6   4     1.510   115.000   180.000   0.02346
+  12  ND1   NA    B   11   8   6     1.390   122.000   180.000  -0.05199
+  13  HD1   H     E   12  11   8     1.010   126.000     0.000   0.29344
+  14  CE1   CR    B   12  11   8     1.320   108.000   180.000  -0.10727
+  15  HE1   H5    E   14  12  11     1.090   120.000   180.000   0.19291
+  16  NE2   N8    S   14  12  11     1.310   109.000     0.000  -0.23431
+  17  CD2   CV    S   16  14  12     1.360   110.000     0.000  -0.10958
+  18  HD2   H4    E   17  16  14     1.090   120.000   180.000   0.13029
+  19  C     C     M    6   4   3     1.522   111.100   180.000   0.59730
+  20  O     O     E   19   6   4     1.229   120.500     0.000  -0.56790
+ 
+LOOP
+ CG   CD2
+ 
+IMPROPER
+ -M   CA   N    H  
+ CA   +M   C    O  
+ CG   CE1  ND1  HD1
+ CG   NE2  CD2  HD2
+ ND1  NE2  CE1  HE1
+ ND1  CD2  CG   CB 
+ 
+DONE
+HISTIDINE DELTAH
+
+ HD7 INT 1
+ CORR OMIT DU   BEG 
+0.00000
+   1  DUMM  DU    M    0  -1  -2     0.000      .0        .0      .00000
+   2  DUMM  DU    M    1   0  -1     1.449      .0        .0      .00000
+   3  DUMM  DU    M    2   1   0     1.522   111.1        .0      .00000
+   4  N     N     M    3   2   1     1.335   116.600   180.000  -0.41570
+   5  H     H     E    4   3   2     1.010   119.800     0.000   0.27190
+   6  CA    CT    M    4   3   2     1.449   121.900   180.000   0.01880
+   7  HA    H1    E    6   4   3     1.090   109.500   300.000   0.08810
+   8  CB    CT    3    6   4   3     1.525   111.100    60.000   0.41121
+   9  HB2   HC    E    8   6   4     1.090   109.500   300.000  -0.05230
+  10  HB3   HC    E    8   6   4     1.090   109.500    60.000  -0.05230
+  11  CG    CC    S    8   6   4     1.510   115.000   180.000  -0.22655
+  12  ND1   NA    B   11   8   6     1.390   122.000   180.000  -0.13679
+  13  HD1   H     E   12  11   8     1.010   126.000     0.000   0.30149
+  14  CE1   CR    B   12  11   8     1.320   108.000   180.000   0.03317
+  15  HE1   H5    E   14  12  11     1.090   120.000   180.000   0.16396
+  16  NE2   N9    S   14  12  11     1.310   109.000     0.000  -0.24026
+  17  CD2   CV    S   16  14  12     1.360   110.000     0.000   0.05443
+  18  HD2   H4    E   17  16  14     1.090   120.000   180.000   0.04564
+  19  C     C     M    6   4   3     1.522   111.100   180.000   0.59730
+  20  O     O     E   19   6   4     1.229   120.500     0.000  -0.56790
+ 
+LOOP
+ CG   CD2
+ 
+IMPROPER
+ -M   CA   N    H  
+ CA   +M   C    O  
+ CG   CE1  ND1  HD1
+ CG   NE2  CD2  HD2
+ ND1  NE2  CE1  HE1
+ ND1  CD2  CG   CB 
+ 
+DONE
+HISTIDINE EPSILONH
+
+ HE3 INT 1
+ CORR OMIT DU   BEG 
+0.00000
+   1  DUMM  DU    M    0  -1  -2     0.000      .0        .0      .00000
+   2  DUMM  DU    M    1   0  -1     1.449      .0        .0      .00000
+   3  DUMM  DU    M    2   1   0     1.522   111.1        .0      .00000
+   4  N     N     M    3   2   1     1.335   116.600   180.000  -0.41570
+   5  H     H     E    4   3   2     1.010   119.800     0.000   0.27190
+   6  CA    CT    M    4   3   2     1.449   121.900   180.000  -0.05810
+   7  HA    H1    E    6   4   3     1.090   109.500   300.000   0.13600
+   8  CB    CT    3    6   4   3     1.525   111.100    60.000   0.47187
+   9  HB2   HC    E    8   6   4     1.090   109.500   300.000  -0.07714
+  10  HB3   HC    E    8   6   4     1.090   109.500    60.000  -0.07714
+  11  CG    CC    S    8   6   4     1.510   115.000   180.000  -0.24053
+  12  ND1   N0    S   11   8   6     1.390   122.000   180.000   0.04467
+  13  CE1   CR    B   12  11   8     1.320   108.000   180.000  -0.08704
+  14  HE1   H5    E   13  12  11     1.090   120.000   180.000   0.16785
+  15  NE2   NA    B   13  12  11     1.310   109.000     0.000  -0.13156
+  16  HE2   H     E   15  13  12     1.010   125.000   180.000   0.33211
+  17  CD2   CW    S   15  13  12     1.360   110.000     0.000  -0.11505
+  18  HD2   H4    E   17  15  13     1.090   120.000   180.000   0.14818
+  19  C     C     M    6   4   3     1.522   111.100   180.000   0.59730
+  20  O     O     E   19   6   4     1.229   120.500     0.000  -0.56790
+ 
+LOOP
+ CG   CD2
+ 
+IMPROPER
+ -M   CA   N    H  
+ CA   +M   C    O  
+ CE1  CD2  NE2  HE2
+ CG   NE2  CD2  HD2
+ ND1  NE2  CE1  HE1
+ ND1  CD2  CG   CB 
+ 
+DONE
+hydroxyl
+
+ OH1 INT 1
+ CORR OMIT DU   BEG 
+0.00000
+   1  DUMM  DU    M    0  -1  -2     0.000      .0        .0      .00000
+   2  DUMM  DU    M    1   0  -1     1.449      .0        .0      .00000
+   3  DUMM  DU    M    2   1   0     1.522   111.1        .0      .00000
+   4  O     O2    M    3   2   1     1.540   111.208   180.000  -1.00476
+   5  H1    HO    E    4   3   2     0.947    97.223    90.000   0.41281
+ 
+DONE
+Zinc(II) Ion
+
+ ZN7 INT 1
+ CORR OMIT DU   BEG 
+0.00000
+   1  DUMM  DU    M    0  -1  -2     0.000      .0        .0      .00000
+   2  DUMM  DU    M    1   0  -1     1.449      .0        .0      .00000
+   3  DUMM  DU    M    2   1   0     1.522   111.1        .0      .00000
+   4 ZN     ZN    M    3   2   1     1.000    90.000   180.000   0.66660
+ 
+DONE
+HISTIDINE DELTAH
+
+ HDA INT 1
+ CORR OMIT DU   BEG 
+0.00000
+   1  DUMM  DU    M    0  -1  -2     0.000      .0        .0      .00000
+   2  DUMM  DU    M    1   0  -1     1.449      .0        .0      .00000
+   3  DUMM  DU    M    2   1   0     1.522   111.1        .0      .00000
+   4  N     N     M    3   2   1     1.335   116.600   180.000  -0.41570
+   5  H     H     E    4   3   2     1.010   119.800     0.000   0.27190
+   6  CA    CT    M    4   3   2     1.449   121.900   180.000   0.01880
+   7  HA    H1    E    6   4   3     1.090   109.500   300.000   0.08810
+   8  CB    CT    3    6   4   3     1.525   111.100    60.000   0.74837
+   9  HB2   HC    E    8   6   4     1.090   109.500   300.000  -0.11954
+  10  HB3   HC    E    8   6   4     1.090   109.500    60.000  -0.11954
+  11  CG    CC    S    8   6   4     1.510   115.000   180.000  -0.41256
+  12  ND1   NA    B   11   8   6     1.390   122.000   180.000  -0.12169
+  13  HD1   H     E   12  11   8     1.010   126.000     0.000   0.32152
+  14  CE1   CR    B   12  11   8     1.320   108.000   180.000   0.15077
+  15  HE1   H5    E   14  12  11     1.090   120.000   180.000   0.16196
+  16  NE2   NT    S   14  12  11     1.310   109.000     0.000  -0.61460
+  17  CD2   CV    S   16  14  12     1.360   110.000     0.000   0.33532
+  18  HD2   H4    E   17  16  14     1.090   120.000   180.000   0.01604
+  19  C     C     M    6   4   3     1.522   111.100   180.000   0.59730
+  20  O     O     E   19   6   4     1.229   120.500     0.000  -0.56790
+ 
+LOOP
+ CG   CD2
+ 
+IMPROPER
+ -M   CA   N    H  
+ CA   +M   C    O  
+ CG   CE1  ND1  HD1
+ CG   NE2  CD2  HD2
+ ND1  NE2  CE1  HE1
+ ND1  CD2  CG   CB 
+ 
+DONE
+WATER, TIP3P MODEL
+
+ WT2 INT 1
+ CORR OMIT DU   BEG 
+0.00000
+   1  DUMM  DU    M    0  -1  -2     0.000      .0        .0      .00000
+   2  DUMM  DU    M    1   0  -1     1.449      .0        .0      .00000
+   3  DUMM  DU    M    2   1   0     1.522   111.1        .0      .00000
+   4  H1    HW    M    3   2   1     1.000   101.430   -98.890   0.44434
+   5  O     O3    M    4   3   2     0.957   104.520   -39.220  -0.78345
+   6  H2    HW    E    5   4   3     0.957   104.520  -151.000   0.44434
+ 
+LOOP
+ H1   H2 
+ 
+DONE
+Zinc(II) Ion
+
+ Z11 INT 1
+ CORR OMIT DU   BEG 
+0.00000
+   1  DUMM  DU    M    0  -1  -2     0.000      .0        .0      .00000
+   2  DUMM  DU    M    1   0  -1     1.449      .0        .0      .00000
+   3  DUMM  DU    M    2   1   0     1.522   111.1        .0      .00000
+   4 ZN     ZN    M    3   2   1     1.000    90.000   180.000   1.11246
+ 
+DONE
+HISTIDINE EPSILONH
+
+ HE6 INT 1
+ CORR OMIT DU   BEG 
+0.00000
+   1  DUMM  DU    M    0  -1  -2     0.000      .0        .0      .00000
+   2  DUMM  DU    M    1   0  -1     1.449      .0        .0      .00000
+   3  DUMM  DU    M    2   1   0     1.522   111.1        .0      .00000
+   4  N     N     M    3   2   1     1.335   116.600   180.000  -0.41570
+   5  H     H     E    4   3   2     1.010   119.800     0.000   0.27190
+   6  CA    CT    M    4   3   2     1.449   121.900   180.000  -0.05810
+   7  HA    H1    E    6   4   3     1.090   109.500   300.000   0.13600
+   8  CB    CT    3    6   4   3     1.525   111.100    60.000   1.05997
+   9  HB2   HC    E    8   6   4     1.090   109.500   300.000  -0.21528
+  10  HB3   HC    E    8   6   4     1.090   109.500    60.000  -0.21528
+  11  CG    CC    S    8   6   4     1.510   115.000   180.000  -0.28845
+  12  ND1   NY    S   11   8   6     1.390   122.000   180.000  -0.49024
+  13  CE1   CR    B   12  11   8     1.320   108.000   180.000  -0.00101
+  14  HE1   H5    E   13  12  11     1.090   120.000   180.000   0.15620
+  15  NE2   NA    B   13  12  11     1.310   109.000     0.000  -0.04727
+  16  HE2   H     E   15  13  12     1.010   125.000   180.000   0.34231
+  17  CD2   CW    S   15  13  12     1.360   110.000     0.000  -0.12203
+  18  HD2   H4    E   17  15  13     1.090   120.000   180.000   0.26454
+  19  C     C     M    6   4   3     1.522   111.100   180.000   0.59730
+  20  O     O     E   19   6   4     1.229   120.500     0.000  -0.56790
+ 
+LOOP
+ CG   CD2
+ 
+IMPROPER
+ -M   CA   N    H  
+ CA   +M   C    O  
+ CE1  CD2  NE2  HE2
+ CG   NE2  CD2  HD2
+ ND1  NE2  CE1  HE1
+ ND1  CD2  CG   CB 
+ 
+DONE
+WATER, TIP3P MODEL
+
+ WT3 INT 1
+ CORR OMIT DU   BEG 
+0.00000
+   1  DUMM  DU    M    0  -1  -2     0.000      .0        .0      .00000
+   2  DUMM  DU    M    1   0  -1     1.449      .0        .0      .00000
+   3  DUMM  DU    M    2   1   0     1.522   111.1        .0      .00000
+   4  H1    HW    M    3   2   1     1.000   101.430   -98.890   0.40063
+   5  O     O4    M    4   3   2     0.957   104.520   -39.220  -0.60020
+   6  H2    HW    E    5   4   3     0.957   104.520  -151.000   0.40063
+ 
+LOOP
+ H1   H2 
+ 
+DONE
+Zinc(II) Ion
+
+ Z12 INT 1
+ CORR OMIT DU   BEG 
+0.00000
+   1  DUMM  DU    M    0  -1  -2     0.000      .0        .0      .00000
+   2  DUMM  DU    M    1   0  -1     1.449      .0        .0      .00000
+   3  DUMM  DU    M    2   1   0     1.522   111.1        .0      .00000
+   4 ZN     ZN    M    3   2   1     1.000    90.000   180.000   0.98985
+ 
+DONE
+STOP
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/base_GMX.gro	Thu Jan 27 17:17:54 2022 +0000
@@ -0,0 +1,25 @@
+base6_GMX.gro created by acpype (v: 2018-04-24T22:34:57UTC) on Tue Jun 11 14:15:01 2019
+ 22
+    1  JZ4   C4    1   0.079   0.137   0.220
+    1  JZ4   C7    2   0.660   0.042   0.244
+    1  JZ4   C8    3   0.732   0.091   0.136
+    1  JZ4   C9    4   0.665   0.133   0.022
+    1  JZ4  C10    5   0.525   0.126   0.016
+    1  JZ4  C11    6   0.521   0.034   0.238
+    1  JZ4  C12    7   0.451   0.077   0.124
+    1  JZ4  C13    8   0.300   0.067   0.120
+    1  JZ4  C14    9   0.231   0.148   0.230
+    1  JZ4  OAB   10   0.460   0.167  -0.097
+    1  JZ4    H   11   0.032   0.193   0.301
+    1  JZ4   H1   12   0.047   0.033   0.227
+    1  JZ4   H2   13   0.043   0.178   0.125
+    1  JZ4   H3   14   0.712   0.009   0.334
+    1  JZ4   H4   15   0.840   0.097   0.141
+    1  JZ4   H5   16   0.722   0.171  -0.062
+    1  JZ4   H6   17   0.466  -0.006   0.324
+    1  JZ4   H7   18   0.273  -0.039   0.128
+    1  JZ4   H8   19   0.262   0.100   0.023
+    1  JZ4   H9   20   0.260   0.253   0.223
+    1  JZ4  H10   21   0.262   0.113   0.329
+    1  JZ4  H11   22   0.526   0.196  -0.162
+   16.16600     5.85200     9.92000
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/base_GMX.itp	Thu Jan 27 17:17:54 2022 +0000
@@ -0,0 +1,218 @@
+; base_GMX.itp created by acpype (v: 2019-03-22T14:36:00UTC) on Fri May 31 15:21:44 2019
+
+[ atomtypes ]
+;name   bond_type     mass     charge   ptype   sigma         epsilon       Amb
+ c3       c3          0.00000  0.00000   A     3.39967e-01   4.57730e-01 ; 1.91  0.1094
+ ca       ca          0.00000  0.00000   A     3.39967e-01   3.59824e-01 ; 1.91  0.0860
+ oh       oh          0.00000  0.00000   A     3.06647e-01   8.80314e-01 ; 1.72  0.2104
+ hc       hc          0.00000  0.00000   A     2.64953e-01   6.56888e-02 ; 1.49  0.0157
+ ha       ha          0.00000  0.00000   A     2.59964e-01   6.27600e-02 ; 1.46  0.0150
+ ho       ho          0.00000  0.00000   A     0.00000e+00   0.00000e+00 ; 0.00  0.0000
+
+[ moleculetype ]
+;name            nrexcl
+ base             3
+
+[ atoms ]
+;   nr  type  resi  res  atom  cgnr     charge      mass       ; qtot   bond_type
+     1   c3     1   JZ4    C4    1    -0.093100     12.01000 ; qtot -0.093
+     2   ca     1   JZ4    C7    2    -0.162000     12.01000 ; qtot -0.255
+     3   ca     1   JZ4    C8    3    -0.095000     12.01000 ; qtot -0.350
+     4   ca     1   JZ4    C9    4    -0.211000     12.01000 ; qtot -0.561
+     5   ca     1   JZ4   C10    5     0.124100     12.01000 ; qtot -0.437
+     6   ca     1   JZ4   C11    6    -0.099000     12.01000 ; qtot -0.536
+     7   ca     1   JZ4   C12    7    -0.098300     12.01000 ; qtot -0.634
+     8   c3     1   JZ4   C13    8    -0.032100     12.01000 ; qtot -0.666
+     9   c3     1   JZ4   C14    9    -0.075400     12.01000 ; qtot -0.742
+    10   oh     1   JZ4   OAB   10    -0.500101     16.00000 ; qtot -1.242
+    11   hc     1   JZ4     H   11     0.032700      1.00800 ; qtot -1.209
+    12   hc     1   JZ4    H1   12     0.032700      1.00800 ; qtot -1.177
+    13   hc     1   JZ4    H2   13     0.032700      1.00800 ; qtot -1.144
+    14   ha     1   JZ4    H3   14     0.133000      1.00800 ; qtot -1.011
+    15   ha     1   JZ4    H4   15     0.132000      1.00800 ; qtot -0.879
+    16   ha     1   JZ4    H5   16     0.132000      1.00800 ; qtot -0.747
+    17   ha     1   JZ4    H6   17     0.134000      1.00800 ; qtot -0.613
+    18   hc     1   JZ4    H7   18     0.055700      1.00800 ; qtot -0.557
+    19   hc     1   JZ4    H8   19     0.055700      1.00800 ; qtot -0.501
+    20   hc     1   JZ4    H9   20     0.041700      1.00800 ; qtot -0.460
+    21   hc     1   JZ4   H10   21     0.041700      1.00800 ; qtot -0.418
+    22   ho     1   JZ4   H11   22     0.418000      1.00800 ; qtot -0.000
+
+[ bonds ]
+;   ai     aj funct   r             k
+     1      9   1    1.5375e-01    2.5179e+05 ;     C4 - C14   
+     1     11   1    1.0969e-01    2.7665e+05 ;     C4 - H     
+     1     12   1    1.0969e-01    2.7665e+05 ;     C4 - H1    
+     1     13   1    1.0969e-01    2.7665e+05 ;     C4 - H2    
+     2      3   1    1.3984e-01    3.8585e+05 ;     C7 - C8    
+     2      6   1    1.3984e-01    3.8585e+05 ;     C7 - C11   
+     2     14   1    1.0860e-01    2.8937e+05 ;     C7 - H3    
+     3      4   1    1.3984e-01    3.8585e+05 ;     C8 - C9    
+     3     15   1    1.0860e-01    2.8937e+05 ;     C8 - H4    
+     4      5   1    1.3984e-01    3.8585e+05 ;     C9 - C10   
+     4     16   1    1.0860e-01    2.8937e+05 ;     C9 - H5    
+     5      7   1    1.3984e-01    3.8585e+05 ;    C10 - C12   
+     5     10   1    1.3637e-01    3.2133e+05 ;    C10 - OAB   
+     6      7   1    1.3984e-01    3.8585e+05 ;    C11 - C12   
+     6     17   1    1.0860e-01    2.8937e+05 ;    C11 - H6    
+     7      8   1    1.5156e-01    2.6861e+05 ;    C12 - C13   
+     8      9   1    1.5375e-01    2.5179e+05 ;    C13 - C14   
+     8     18   1    1.0969e-01    2.7665e+05 ;    C13 - H7    
+     8     19   1    1.0969e-01    2.7665e+05 ;    C13 - H8    
+     9     20   1    1.0969e-01    2.7665e+05 ;    C14 - H9    
+     9     21   1    1.0969e-01    2.7665e+05 ;    C14 - H10   
+    10     22   1    9.7300e-02    3.1079e+05 ;    OAB - H11   
+
+[ pairs ]
+;   ai     aj    funct
+     1      7      1 ;     C4 - C12   
+     1     18      1 ;     C4 - H7    
+     1     19      1 ;     C4 - H8    
+     2      5      1 ;     C7 - C10   
+     2      8      1 ;     C7 - C13   
+     2     16      1 ;     C7 - H5    
+     3      7      1 ;     C8 - C12   
+     3     10      1 ;     C8 - OAB   
+     3     17      1 ;     C8 - H6    
+     4      6      1 ;     C9 - C11   
+     4      8      1 ;     C9 - C13   
+     4     14      1 ;     C9 - H3    
+     4     22      1 ;     C9 - H11   
+     5      9      1 ;    C10 - C14   
+     5     15      1 ;    C10 - H4    
+     5     17      1 ;    C10 - H6    
+     5     18      1 ;    C10 - H7    
+     5     19      1 ;    C10 - H8    
+     6      9      1 ;    C11 - C14   
+     6     10      1 ;    C11 - OAB   
+     6     15      1 ;    C11 - H4    
+     6     18      1 ;    C11 - H7    
+     6     19      1 ;    C11 - H8    
+     7     14      1 ;    C12 - H3    
+     7     16      1 ;    C12 - H5    
+     7     20      1 ;    C12 - H9    
+     7     21      1 ;    C12 - H10   
+     7     22      1 ;    C12 - H11   
+     8     10      1 ;    C13 - OAB   
+     8     17      1 ;    C13 - H6    
+    10     16      1 ;    OAB - H5    
+    11      8      1 ;      H - C13   
+    11     20      1 ;      H - H9    
+    11     21      1 ;      H - H10   
+    12      8      1 ;     H1 - C13   
+    12     20      1 ;     H1 - H9    
+    12     21      1 ;     H1 - H10   
+    13      8      1 ;     H2 - C13   
+    13     20      1 ;     H2 - H9    
+    13     21      1 ;     H2 - H10   
+    14     15      1 ;     H3 - H4    
+    14     17      1 ;     H3 - H6    
+    15     16      1 ;     H4 - H5    
+    18     20      1 ;     H7 - H9    
+    18     21      1 ;     H7 - H10   
+    19     20      1 ;     H8 - H9    
+    19     21      1 ;     H8 - H10   
+
+[ angles ]
+;   ai     aj     ak    funct   theta         cth
+     1      9      8      1    1.1151e+02    5.2635e+02 ;     C4 - C14    - C13   
+     1      9     20      1    1.0980e+02    3.8744e+02 ;     C4 - C14    - H9    
+     1      9     21      1    1.0980e+02    3.8744e+02 ;     C4 - C14    - H10   
+     2      3      4      1    1.2002e+02    5.5731e+02 ;     C7 - C8     - C9    
+     2      3     15      1    1.1988e+02    4.0334e+02 ;     C7 - C8     - H4    
+     2      6      7      1    1.2002e+02    5.5731e+02 ;     C7 - C11    - C12   
+     2      6     17      1    1.1988e+02    4.0334e+02 ;     C7 - C11    - H6    
+     3      2      6      1    1.2002e+02    5.5731e+02 ;     C8 - C7     - C11   
+     3      2     14      1    1.1988e+02    4.0334e+02 ;     C8 - C7     - H3    
+     3      4      5      1    1.2002e+02    5.5731e+02 ;     C8 - C9     - C10   
+     3      4     16      1    1.1988e+02    4.0334e+02 ;     C8 - C9     - H5    
+     4      3     15      1    1.1988e+02    4.0334e+02 ;     C9 - C8     - H4    
+     4      5      7      1    1.2002e+02    5.5731e+02 ;     C9 - C10    - C12   
+     4      5     10      1    1.1990e+02    5.8158e+02 ;     C9 - C10    - OAB   
+     5      4     16      1    1.1988e+02    4.0334e+02 ;    C10 - C9     - H5    
+     5      7      6      1    1.2002e+02    5.5731e+02 ;    C10 - C12    - C11   
+     5      7      8      1    1.2077e+02    5.3137e+02 ;    C10 - C12    - C13   
+     5     10     22      1    1.0858e+02    4.1003e+02 ;    C10 - OAB    - H11   
+     6      2     14      1    1.1988e+02    4.0334e+02 ;    C11 - C7     - H3    
+     6      7      8      1    1.2077e+02    5.3137e+02 ;    C11 - C12    - C13   
+     7      5     10      1    1.1990e+02    5.8158e+02 ;    C12 - C10    - OAB   
+     7      6     17      1    1.1988e+02    4.0334e+02 ;    C12 - C11    - H6    
+     7      8      9      1    1.1207e+02    5.2802e+02 ;    C12 - C13    - C14   
+     7      8     18      1    1.1047e+02    3.9162e+02 ;    C12 - C13    - H7    
+     7      8     19      1    1.1047e+02    3.9162e+02 ;    C12 - C13    - H8    
+     8      9     20      1    1.0980e+02    3.8744e+02 ;    C13 - C14    - H9    
+     8      9     21      1    1.0980e+02    3.8744e+02 ;    C13 - C14    - H10   
+     9      1     11      1    1.0980e+02    3.8744e+02 ;    C14 - C4     - H     
+     9      1     12      1    1.0980e+02    3.8744e+02 ;    C14 - C4     - H1    
+     9      1     13      1    1.0980e+02    3.8744e+02 ;    C14 - C4     - H2    
+     9      8     18      1    1.0980e+02    3.8744e+02 ;    C14 - C13    - H7    
+     9      8     19      1    1.0980e+02    3.8744e+02 ;    C14 - C13    - H8    
+    11      1     12      1    1.0758e+02    3.2970e+02 ;      H - C4     - H1    
+    11      1     13      1    1.0758e+02    3.2970e+02 ;      H - C4     - H2    
+    12      1     13      1    1.0758e+02    3.2970e+02 ;     H1 - C4     - H2    
+    18      8     19      1    1.0758e+02    3.2970e+02 ;     H7 - C13    - H8    
+    20      9     21      1    1.0758e+02    3.2970e+02 ;     H9 - C14    - H10   
+
+[ dihedrals ] ; propers
+; for gromacs 4.5 or higher, using funct 9
+;    i      j      k      l   func   phase     kd      pn
+     1      9      8      7      9     0.00   0.65084   3 ;     C4-   C14-   C13-   C12
+     1      9      8     18      9     0.00   0.66944   3 ;     C4-   C14-   C13-    H7
+     1      9      8     19      9     0.00   0.66944   3 ;     C4-   C14-   C13-    H8
+     2      3      4      5      9   180.00  15.16700   2 ;     C7-    C8-    C9-   C10
+     2      3      4     16      9   180.00  15.16700   2 ;     C7-    C8-    C9-    H5
+     2      6      7      5      9   180.00  15.16700   2 ;     C7-   C11-   C12-   C10
+     2      6      7      8      9   180.00  15.16700   2 ;     C7-   C11-   C12-   C13
+     3      2      6      7      9   180.00  15.16700   2 ;     C8-    C7-   C11-   C12
+     3      2      6     17      9   180.00  15.16700   2 ;     C8-    C7-   C11-    H6
+     3      4      5      7      9   180.00  15.16700   2 ;     C8-    C9-   C10-   C12
+     3      4      5     10      9   180.00  15.16700   2 ;     C8-    C9-   C10-   OAB
+     4      3      2      6      9   180.00  15.16700   2 ;     C9-    C8-    C7-   C11
+     4      3      2     14      9   180.00  15.16700   2 ;     C9-    C8-    C7-    H3
+     4      5      7      6      9   180.00  15.16700   2 ;     C9-   C10-   C12-   C11
+     4      5      7      8      9   180.00  15.16700   2 ;     C9-   C10-   C12-   C13
+     4      5     10     22      9   180.00   3.76560   2 ;     C9-   C10-   OAB-   H11
+     5      4      3     15      9   180.00  15.16700   2 ;    C10-    C9-    C8-    H4
+     5      7      6     17      9   180.00  15.16700   2 ;    C10-   C12-   C11-    H6
+     5      7      8      9      9     0.00   0.00000   0 ;    C10-   C12-   C13-   C14
+     5      7      8     18      9     0.00   0.00000   0 ;    C10-   C12-   C13-    H7
+     5      7      8     19      9     0.00   0.00000   0 ;    C10-   C12-   C13-    H8
+     6      2      3     15      9   180.00  15.16700   2 ;    C11-    C7-    C8-    H4
+     6      7      5     10      9   180.00  15.16700   2 ;    C11-   C12-   C10-   OAB
+     6      7      8      9      9     0.00   0.00000   0 ;    C11-   C12-   C13-   C14
+     6      7      8     18      9     0.00   0.00000   0 ;    C11-   C12-   C13-    H7
+     6      7      8     19      9     0.00   0.00000   0 ;    C11-   C12-   C13-    H8
+     7      5      4     16      9   180.00  15.16700   2 ;    C12-   C10-    C9-    H5
+     7      5     10     22      9   180.00   3.76560   2 ;    C12-   C10-   OAB-   H11
+     7      6      2     14      9   180.00  15.16700   2 ;    C12-   C11-    C7-    H3
+     7      8      9     20      9     0.00   0.65084   3 ;    C12-   C13-   C14-    H9
+     7      8      9     21      9     0.00   0.65084   3 ;    C12-   C13-   C14-   H10
+     8      7      5     10      9   180.00  15.16700   2 ;    C13-   C12-   C10-   OAB
+     8      7      6     17      9   180.00  15.16700   2 ;    C13-   C12-   C11-    H6
+    10      5      4     16      9   180.00  15.16700   2 ;    OAB-   C10-    C9-    H5
+    11      1      9      8      9     0.00   0.66944   3 ;      H-    C4-   C14-   C13
+    11      1      9     20      9     0.00   0.62760   3 ;      H-    C4-   C14-    H9
+    11      1      9     21      9     0.00   0.62760   3 ;      H-    C4-   C14-   H10
+    12      1      9      8      9     0.00   0.66944   3 ;     H1-    C4-   C14-   C13
+    12      1      9     20      9     0.00   0.62760   3 ;     H1-    C4-   C14-    H9
+    12      1      9     21      9     0.00   0.62760   3 ;     H1-    C4-   C14-   H10
+    13      1      9      8      9     0.00   0.66944   3 ;     H2-    C4-   C14-   C13
+    13      1      9     20      9     0.00   0.62760   3 ;     H2-    C4-   C14-    H9
+    13      1      9     21      9     0.00   0.62760   3 ;     H2-    C4-   C14-   H10
+    14      2      3     15      9   180.00  15.16700   2 ;     H3-    C7-    C8-    H4
+    14      2      6     17      9   180.00  15.16700   2 ;     H3-    C7-   C11-    H6
+    15      3      4     16      9   180.00  15.16700   2 ;     H4-    C8-    C9-    H5
+    18      8      9     20      9     0.00   0.62760   3 ;     H7-   C13-   C14-    H9
+    18      8      9     21      9     0.00   0.62760   3 ;     H7-   C13-   C14-   H10
+    19      8      9     20      9     0.00   0.62760   3 ;     H8-   C13-   C14-    H9
+    19      8      9     21      9     0.00   0.62760   3 ;     H8-   C13-   C14-   H10
+
+[ dihedrals ] ; impropers
+; treated as propers in GROMACS to use correct AMBER analytical function
+;    i      j      k      l   func   phase     kd      pn
+     2      4      3     15      4   180.00   4.60240   2 ;     C7-    C9-    C8-    H4
+     2      7      6     17      4   180.00   4.60240   2 ;     C7-   C12-   C11-    H6
+     3      5      4     16      4   180.00   4.60240   2 ;     C8-   C10-    C9-    H5
+     3      6      2     14      4   180.00   4.60240   2 ;     C8-   C11-    C7-    H3
+     4      7      5     10      4   180.00   4.60240   2 ;     C9-   C12-   C10-   OAB
+     5      6      7      8      4   180.00   4.60240   2 ;    C10-   C11-   C12-   C13
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cid1.inpcrd	Thu Jan 27 17:17:54 2022 +0000
@@ -0,0 +1,23 @@
+default_name
+    42
+ 413.7160000 -23.8940000  73.9880000 413.0110000 -23.1360000  73.0600000
+ 410.4130000 -22.8270000  77.7640000 413.0830000 -24.9950000  74.5420000
+ 411.1680000 -24.6150000  73.3300000 412.1350000 -21.4560000  78.2360000
+ 411.7120000 -23.4970000  72.7190000 411.3590000 -22.4680000  78.7560000
+ 410.6390000 -22.0230000  76.6690000 409.9160000 -22.0060000  75.3710000
+ 410.3560000 -20.6120000  70.7060000 411.2760000 -21.2970000  69.7140000
+ 410.9200000 -22.6950000  71.7140000 410.7700000 -21.2020000  72.0480000
+ 411.0860000 -23.8010000  69.4340000 409.7500000 -20.9270000  73.1430000
+ 411.8220000 -25.3760000  74.2360000 411.6890000 -21.1940000  76.9670000
+ 410.3570000 -21.0800000  74.4240000 411.5380000 -22.6710000  70.3070000
+ 408.9730000 -22.7740000  75.2000000 411.4870000 -23.1760000  80.2920000
+ 414.7300000 -23.6320000  74.2690000 413.4810000 -22.2670000  72.6080000
+ 409.6480000 -23.5890000  77.8390000 413.5900000 -25.6180000  75.2710000
+ 410.1590000 -24.9450000  73.1040000 412.9630000 -20.8980000  78.6520000
+ 410.4620000 -19.5230000  70.6760000 409.3110000 -20.8540000  70.4760000
+ 410.8360000 -21.3960000  68.7180000 412.2480000 -20.7980000  69.6480000
+ 409.9150000 -23.1650000  71.6000000 411.7370000 -20.7780000  72.3500000
+ 410.0030000 -23.7210000  69.3180000 411.5930000 -23.7040000  68.4720000
+ 411.3590000 -24.7350000  69.9290000 408.9340000 -21.6350000  73.0500000
+ 409.3820000 -19.9130000  73.0430000 412.0760000 -20.4940000  76.3480000
+ 411.1120000 -20.4360000  74.6780000 412.5590000 -22.7580000  70.4090000
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cid1.prmtop	Thu Jan 27 17:17:54 2022 +0000
@@ -0,0 +1,402 @@
+%VERSION  VERSION_STAMP = V0001.000  DATE = 11/24/21  10:22:01                  
+%FLAG TITLE                                                                     
+%FORMAT(20a4)                                                                   
+default_name                                                                    
+%FLAG POINTERS                                                                  
+%FORMAT(10I8)                                                                   
+      42      11      20      24      46      33      89      56       0       0
+     240       1      24      33      56      23      41      20      17       0
+       0       0       0       0       0       0       0       0      42       0
+       0
+%FLAG ATOM_NAME                                                                 
+%FORMAT(20a4)                                                                   
+C1  C2  C3  C4  C5  C6  C7  C8  C9  C10 C11 C12 C13 C14 C15 C16 N17 N18 N19 N20 
+O21 CL22H23 H24 H25 H26 H27 H28 H29 H30 H31 H32 H33 H34 H35 H36 H37 H38 H39 H40 
+H41 H42 
+%FLAG CHARGE                                                                    
+%FORMAT(5E16.8)                                                                 
+ -4.30592949E+00 -1.43956170E+00 -1.23911640E+00  8.03967876E+00  7.94856726E+00
+ -1.60902909E+00 -5.47762338E+00 -1.52338428E+00 -4.18930677E+00  1.31874785E+01
+ -1.81129662E+00  1.98258624E+00  3.58614864E+00 -1.83498561E+00  1.45960623E+00
+  1.80400770E+00 -1.16804943E+01 -2.82627873E+00 -1.06946679E+01 -1.25260090E+01
+ -1.19556510E+01 -3.71734920E-01  3.07956870E+00  2.51467740E+00  3.29823630E+00
+  9.49381830E-01  7.12491930E-01  3.55334850E+00  1.61631801E+00  1.61631801E+00
+  1.88965251E+00  1.88965251E+00  2.61854451E+00  1.88965251E+00  2.01114058E+00
+  2.01114058E+00  2.01114058E+00  1.27009431E+00  1.27009431E+00  5.51589021E+00
+  5.87669175E+00  8.14172364E+00
+%FLAG ATOMIC_NUMBER                                                             
+%FORMAT(10I8)                                                                   
+       6       6       6       6       6       6       6       6       6       6
+       6       6       6       6       6       6       7       7       7       7
+       8      17       1       1       1       1       1       1       1       1
+       1       1       1       1       1       1       1       1       1       1
+       1       1
+%FLAG MASS                                                                      
+%FORMAT(5E16.8)                                                                 
+  1.20100000E+01  1.20100000E+01  1.20100000E+01  1.20100000E+01  1.20100000E+01
+  1.20100000E+01  1.20100000E+01  1.20100000E+01  1.20100000E+01  1.20100000E+01
+  1.20100000E+01  1.20100000E+01  1.20100000E+01  1.20100000E+01  1.20100000E+01
+  1.20100000E+01  1.40100000E+01  1.40100000E+01  1.40100000E+01  1.40100000E+01
+  1.60000000E+01  3.54500000E+01  1.00800000E+00  1.00800000E+00  1.00800000E+00
+  1.00800000E+00  1.00800000E+00  1.00800000E+00  1.00800000E+00  1.00800000E+00
+  1.00800000E+00  1.00800000E+00  1.00800000E+00  1.00800000E+00  1.00800000E+00
+  1.00800000E+00  1.00800000E+00  1.00800000E+00  1.00800000E+00  1.00800000E+00
+  1.00800000E+00  1.00800000E+00
+%FLAG ATOM_TYPE_INDEX                                                           
+%FORMAT(10I8)                                                                   
+       1       1       1       1       1       1       1       1       1       1
+       2       2       2       2       2       2       3       3       3       3
+       4       5       6       6       6       7       7       7       8       8
+       9       9       9       8       9       9       9      10      10      11
+      11      11
+%FLAG NUMBER_EXCLUDED_ATOMS                                                     
+%FORMAT(10I8)                                                                   
+       9      12      11       7       9       8      14       7      10      10
+      16      15      20      14       8      10       3       6       5      10
+       1       2       2       1       1       1       1       1       4       3
+       2       1       2       2       3       2       1       2       1       1
+       1       1
+%FLAG NONBONDED_PARM_INDEX                                                      
+%FORMAT(10I8)                                                                   
+       1       2       4       7      11      16      22      29      37      46
+      56       2       3       5       8      12      17      23      30      38
+      47      57       4       5       6       9      13      18      24      31
+      39      48      58       7       8       9      10      14      19      25
+      32      40      49      59      11      12      13      14      15      20
+      26      33      41      50      60      16      17      18      19      20
+      21      27      34      42      51      61      22      23      24      25
+      26      27      28      35      43      52      62      29      30      31
+      32      33      34      35      36      44      53      63      37      38
+      39      40      41      42      43      44      45      54      64      46
+      47      48      49      50      51      52      53      54      55      65
+      56      57      58      59      60      61      62      63      64      65
+      66
+%FLAG RESIDUE_LABEL                                                             
+%FORMAT(20a4)                                                                   
+UNL 
+%FLAG RESIDUE_POINTER                                                           
+%FORMAT(10I8)                                                                   
+       1
+%FLAG BOND_FORCE_CONSTANT                                                       
+%FORMAT(5E16.8)                                                                 
+  3.73200000E+02  4.03200000E+02  4.08400000E+02  3.28700000E+02  3.30600000E+02
+  2.83300000E+02  3.38700000E+02  3.00900000E+02  3.30600000E+02  4.27600000E+02
+  6.37700000E+02  3.71000000E+02  4.25800000E+02  3.17500000E+02  3.21000000E+02
+  5.00900000E+02  3.52000000E+02  4.61100000E+02  4.88000000E+02  3.41500000E+02
+  4.19800000E+02  3.49100000E+02  3.45800000E+02
+%FLAG BOND_EQUIL_VALUE                                                          
+%FORMAT(5E16.8)                                                                 
+  1.03040000E+00  1.01290000E+00  1.01000000E+00  1.46190000E+00  1.09690000E+00
+  1.51100000E+00  1.09100000E+00  1.53750000E+00  1.09690000E+00  1.37890000E+00
+  1.21830000E+00  1.46760000E+00  1.38020000E+00  1.73540000E+00  1.51560000E+00
+  1.37290000E+00  1.08170000E+00  1.39840000E+00  1.33900000E+00  1.08900000E+00
+  1.42780000E+00  1.08370000E+00  1.08600000E+00
+%FLAG ANGLE_FORCE_CONSTANT                                                      
+%FORMAT(5E16.8)                                                                 
+  3.92000000E+01  3.92000000E+01  3.94000000E+01  4.86000000E+01  7.42000000E+01
+  4.98000000E+01  4.98000000E+01  5.19000000E+01  4.63000000E+01  4.58000000E+01
+  4.59000000E+01  6.42000000E+01  4.62000000E+01  6.59000000E+01  4.64000000E+01
+  6.29000000E+01  6.26000000E+01  6.86950000E+01  6.34000000E+01  4.83000000E+01
+  4.85000000E+01  6.91000000E+01  6.91000000E+01  4.68000000E+01  6.82000000E+01
+  4.71000000E+01  7.34000000E+01  4.73000000E+01  4.82000000E+01  6.88000000E+01
+  4.81000000E+01  6.31000000E+01  6.48000000E+01  4.66000000E+01  5.75000000E+01
+  6.85000000E+01  6.35000000E+01  6.83000000E+01  5.78000000E+01  6.51000000E+01
+  6.66000000E+01
+%FLAG ANGLE_EQUIL_VALUE                                                         
+%FORMAT(5E16.8)                                                                 
+  1.89298492E+00  1.91549968E+00  1.87762601E+00  1.88513093E+00  2.14762857E+00
+  1.90031530E+00  2.10364625E+00  2.02510640E+00  1.91637234E+00  2.05390434E+00
+  1.92178286E+00  1.99334139E+00  1.92963685E+00  1.94796281E+00  1.91218355E+00
+  1.94621748E+00  1.91392888E+00  1.98679641E+00  2.10643878E+00  2.05163542E+00
+  2.12511381E+00  1.96698691E+00  2.16298747E+00  2.19038915E+00  1.99299233E+00
+  2.11307103E+00  1.86732857E+00  2.24239998E+00  2.09230160E+00  2.14570870E+00
+  2.10033012E+00  1.95599133E+00  1.98618554E+00  1.94517029E+00  2.15391175E+00
+  1.91811767E+00  2.10783504E+00  2.04587583E+00  2.09422147E+00  2.11795796E+00
+  2.09474507E+00
+%FLAG DIHEDRAL_FORCE_CONSTANT                                                   
+%FORMAT(5E16.8)                                                                 
+  0.00000000E+00  1.55555556E-01  1.50000000E-01  1.70000000E+00  3.62500000E+00
+  4.00000000E+00  2.00000000E+00  2.50000000E+00  2.87500000E+00  1.60000000E-01
+  2.00000000E-01  2.50000000E-01  1.80000000E-01  5.30000000E-01  1.50000000E-01
+  5.00000000E-01  7.00000000E-01  4.80000000E+00  1.10000000E+00  1.05000000E+01
+%FLAG DIHEDRAL_PERIODICITY                                                      
+%FORMAT(5E16.8)                                                                 
+  2.00000000E+00  3.00000000E+00  3.00000000E+00  2.00000000E+00  2.00000000E+00
+  2.00000000E+00  1.00000000E+00  2.00000000E+00  2.00000000E+00  3.00000000E+00
+  1.00000000E+00  2.00000000E+00  3.00000000E+00  1.00000000E+00  3.00000000E+00
+  4.00000000E+00  2.00000000E+00  2.00000000E+00  2.00000000E+00  2.00000000E+00
+%FLAG DIHEDRAL_PHASE                                                            
+%FORMAT(5E16.8)                                                                 
+  0.00000000E+00  0.00000000E+00  0.00000000E+00  3.14159400E+00  3.14159400E+00
+  3.14159400E+00  0.00000000E+00  3.14159400E+00  3.14159400E+00  0.00000000E+00
+  3.14159400E+00  3.14159400E+00  0.00000000E+00  0.00000000E+00  3.14159400E+00
+  3.14159400E+00  0.00000000E+00  3.14159400E+00  3.14159400E+00  3.14159400E+00
+%FLAG SCEE_SCALE_FACTOR                                                         
+%FORMAT(5E16.8)                                                                 
+  1.20000000E+00  1.20000000E+00  1.20000000E+00  1.20000000E+00  1.20000000E+00
+  1.20000000E+00  1.20000000E+00  1.20000000E+00  1.20000000E+00  1.20000000E+00
+  1.20000000E+00  1.20000000E+00  1.20000000E+00  1.20000000E+00  1.20000000E+00
+  1.20000000E+00  1.20000000E+00  1.20000000E+00  0.00000000E+00  0.00000000E+00
+%FLAG SCNB_SCALE_FACTOR                                                         
+%FORMAT(5E16.8)                                                                 
+  2.00000000E+00  2.00000000E+00  2.00000000E+00  2.00000000E+00  2.00000000E+00
+  2.00000000E+00  2.00000000E+00  2.00000000E+00  2.00000000E+00  2.00000000E+00
+  2.00000000E+00  2.00000000E+00  2.00000000E+00  2.00000000E+00  2.00000000E+00
+  2.00000000E+00  2.00000000E+00  2.00000000E+00  0.00000000E+00  0.00000000E+00
+%FLAG SOLTY                                                                     
+%FORMAT(5E16.8)                                                                 
+  0.00000000E+00  0.00000000E+00  0.00000000E+00  0.00000000E+00  0.00000000E+00
+  0.00000000E+00  0.00000000E+00  0.00000000E+00  0.00000000E+00  0.00000000E+00
+  0.00000000E+00  0.00000000E+00  0.00000000E+00  0.00000000E+00  0.00000000E+00
+  0.00000000E+00  0.00000000E+00
+%FLAG LENNARD_JONES_ACOEF                                                       
+%FORMAT(5E16.8)                                                                 
+  8.19971662E+05  9.24822270E+05  1.04308023E+06  8.82619071E+05  9.95480466E+05
+  9.44293233E+05  5.74393458E+05  6.47841731E+05  6.06829342E+05  3.79876399E+05
+  1.63123475E+06  1.83982239E+06  1.76079018E+06  1.15256113E+06  3.24095688E+06
+  7.62451550E+04  8.59947003E+04  7.91627154E+04  4.77908183E+04  1.54217681E+05
+  5.71629601E+03  6.37148278E+04  7.18621074E+04  6.58473870E+04  3.93690817E+04
+  1.29147101E+05  4.64559155E+03  3.76169105E+03  8.61541883E+04  9.71708117E+04
+  8.96776989E+04  5.44261042E+04  1.74057868E+05  6.55825601E+03  5.34045360E+03
+  7.51607703E+03  2.01619733E+04  2.27401052E+04  2.01791425E+04  1.12780457E+04
+  4.14717455E+04  1.21014911E+03  9.55000044E+02  1.41077189E+03  2.01823541E+02
+  6.01816484E+04  6.78771368E+04  6.20665997E+04  3.69471530E+04  1.22102013E+05
+  4.33325458E+03  3.50301067E+03  4.98586848E+03  8.79040886E+02  3.25969625E+03
+  2.27577561E+03  2.56678134E+03  2.12601181E+03  1.02595236E+03  4.83020816E+03
+  8.90987508E+01  6.63368273E+01  1.07193646E+02  9.14716912E+00  5.94667300E+01
+  1.39982777E-01
+%FLAG LENNARD_JONES_BCOEF                                                       
+%FORMAT(5E16.8)                                                                 
+  5.31102864E+02  5.99015525E+02  6.75612247E+02  6.53361429E+02  7.36907417E+02
+  8.01323529E+02  5.55666448E+02  6.26720080E+02  6.77220874E+02  5.64885984E+02
+  9.92485818E+02  1.11939599E+03  1.22266505E+03  1.04286543E+03  1.85348706E+03
+  1.04660679E+02  1.18043746E+02  1.26451907E+02  1.03580945E+02  1.97211104E+02
+  1.85196588E+01  9.56748258E+01  1.07908863E+02  1.15327881E+02  9.40124296E+01
+  1.80470661E+02  1.66953734E+01  1.50233639E+01  1.12529845E+02  1.26919150E+02
+  1.36131731E+02  1.11805549E+02  2.11915736E+02  2.00642027E+01  1.81057616E+01
+  2.17257828E+01  5.44372326E+01  6.13981767E+01  6.45756063E+01  5.08951803E+01
+  1.03440958E+02  8.61880722E+00  7.65648470E+00  9.41257003E+00  3.56012899E+00
+  9.40505980E+01  1.06076943E+02  1.13252061E+02  9.21192136E+01  1.77491593E+02
+  1.63092814E+01  1.46638650E+01  1.76949863E+01  7.42992380E+00  1.43076527E+01
+  1.82891803E+01  2.06278363E+01  2.09604198E+01  1.53505284E+01  3.53019992E+01
+  2.33864085E+00  2.01792524E+00  2.59456373E+00  7.57919667E-01  1.93248820E+00
+  9.37598976E-02
+%FLAG BONDS_INC_HYDROGEN                                                        
+%FORMAT(10I8)                                                                   
+      57     123       1      54     120       2      51     117       3      45
+     111       5      45     114       5      42     102       7      42     105
+       7      42     108       7      39      99       9      36      96       7
+      33      90       7      33      93       7      30      84       9      30
+      87       9      15      81      17      12      78      20       9      75
+      20       6      72      22       3      69      23       0      66      23
+%FLAG BONDS_WITHOUT_HYDROGEN                                                    
+%FORMAT(10I8)                                                                   
+      45      54       4      42      57       6      39      45       8      36
+      39       8      36      57       6      33      57       6      30      33
+       8      30      39       8      27      54      10      27      60      11
+      24      27      12      24      51      13      21      63      14      18
+      36      15      15      21      16      15      51      13      12      18
+      18      12      48      19       9      48      19       6      21      21
+       6      24      16       3      18      18       0       3      18       0
+       9      18
+%FLAG ANGLES_INC_HYDROGEN                                                       
+%FORMAT(10I8)                                                                   
+     111      45     114       1     105      42     108       2     102      42
+     105       2     102      42     108       2      90      33      93       2
+      84      30      87       3      57      33      90       4      57      33
+      93       4      57      36      96       4      57      42     102       4
+      57      42     105       4      57      42     108       4      54      45
+     111       6      54      45     114       6      51      15      81       7
+      48       9      75       8      48      12      78       8      45      39
+      99       9      45      54     120      10      42      57     123      11
+      39      30      84       9      39      30      87       9      39      36
+      96      13      39      45     111      15      39      45     114      15
+      36      39      99       9      36      57     123      11      33      30
+      84       9      33      30      87       9      33      57     123      11
+      30      33      90      13      30      33      93      13      30      39
+      99       9      27      54     120      20      24       6      72      21
+      24      51     117      24      21       6      72      26      21      15
+      81      28      18       3      69      29      18      12      78      31
+      18      36      96      34      15      51     117      24       9       0
+      66      29       3       0      66      29       0       3      69      29
+       0       9      75      31
+%FLAG ANGLES_WITHOUT_HYDROGEN                                                   
+%FORMAT(10I8)                                                                   
+      54      27      60       5      39      36      57      12      39      45
+      54      14      36      39      45      16      36      57      42      17
+      33      30      39      16      33      57      36      17      33      57
+      42      17      30      33      57      12      30      39      36      16
+      30      39      45      16      27      24      51      18      27      54
+      45      19      24      27      54      22      24      27      60      23
+      21       6      24      25      21      15      51      27      18      12
+      48      30      18      36      39      32      18      36      57      33
+      15      21      63      35      15      51      24      36      12      18
+      36      37       9      48      12      38       6      21      15      25
+       6      21      63      39       6      24      27      40       6      24
+      51      27       3       0       9      41       3      18      12      41
+       3      18      36      37       0       3      18      41       0       9
+      48      30
+%FLAG DIHEDRALS_INC_HYDROGEN                                                    
+%FORMAT(10I8)                                                                   
+     114      45      54     120       1     111      45      54     120       1
+     108      42      57     123       2     105      42      57     123       2
+     102      42      57     123       2      99      39      45     111       2
+      99      39      45     114       2      96      36      39      99       2
+      96      36      57     123       2      93      33      57     123       2
+      90      33      57     123       2      87      30      33      90       2
+      87      30      33      93       2      87      30      39      99       3
+      84      30      33      90       2      84      30      33      93       2
+      84      30      39      99       3      81      15      51     117       4
+      66       0       3      69       5      66       0       9      75       5
+      63      21       6      72       6      63      21      15      81       6
+      60      27      54     120       7      60      27     -54     120       8
+      57      33      30      84       2      57      33      30      87       2
+      57      36      39      99       2      54      45      39      99       2
+      51      24       6      72       6      66       0       9      48       5
+      45      39      30      84      10      45      39      30      87      10
+      45      39      36      96       2      42      57      33      90       2
+      42      57      33      93       2      42      57      36      96       2
+      39      30      33      90       2      39      30      33      93       2
+      39      36      57     123       2      39      45      54     120       1
+      36      18       3      69       5      36      18      12      78       5
+      36      39      30      84      10      36      39      30      87      10
+      36      39      45     111       2      36      39      45     114       2
+      36      57      33      90       2      36      57      33      93       2
+      36      57      42     102       2      36      57      42     105       2
+      36      57      42     108       2      33      30      39      99      10
+      33      57      36      96       2      33      57      42     102       2
+      33      57      42     105       2      33      57      42     108       2
+      30      33      57     123       2      30      39      36      96       2
+      30      39      45     111       2      30      39      45     114       2
+      27      24       6      72       6      27      24      51     117       4
+      27      54      45     111       1      27      54      45     114       1
+      24      27      54     120       8      24      51      15      81       4
+      21      15      51     117       4      66       0       3      18       5
+      18      36      39      99       2      18      36      57     123       2
+      15      21       6      72       6      12      18       3      69       5
+      12      18      36      96       1      12      48       9      75      18
+       9       0       3      69       5       9      48      12      78      18
+       6      21      15      81       6       6      24      51     117       4
+       3       0       9      75       5       3      18      12      78       5
+       3      18      36      96       1      27      45     -54    -120      19
+      15      24     -51    -117      19      21      81     -15     -51      19
+      18      78     -12     -48      19       0      75      -9     -48      19
+      21      24      -6     -72      19       0      18      -3     -69      19
+      66       0      -9      -3      19
+%FLAG DIHEDRALS_WITHOUT_HYDROGEN                                                
+%FORMAT(10I8)                                                                   
+      51      15      21      63       6      51      24      27      54       9
+      51      24      27      60       9      45      39      36      57       2
+      45      54      27      60       8      39      30     -33      57       2
+      39      36      57      42       2      36      18      12      48       5
+      36      39      45      54       2      33      30     -39      36      11
+      33      30     -39      36      12      33      30     -39      36      13
+      33      30      39      45      11      33      30     -39      45      12
+      33      30     -39      45      13      33      57     -36      39       2
+      30      33     -57      36       2      30      33      57      42       2
+      30      39     -36      57       2      30      39      45      54       2
+      27      54      45      39      14      27      54     -45      39       1
+      27      54     -45      39      15      27      54     -45      39      16
+      24       6      21      63       6      24      27      54      45       8
+      21       6      24      27       6      21       6     -24      51       6
+      21      15     -51      24       4      18      36      39      30       2
+      18      36      39      45       2      18      36      57      33      17
+      18      36     -57      33       2      18      36      57      42      17
+      18      36     -57      42       2      15      21      -6      24       6
+      15      51      24      27       4      12      18      36      39       1
+      12      18      36      57       1       9       0       3      18       5
+       9      48     -12      18      18       6      21     -15      51       6
+       6      24      27      54       9       6      24      27      60       9
+       6      24     -51      15       4       3       0       9      48       5
+       3      18     -12      48       5       3      18      36      39       1
+       3      18      36      57       1       0       3      18      12       5
+       0       3      18      36       5       0       9     -48      12      18
+      24      54     -27     -60      20      27       6     -24     -51      19
+       6      15     -21     -63      19       3      12     -18     -36      19
+%FLAG EXCLUDED_ATOMS_LIST                                                       
+%FORMAT(10I8)                                                                   
+       2       4       5       7      13      17      23      24      26       4
+       5       7      13      14      17      20      23      24      26      27
+      33       6       8       9      10      18      19      21      22      25
+      28      40       5       7      17      23      24      26      27       7
+      13      14      17      20      24      26      27      33       8       9
+      10      18      22      25      28      40      11      12      13      14
+      15      16      17      20      23      24      27      33      34      42
+       9      10      18      22      25      28      40      10      16      18
+      19      21      22      25      28      40      41      14      16      18
+      19      21      25      38      39      40      41      12      13      14
+      15      16      19      20      29      30      31      32      33      34
+      38      39      42      13      14      15      16      20      29      30
+      31      32      33      34      35      36      37      42      14      15
+      16      17      19      20      24      27      29      30      31      32
+      33      34      35      36      37      38      39      42      15      16
+      19      20      29      30      31      32      33      34      38      39
+      41      42      20      31      32      33      35      36      37      42
+      19      20      21      29      30      33      34      38      39      41
+      23      26      27      19      21      22      25      28      40      21
+      34      38      39      41      29      30      31      32      33      34
+      35      36      37      42      41      25      28      24      26       0
+       0       0       0      40      30      31      32      34      31      32
+      34      32      42      42      34      42      38      39      36      37
+      42      37      42      42      39      41      41       0       0       0
+%FLAG HBOND_ACOEF                                                               
+%FORMAT(5E16.8)                                                                 
+
+%FLAG HBOND_BCOEF                                                               
+%FORMAT(5E16.8)                                                                 
+
+%FLAG HBCUT                                                                     
+%FORMAT(5E16.8)                                                                 
+
+%FLAG AMBER_ATOM_TYPE                                                           
+%FORMAT(20a4)                                                                   
+ca  ca  cc  ca  ca  cd  ca  cc  cd  c   c3  c3  c3  c3  c3  c3  nb  na  n   n4  
+o   cl  ha  ha  ha  h4  h4  h4  hc  hc  hx  hx  hx  hc  hx  hx  hx  h1  h1  hn  
+hn  hn  
+%FLAG TREE_CHAIN_CLASSIFICATION                                                 
+%FORMAT(20a4)                                                                   
+BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA 
+BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA 
+BLA BLA 
+%FLAG JOIN_ARRAY                                                                
+%FORMAT(10I8)                                                                   
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0
+%FLAG IROTAT                                                                    
+%FORMAT(10I8)                                                                   
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0
+%FLAG RADIUS_SET                                                                
+%FORMAT(1a80)                                                                   
+modified Bondi radii (mbondi)                                                   
+%FLAG RADII                                                                     
+%FORMAT(5E16.8)                                                                 
+  1.70000000E+00  1.70000000E+00  1.70000000E+00  1.70000000E+00  1.70000000E+00
+  1.70000000E+00  1.70000000E+00  1.70000000E+00  1.70000000E+00  1.70000000E+00
+  1.70000000E+00  1.70000000E+00  1.70000000E+00  1.70000000E+00  1.70000000E+00
+  1.70000000E+00  1.55000000E+00  1.55000000E+00  1.55000000E+00  1.55000000E+00
+  1.50000000E+00  1.70000000E+00  1.30000000E+00  1.30000000E+00  1.30000000E+00
+  1.30000000E+00  1.30000000E+00  1.30000000E+00  1.30000000E+00  1.30000000E+00
+  1.30000000E+00  1.30000000E+00  1.30000000E+00  1.30000000E+00  1.30000000E+00
+  1.30000000E+00  1.30000000E+00  1.30000000E+00  1.30000000E+00  1.30000000E+00
+  1.30000000E+00  1.30000000E+00
+%FLAG SCREEN                                                                    
+%FORMAT(5E16.8)                                                                 
+  7.20000000E-01  7.20000000E-01  7.20000000E-01  7.20000000E-01  7.20000000E-01
+  7.20000000E-01  7.20000000E-01  7.20000000E-01  7.20000000E-01  7.20000000E-01
+  7.20000000E-01  7.20000000E-01  7.20000000E-01  7.20000000E-01  7.20000000E-01
+  7.20000000E-01  7.90000000E-01  7.90000000E-01  7.90000000E-01  7.90000000E-01
+  8.50000000E-01  8.00000000E-01  8.50000000E-01  8.50000000E-01  8.50000000E-01
+  8.50000000E-01  8.50000000E-01  8.50000000E-01  8.50000000E-01  8.50000000E-01
+  8.50000000E-01  8.50000000E-01  8.50000000E-01  8.50000000E-01  8.50000000E-01
+  8.50000000E-01  8.50000000E-01  8.50000000E-01  8.50000000E-01  8.50000000E-01
+  8.50000000E-01  8.50000000E-01
+%FLAG IPOL                                                                      
+%FORMAT(1I8)                                                                    
+       0
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/complex.prmtop	Thu Jan 27 17:17:54 2022 +0000
@@ -0,0 +1,19476 @@
+%VERSION  VERSION_STAMP = V0001.000  DATE = 10/09/09  16:22:47                  
+%FLAG TITLE                                                                     
+%FORMAT(20a4)                                                                   
+                                                                                
+%FLAG POINTERS                                                                  
+%FORMAT(10I8)                                                                   
+    3941      15    1991    1991    4536    2694    8432    6711       0       0
+   21774     241    1991    2694    6711      59     119      51      42       0
+       0       0       0       0       0       0       0       0      61       0
+       0
+%FLAG ATOM_NAME                                                                 
+%FORMAT(20a4)                                                                   
+N   H1  H2  H3  CA  HA  CB  HB1 HB2 HB3 C   O   N   H   CA  HA  CB  HB2 HB3 CG  
+HG  CD1 HD11HD12HD13CD2 HD21HD22HD23C   O   N   H   CA  HA  CB  HB2 HB3 OG  HG  
+C   O   N   H   CA  HA  CB  HB2 HB3 CG  HG  CD1 HD11HD12HD13CD2 HD21HD22HD23C   
+O   N   H   CA  HA  CB  HB  CG2 HG21HG22HG23OG1 HG1 C   O   N   H   CA  HA  CB  
+HB1 HB2 HB3 C   O   N   H   CA  HA  CB  HB2 HB3 CG  OD1 OD2 C   O   N   H   CA  
+HA  CB  HB2 HB3 CG  HG2 HG3 CD  OE1 NE2 HE21HE22C   O   N   H   CA  HA  CB  HB2 
+HB3 CG  HG2 HG3 SD  CE  HE1 HE2 HE3 C   O   N   H   CA  HA  CB  HB  CG1 HG11HG12
+HG13CG2 HG21HG22HG23C   O   N   H   CA  HA  CB  HB2 HB3 OG  HG  C   O   N   H   
+CA  HA  CB  HB1 HB2 HB3 C   O   N   H   CA  HA  CB  HB2 HB3 CG  HG  CD1 HD11HD12
+HD13CD2 HD21HD22HD23C   O   N   H   CA  HA  CB  HB2 HB3 CG  HG  CD1 HD11HD12HD13
+CD2 HD21HD22HD23C   O   N   H   CA  HA  CB  HB2 HB3 CG  OD1 OD2 C   O   N   H   
+CA  HA  CB  HB1 HB2 HB3 C   O   N   H   CA  HA  CB  HB2 HB3 CG  HG2 HG3 CD  OE1 
+OE2 C   O   N   CD  HD2 HD3 CG  HG2 HG3 CB  HB2 HB3 CA  HA  C   O   N   CD  HD2 
+HD3 CG  HG2 HG3 CB  HB2 HB3 CA  HA  C   O   N   H   CA  HA  CB  HB  CG2 HG21HG22
+HG23CG1 HG12HG13CD1 HD11HD12HD13C   O   N   H   CA  HA  CB  HB2 HB3 CG  HG  CD1 
+HD11HD12HD13CD2 HD21HD22HD23C   O   N   H   CA  HA  CB  HB2 HB3 CG  CD1 HD1 CE1 
+HE1 CZ  OH  HH  CE2 HE2 CD2 HD2 C   O   N   H   CA  HA  CB  HB2 HB3 OG  HG  C   
+O   N   H   CA  HA  CB  HB2 HB3 CG  HG2 HG3 CD  OE1 OE2 C   O   N   H   CA  HA  
+CB  HB2 HB3 CG  CD1 HD1 CE1 HE1 CZ  OH  HH  CE2 HE2 CD2 HD2 C   O   N   H   CA  
+HA  CB  HB2 HB3 CG  OD1 OD2 C   O   N   CD  HD2 HD3 CG  HG2 HG3 CB  HB2 HB3 CA  
+HA  C   O   N   H   CA  HA  CB  HB  CG2 HG21HG22HG23OG1 HG1 C   O   N   H   CA  
+HA  CB  HB2 HB3 CG  HG2 HG3 CD  HD2 HD3 NE  HE  CZ  NH1 HH11HH12NH2 HH21HH22C   
+O   N   CD  HD2 HD3 CG  HG2 HG3 CB  HB2 HB3 CA  HA  C   O   N   H   CA  HA  CB  
+HB2 HB3 CG  CD1 HD1 CE1 HE1 CZ  HZ  CE2 HE2 CD2 HD2 C   O   N   H   CA  HA  CB  
+HB2 HB3 OG  HG  C   O   N   H   CA  HA  CB  HB2 HB3 CG  HG2 HG3 CD  OE1 OE2 C   
+O   N   H   CA  HA  CB  HB1 HB2 HB3 C   O   N   H   CA  HA  CB  HB2 HB3 OG  HG  
+C   O   N   H   CA  HA  CB  HB2 HB3 CG  HG2 HG3 SD  CE  HE1 HE2 HE3 C   O   N   
+H   CA  HA  CB  HB2 HB3 CG  HG2 HG3 SD  CE  HE1 HE2 HE3 C   O   N   H   CA  HA2 
+HA3 C   O   N   H   CA  HA  CB  HB2 HB3 CG  HG  CD1 HD11HD12HD13CD2 HD21HD22HD23
+C   O   N   H   CA  HA  CB  HB2 HB3 CG  HG  CD1 HD11HD12HD13CD2 HD21HD22HD23C   
+O   N   H   CA  HA  CB  HB  CG2 HG21HG22HG23OG1 HG1 C   O   N   H   CA  HA  CB  
+HB2 HB3 CG  OD1 ND2 HD21HD22C   O   N   H   CA  HA  CB  HB2 HB3 CG  HG  CD1 HD11
+HD12HD13CD2 HD21HD22HD23C   O   N   H   CA  HA  CB  HB1 HB2 HB3 C   O   N   H   
+CA  HA  CB  HB2 HB3 CG  OD1 OD2 C   O   N   H   CA  HA  CB  HB2 HB3 CG  HG2 HG3 
+CD  HD2 HD3 NE  HE  CZ  NH1 HH11HH12NH2 HH21HH22C   O   N   H   CA  HA  CB  HB2 
+HB3 CG  HG2 HG3 CD  OE1 OE2 C   O   N   H   CA  HA  CB  HB2 HB3 CG  HG  CD1 HD11
+HD12HD13CD2 HD21HD22HD23C   O   N   H   CA  HA  CB  HB  CG1 HG11HG12HG13CG2 HG21
+HG22HG23C   O   N   H   CA  HA  CB  HB2 HB3 CG  ND1 CE1 HE1 NE2 HE2 CD2 HD2 C   
+O   N   H   CA  HA  CB  HB2 HB3 CG  HG2 HG3 SD  CE  HE1 HE2 HE3 C   O   N   H   
+CA  HA  CB  HB  CG2 HG21HG22HG23CG1 HG12HG13CD1 HD11HD12HD13C   O   N   H   CA  
+HA  CB  HB2 HB3 CG  OD1 ND2 HD21HD22C   O   N   H   CA  HA  CB  HB2 HB3 CG  CD1 
+HD1 NE1 HE1 CE2 CZ2 HZ2 CH2 HH2 CZ3 HZ3 CE3 HE3 CD2 C   O   N   H   CA  HA  CB  
+HB1 HB2 HB3 C   O   N   H   CA  HA  CB  HB2 HB3 CG  HG2 HG3 CD  HD2 HD3 CE  HE2 
+HE3 NZ  HZ1 HZ2 HZ3 C   O   N   H   CA  HA  CB  HB2 HB3 CG  HG2 HG3 CD  HD2 HD3 
+NE  HE  CZ  NH1 HH11HH12NH2 HH21HH22C   O   N   H   CA  HA  CB  HB  CG1 HG11HG12
+HG13CG2 HG21HG22HG23C   O   N   CD  HD2 HD3 CG  HG2 HG3 CB  HB2 HB3 CA  HA  C   
+O   N   H   CA  HA2 HA3 C   O   N   H   CA  HA  CB  HB2 HB3 CG  CD1 HD1 CE1 HE1 
+CZ  HZ  CE2 HE2 CD2 HD2 C   O   N   H   CA  HA  CB  HB  CG1 HG11HG12HG13CG2 HG21
+HG22HG23C   O   N   H   CA  HA  CB  HB2 HB3 CG  OD1 OD2 C   O   N   H   CA  HA  
+CB  HB2 HB3 CG  HG  CD1 HD11HD12HD13CD2 HD21HD22HD23C   O   N   H   CA  HA  CB  
+HB  CG2 HG21HG22HG23OG1 HG1 C   O   N   H   CA  HA  CB  HB2 HB3 CG  HG  CD1 HD11
+HD12HD13CD2 HD21HD22HD23C   O   N   H   CA  HA  CB  HB2 HB3 CG  ND1 CE1 HE1 NE2 
+HE2 CD2 HD2 C   O   N   H   CA  HA  CB  HB2 HB3 CG  OD1 OD2 C   O   N   H   CA  
+HA  CB  HB2 HB3 CG  HG2 HG3 CD  OE1 NE2 HE21HE22C   O   N   H   CA  HA  CB  HB  
+CG1 HG11HG12HG13CG2 HG21HG22HG23C   O   N   H   CA  HA  CB  HB2 HB3 CG  ND1 CE1 
+HE1 NE2 HE2 CD2 HD2 C   O   N   H   CA  HA  CB  HB2 HB3 CG  HG  CD1 HD11HD12HD13
+CD2 HD21HD22HD23C   O   N   H   CA  HA  CB  HB2 HB3 CG  HG  CD1 HD11HD12HD13CD2 
+HD21HD22HD23C   O   N   H   CA  HA  CB  HB2 HB3 CG  HG2 HG3 CD  OE1 OE2 C   O   
+N   H   CA  HA  CB  HB2 HB3 SG  HG  C   O   N   H   CA  HA  CB  HB1 HB2 HB3 C   
+O   N   H   CA  HA  CB  HB2 HB3 CG  CD1 HD1 NE1 HE1 CE2 CZ2 HZ2 CH2 HH2 CZ3 HZ3 
+CE3 HE3 CD2 C   O   N   H   CA  HA  CB  HB2 HB3 CG  HG  CD1 HD11HD12HD13CD2 HD21
+HD22HD23C   O   N   H   CA  HA  CB  HB2 HB3 CG  HG2 HG3 CD  OE1 OE2 C   O   N   
+H   CA  HA  CB  HB  CG2 HG21HG22HG23CG1 HG12HG13CD1 HD11HD12HD13C   O   N   H   
+CA  HA  CB  HB2 HB3 CG  HG  CD1 HD11HD12HD13CD2 HD21HD22HD23C   O   N   H   CA  
+HA  CB  HB2 HB3 CG  HG2 HG3 SD  CE  HE1 HE2 HE3 C   O   N   H   CA  HA  CB  HB  
+CG2 HG21HG22HG23CG1 HG12HG13CD1 HD11HD12HD13C   O   N   H   CA  HA2 HA3 C   O   
+N   H   CA  HA  CB  HB2 HB3 CG  HG  CD1 HD11HD12HD13CD2 HD21HD22HD23C   O   N   
+H   CA  HA  CB  HB  CG1 HG11HG12HG13CG2 HG21HG22HG23C   O   N   H   CA  HA  CB  
+HB2 HB3 CG  CD1 HD1 NE1 HE1 CE2 CZ2 HZ2 CH2 HH2 CZ3 HZ3 CE3 HE3 CD2 C   O   N   
+H   CA  HA  CB  HB2 HB3 CG  HG2 HG3 CD  HD2 HD3 NE  HE  CZ  NH1 HH11HH12NH2 HH21
+HH22C   O   N   H   CA  HA  CB  HB2 HB3 OG  HG  C   O   N   H   CA  HA  CB  HB2 
+HB3 CG  HG2 HG3 SD  CE  HE1 HE2 HE3 C   O   N   H   CA  HA  CB  HB2 HB3 CG  HG2 
+HG3 CD  OE1 OE2 C   O   N   H   CA  HA  CB  HB2 HB3 CG  ND1 CE1 HE1 NE2 HE2 CD2 
+HD2 C   O   N   CD  HD2 HD3 CG  HG2 HG3 CB  HB2 HB3 CA  HA  C   O   N   H   CA  
+HA2 HA3 C   O   N   H   CA  HA  CB  HB2 HB3 CG  HG2 HG3 CD  HD2 HD3 CE  HE2 HE3 
+NZ  HZ1 HZ2 HZ3 C   O   N   H   CA  HA  CB  HB2 HB3 CG  HG  CD1 HD11HD12HD13CD2 
+HD21HD22HD23C   O   N   H   CA  HA  CB  HB2 HB3 CG  HG  CD1 HD11HD12HD13CD2 HD21
+HD22HD23C   O   N   H   CA  HA  CB  HB2 HB3 CG  CD1 HD1 CE1 HE1 CZ  HZ  CE2 HE2 
+CD2 HD2 C   O   N   H   CA  HA  CB  HB1 HB2 HB3 C   O   N   CD  HD2 HD3 CG  HG2 
+HG3 CB  HB2 HB3 CA  HA  C   O   N   H   CA  HA  CB  HB2 HB3 CG  OD1 ND2 HD21HD22
+C   O   N   H   CA  HA  CB  HB2 HB3 CG  HG  CD1 HD11HD12HD13CD2 HD21HD22HD23C   
+O   N   H   CA  HA  CB  HB2 HB3 CG  HG  CD1 HD11HD12HD13CD2 HD21HD22HD23C   O   
+N   H   CA  HA  CB  HB2 HB3 CG  HG  CD1 HD11HD12HD13CD2 HD21HD22HD23C   O   N   
+H   CA  HA  CB  HB2 HB3 CG  OD1 OD2 C   O   N   H   CA  HA  CB  HB2 HB3 CG  HG2 
+HG3 CD  HD2 HD3 NE  HE  CZ  NH1 HH11HH12NH2 HH21HH22C   O   N   H   CA  HA  CB  
+HB2 HB3 CG  OD1 ND2 HD21HD22C   O   N   H   CA  HA  CB  HB2 HB3 CG  HG2 HG3 CD  
+OE1 NE2 HE21HE22C   O   N   H   CA  HA2 HA3 C   O   N   H   CA  HA  CB  HB2 HB3 
+CG  HG2 HG3 CD  HD2 HD3 CE  HE2 HE3 NZ  HZ1 HZ2 HZ3 C   O   N   H   CA  HA  CB  
+HB2 HB3 SG  HG  C   O   N   H   CA  HA  CB  HB  CG1 HG11HG12HG13CG2 HG21HG22HG23
+C   O   N   H   CA  HA  CB  HB2 HB3 CG  HG2 HG3 CD  OE1 OE2 C   O   N   H   CA  
+HA2 HA3 C   O   N   H   CA  HA  CB  HB2 HB3 CG  HG2 HG3 SD  CE  HE1 HE2 HE3 C   
+O   N   H   CA  HA  CB  HB  CG1 HG11HG12HG13CG2 HG21HG22HG23C   O   N   H   CA  
+HA  CB  HB2 HB3 CG  HG2 HG3 CD  OE1 OE2 C   O   N   H   CA  HA  CB  HB  CG2 HG21
+HG22HG23CG1 HG12HG13CD1 HD11HD12HD13C   O   N   H   CA  HA  CB  HB2 HB3 CG  CD1 
+HD1 CE1 HE1 CZ  HZ  CE2 HE2 CD2 HD2 C   O   N   H   CA  HA  CB  HB2 HB3 CG  OD1 
+OD2 C   O   N   H   CA  HA  CB  HB2 HB3 CG  HG2 HG3 SD  CE  HE1 HE2 HE3 C   O   
+N   H   CA  HA  CB  HB2 HB3 CG  HG  CD1 HD11HD12HD13CD2 HD21HD22HD23C   O   N   
+H   CA  HA  CB  HB2 HB3 CG  HG  CD1 HD11HD12HD13CD2 HD21HD22HD23C   O   N   H   
+CA  HA  CB  HB1 HB2 HB3 C   O   N   H   CA  HA  CB  HB  CG2 HG21HG22HG23OG1 HG1 
+C   O   N   H   CA  HA  CB  HB2 HB3 OG  HG  C   O   N   H   CA  HA  CB  HB2 HB3 
+OG  HG  C   O   N   H   CA  HA  CB  HB2 HB3 CG  HG2 HG3 CD  HD2 HD3 NE  HE  CZ  
+NH1 HH11HH12NH2 HH21HH22C   O   N   H   CA  HA  CB  HB2 HB3 CG  CD1 HD1 CE1 HE1 
+CZ  HZ  CE2 HE2 CD2 HD2 C   O   N   H   CA  HA  CB  HB2 HB3 CG  HG2 HG3 CD  HD2 
+HD3 NE  HE  CZ  NH1 HH11HH12NH2 HH21HH22C   O   N   H   CA  HA  CB  HB2 HB3 CG  
+HG2 HG3 SD  CE  HE1 HE2 HE3 C   O   N   H   CA  HA  CB  HB2 HB3 CG  HG2 HG3 SD  
+CE  HE1 HE2 HE3 C   O   N   H   CA  HA  CB  HB2 HB3 CG  OD1 ND2 HD21HD22C   O   
+N   H   CA  HA  CB  HB2 HB3 CG  HG  CD1 HD11HD12HD13CD2 HD21HD22HD23C   O   N   
+H   CA  HA  CB  HB2 HB3 CG  HG2 HG3 CD  OE1 NE2 HE21HE22C   O   N   H   CA  HA2 
+HA3 C   O   N   H   CA  HA  CB  HB2 HB3 CG  HG2 HG3 CD  OE1 OE2 C   O   N   H   
+CA  HA  CB  HB2 HB3 CG  HG2 HG3 CD  OE1 OE2 C   O   N   H   CA  HA  CB  HB2 HB3 
+CG  CD1 HD1 CE1 HE1 CZ  HZ  CE2 HE2 CD2 HD2 C   O   N   H   CA  HA  CB  HB  CG1 
+HG11HG12HG13CG2 HG21HG22HG23C   O   N   H   CA  HA  CB  HB2 HB3 SG  HG  C   O   
+N   H   CA  HA  CB  HB2 HB3 CG  HG  CD1 HD11HD12HD13CD2 HD21HD22HD23C   O   N   
+H   CA  HA  CB  HB2 HB3 CG  HG2 HG3 CD  HD2 HD3 CE  HE2 HE3 NZ  HZ1 HZ2 HZ3 C   
+O   N   H   CA  HA  CB  HB2 HB3 OG  HG  C   O   N   H   CA  HA  CB  HB  CG2 HG21
+HG22HG23CG1 HG12HG13CD1 HD11HD12HD13C   O   N   H   CA  HA  CB  HB  CG2 HG21HG22
+HG23CG1 HG12HG13CD1 HD11HD12HD13C   O   N   H   CA  HA  CB  HB2 HB3 CG  HG  CD1 
+HD11HD12HD13CD2 HD21HD22HD23C   O   N   H   CA  HA  CB  HB2 HB3 CG  HG  CD1 HD11
+HD12HD13CD2 HD21HD22HD23C   O   N   H   CA  HA  CB  HB2 HB3 CG  OD1 ND2 HD21HD22
+C   O   N   H   CA  HA  CB  HB2 HB3 OG  HG  C   O   N   H   CA  HA2 HA3 C   O   
+N   H   CA  HA  CB  HB  CG1 HG11HG12HG13CG2 HG21HG22HG23C   O   N   H   CA  HA  
+CB  HB2 HB3 CG  CD1 HD1 CE1 HE1 CZ  OH  HH  CE2 HE2 CD2 HD2 C   O   N   H   CA  
+HA  CB  HB  CG2 HG21HG22HG23OG1 HG1 C   O   N   H   CA  HA  CB  HB2 HB3 CG  CD1 
+HD1 CE1 HE1 CZ  HZ  CE2 HE2 CD2 HD2 C   O   N   H   CA  HA  CB  HB2 HB3 CG  HG  
+CD1 HD11HD12HD13CD2 HD21HD22HD23C   O   N   H   CA  HA  CB  HB2 HB3 OG  HG  C   
+O   N   H   CA  HA  CB  HB2 HB3 OG  HG  C   O   N   H   CA  HA  CB  HB  CG2 HG21
+HG22HG23OG1 HG1 C   O   N   H   CA  HA  CB  HB2 HB3 CG  HG  CD1 HD11HD12HD13CD2 
+HD21HD22HD23C   O   N   H   CA  HA  CB  HB2 HB3 CG  HG2 HG3 CD  HD2 HD3 CE  HE2 
+HE3 NZ  HZ1 HZ2 HZ3 C   O   N   H   CA  HA  CB  HB2 HB3 OG  HG  C   O   N   H   
+CA  HA  CB  HB2 HB3 CG  HG  CD1 HD11HD12HD13CD2 HD21HD22HD23C   O   N   H   CA  
+HA  CB  HB2 HB3 CG  HG2 HG3 CD  OE1 OE2 C   O   N   H   CA  HA  CB  HB2 HB3 CG  
+HG2 HG3 CD  OE1 OE2 C   O   N   H   CA  HA  CB  HB2 HB3 CG  HG2 HG3 CD  HD2 HD3 
+CE  HE2 HE3 NZ  HZ1 HZ2 HZ3 C   O   N   H   CA  HA  CB  HB2 HB3 CG  OD1 OD2 C   
+O   N   H   CA  HA  CB  HB2 HB3 CG  ND1 CE1 HE1 NE2 HE2 CD2 HD2 C   O   N   H   
+CA  HA  CB  HB  CG2 HG21HG22HG23CG1 HG12HG13CD1 HD11HD12HD13C   O   N   H   CA  
+HA  CB  HB2 HB3 CG  ND1 CE1 HE1 NE2 HE2 CD2 HD2 C   O   N   H   CA  HA  CB  HB2 
+HB3 CG  HG2 HG3 CD  HD2 HD3 NE  HE  CZ  NH1 HH11HH12NH2 HH21HH22C   O   N   H   
+CA  HA  CB  HB  CG1 HG11HG12HG13CG2 HG21HG22HG23C   O   N   H   CA  HA  CB  HB2 
+HB3 CG  HG  CD1 HD11HD12HD13CD2 HD21HD22HD23C   O   N   H   CA  HA  CB  HB2 HB3 
+CG  OD1 OD2 C   O   N   H   CA  HA  CB  HB2 HB3 CG  HG2 HG3 CD  HD2 HD3 CE  HE2 
+HE3 NZ  HZ1 HZ2 HZ3 C   O   N   H   CA  HA  CB  HB  CG2 HG21HG22HG23CG1 HG12HG13
+CD1 HD11HD12HD13C   O   N   H   CA  HA  CB  HB  CG2 HG21HG22HG23OG1 HG1 C   O   
+N   H   CA  HA  CB  HB2 HB3 CG  OD1 OD2 C   O   N   H   CA  HA  CB  HB  CG2 HG21
+HG22HG23OG1 HG1 C   O   N   H   CA  HA  CB  HB2 HB3 CG  HG  CD1 HD11HD12HD13CD2 
+HD21HD22HD23C   O   N   H   CA  HA  CB  HB  CG2 HG21HG22HG23CG1 HG12HG13CD1 HD11
+HD12HD13C   O   N   H   CA  HA  CB  HB2 HB3 CG  ND1 CE1 HE1 NE2 HE2 CD2 HD2 C   
+O   N   H   CA  HA  CB  HB2 HB3 CG  HG  CD1 HD11HD12HD13CD2 HD21HD22HD23C   O   
+N   H   CA  HA  CB  HB2 HB3 CG  HG2 HG3 SD  CE  HE1 HE2 HE3 C   O   N   H   CA  
+HA  CB  HB1 HB2 HB3 C   O   N   H   CA  HA  CB  HB2 HB3 CG  HG2 HG3 CD  HD2 HD3 
+CE  HE2 HE3 NZ  HZ1 HZ2 HZ3 C   O   N   H   CA  HA  CB  HB1 HB2 HB3 C   O   N   
+H   CA  HA2 HA3 C   O   N   H   CA  HA  CB  HB2 HB3 CG  HG  CD1 HD11HD12HD13CD2 
+HD21HD22HD23C   O   N   H   CA  HA  CB  HB  CG2 HG21HG22HG23OG1 HG1 C   O   N   
+H   CA  HA  CB  HB2 HB3 CG  HG  CD1 HD11HD12HD13CD2 HD21HD22HD23C   O   N   H   
+CA  HA  CB  HB2 HB3 CG  HG2 HG3 CD  OE1 NE2 HE21HE22C   O   N   H   CA  HA  CB  
+HB2 HB3 CG  HG2 HG3 CD  OE1 NE2 HE21HE22C   O   N   H   CA  HA  CB  HB2 HB3 CG  
+HG2 HG3 CD  OE1 NE2 HE21HE22C   O   N   H   CA  HA  CB  HB2 HB3 CG  ND1 CE1 HE1 
+NE2 HE2 CD2 HD2 C   O   N   H   CA  HA  CB  HB2 HB3 CG  HG2 HG3 CD  OE1 NE2 HE21
+HE22C   O   N   H   CA  HA  CB  HB2 HB3 CG  HG2 HG3 CD  HD2 HD3 NE  HE  CZ  NH1 
+HH11HH12NH2 HH21HH22C   O   N   H   CA  HA  CB  HB2 HB3 CG  HG  CD1 HD11HD12HD13
+CD2 HD21HD22HD23C   O   N   H   CA  HA  CB  HB1 HB2 HB3 C   O   N   H   CA  HA  
+CB  HB2 HB3 CG  HG2 HG3 CD  OE1 NE2 HE21HE22C   O   N   H   CA  HA  CB  HB2 HB3 
+CG  HG  CD1 HD11HD12HD13CD2 HD21HD22HD23C   O   N   H   CA  HA  CB  HB2 HB3 CG  
+HG  CD1 HD11HD12HD13CD2 HD21HD22HD23C   O   N   H   CA  HA  CB  HB2 HB3 CG  HG  
+CD1 HD11HD12HD13CD2 HD21HD22HD23C   O   N   H   CA  HA  CB  HB  CG2 HG21HG22HG23
+CG1 HG12HG13CD1 HD11HD12HD13C   O   N   H   CA  HA  CB  HB2 HB3 CG  HG  CD1 HD11
+HD12HD13CD2 HD21HD22HD23C   O   N   H   CA  HA  CB  HB2 HB3 OG  HG  C   O   N   
+H   CA  HA  CB  HB2 HB3 CG  ND1 CE1 HE1 NE2 HE2 CD2 HD2 C   O   N   H   CA  HA  
+CB  HB  CG2 HG21HG22HG23CG1 HG12HG13CD1 HD11HD12HD13C   O   N   H   CA  HA  CB  
+HB2 HB3 CG  HG2 HG3 CD  HD2 HD3 NE  HE  CZ  NH1 HH11HH12NH2 HH21HH22C   O   N   
+H   CA  HA  CB  HB2 HB3 CG  ND1 CE1 HE1 NE2 HE2 CD2 HD2 C   O   N   H   CA  HA  
+CB  HB2 HB3 CG  HG2 HG3 SD  CE  HE1 HE2 HE3 C   O   N   H   CA  HA  CB  HB2 HB3 
+OG  HG  C   O   N   H   CA  HA  CB  HB2 HB3 CG  OD1 ND2 HD21HD22C   O   N   H   
+CA  HA  CB  HB2 HB3 CG  HG2 HG3 CD  HD2 HD3 CE  HE2 HE3 NZ  HZ1 HZ2 HZ3 C   O   
+N   H   CA  HA2 HA3 C   O   N   H   CA  HA  CB  HB2 HB3 CG  HG2 HG3 SD  CE  HE1 
+HE2 HE3 C   O   N   H   CA  HA  CB  HB2 HB3 CG  HG2 HG3 CD  OE1 OE2 C   O   N   
+H   CA  HA  CB  HB2 HB3 CG  ND1 CE1 HE1 NE2 HE2 CD2 HD2 C   O   N   H   CA  HA  
+CB  HB2 HB3 CG  HG  CD1 HD11HD12HD13CD2 HD21HD22HD23C   O   N   H   CA  HA  CB  
+HB2 HB3 CG  CD1 HD1 CE1 HE1 CZ  OH  HH  CE2 HE2 CD2 HD2 C   O   N   H   CA  HA  
+CB  HB2 HB3 OG  HG  C   O   N   H   CA  HA  CB  HB2 HB3 CG  HG2 HG3 SD  CE  HE1 
+HE2 HE3 C   O   N   H   CA  HA  CB  HB2 HB3 CG  HG2 HG3 CD  HD2 HD3 CE  HE2 HE3 
+NZ  HZ1 HZ2 HZ3 C   O   N   H   CA  HA  CB  HB2 HB3 SG  HG  C   O   N   H   CA  
+HA  CB  HB2 HB3 CG  HG2 HG3 CD  HD2 HD3 CE  HE2 HE3 NZ  HZ1 HZ2 HZ3 C   O   N   
+H   CA  HA  CB  HB2 HB3 CG  OD1 ND2 HD21HD22C   O   N   H   CA  HA  CB  HB  CG1 
+HG11HG12HG13CG2 HG21HG22HG23C   O   N   H   CA  HA  CB  HB  CG1 HG11HG12HG13CG2 
+HG21HG22HG23C   O   N   CD  HD2 HD3 CG  HG2 HG3 CB  HB2 HB3 CA  HA  C   O   N   
+H   CA  HA  CB  HB2 HB3 CG  CD1 HD1 CE1 HE1 CZ  OH  HH  CE2 HE2 CD2 HD2 C   O   
+N   H   CA  HA  CB  HB2 HB3 CG  OD1 OD2 C   O   N   H   CA  HA  CB  HB2 HB3 CG  
+HG  CD1 HD11HD12HD13CD2 HD21HD22HD23C   O   N   H   CA  HA  CB  HB2 HB3 CG  HG  
+CD1 HD11HD12HD13CD2 HD21HD22HD23C   O   N   H   CA  HA  CB  HB2 HB3 CG  HG  CD1 
+HD11HD12HD13CD2 HD21HD22HD23C   O   N   H   CA  HA  CB  HB2 HB3 CG  HG2 HG3 CD  
+OE1 OE2 C   O   N   H   CA  HA  CB  HB2 HB3 CG  HG2 HG3 SD  CE  HE1 HE2 HE3 C   
+O   N   H   CA  HA  CB  HB2 HB3 CG  HG  CD1 HD11HD12HD13CD2 HD21HD22HD23C   O   
+N   H   CA  HA  CB  HB2 HB3 CG  OD1 OD2 C   O   N   H   CA  HA  CB  HB1 HB2 HB3 
+C   O   N   H   CA  HA  CB  HB2 HB3 CG  ND1 CE1 HE1 NE2 HE2 CD2 HD2 C   O   OXT 
+O11 H7  C11 C12 C13 H9  H8  C10 H6  C9  H5  C8  C7  S6  C5  C4  H4  C3  O3  H3  
+C2  H2  C1  H1  C14 C15 C16 O16 C17 C22 C21 H12 H13 C18 H10 C19 H11 C20 O23 C24 
+H14 H15 C25 H16 H17 N26 C27 H18 H19 C28 H20 H21 C29 H22 H23 C30 H24 H25 C31 H26 
+H27 
+%FLAG CHARGE                                                                    
+%FORMAT(5E16.8)                                                                 
+  2.57663322E+00  3.63899331E+00  3.63899331E+00  3.63899331E+00  1.75298526E+00
+  1.61996247E+00 -1.08787131E+00  5.46669000E-01  5.46669000E-01  5.46669000E-01
+  1.12304035E+01 -1.04268001E+01 -7.57501011E+00  4.95464337E+00 -9.43915140E-01
+  1.68009606E+00 -2.00809746E+00  8.32759110E-01  8.32759110E-01  6.43429413E+00
+ -6.57825030E-01 -7.50940983E+00  1.82223000E+00  1.82223000E+00  1.82223000E+00
+ -7.50940983E+00  1.82223000E+00  1.82223000E+00  1.82223000E+00  1.08841798E+01
+ -1.03484442E+01 -7.57501011E+00  4.95464337E+00 -4.53735270E-01  1.53613989E+00
+  3.85766091E+00  6.41424960E-01  6.41424960E-01 -1.19283176E+01  7.79003325E+00
+  1.08841798E+01 -1.03484442E+01 -7.57501011E+00  4.95464337E+00 -9.43915140E-01
+  1.68009606E+00 -2.00809746E+00  8.32759110E-01  8.32759110E-01  6.43429413E+00
+ -6.57825030E-01 -7.50940983E+00  1.82223000E+00  1.82223000E+00  1.82223000E+00
+ -7.50940983E+00  1.82223000E+00  1.82223000E+00  1.82223000E+00  1.08841798E+01
+ -1.03484442E+01 -7.57501011E+00  4.95464337E+00 -7.08847470E-01  1.83498561E+00
+  6.65842842E+00  7.83558900E-02 -4.44259674E+00  1.16987166E+00  1.16987166E+00
+  1.16987166E+00 -1.23200970E+01  7.47478746E+00  1.08841798E+01 -1.03484442E+01
+ -7.57501011E+00  4.95464337E+00  6.14091510E-01  1.49969529E+00 -3.32556975E+00
+  1.09880469E+00  1.09880469E+00  1.09880469E+00  1.08841798E+01 -1.03484442E+01
+ -9.40817349E+00  5.35006728E+00  6.94269630E-01  1.60356240E+00 -5.52135690E-01
+ -2.22312060E-01 -2.22312060E-01  1.45669066E+01 -1.46033512E+01 -1.46033512E+01
+  9.77808618E+00 -1.06035564E+01 -7.57501011E+00  4.95464337E+00 -5.64891300E-02
+  1.54889550E+00 -6.56002800E-02  3.11601330E-01  3.11601330E-01 -1.17533835E+00
+  6.41424960E-01  6.41424960E-01  1.26663207E+01 -1.10900918E+01 -1.71417176E+01
+  7.74629973E+00  7.74629973E+00  1.08841798E+01 -1.03484442E+01 -7.57501011E+00
+  4.95464337E+00 -4.31868510E-01  1.60356240E+00  6.23202660E-01  4.39157430E-01
+  4.39157430E-01  3.28001400E-02  8.01781200E-01  8.01781200E-01 -4.98744351E+00
+ -9.76715280E-01  1.24640532E+00  1.24640532E+00  1.24640532E+00  1.08841798E+01
+ -1.03484442E+01 -7.57501011E+00  4.95464337E+00 -1.59445125E+00  1.76574087E+00
+  5.43935655E+00 -5.41202310E-01 -5.81655816E+00  1.44138393E+00  1.44138393E+00
+  1.44138393E+00 -5.81655816E+00  1.44138393E+00  1.44138393E+00  1.44138393E+00
+  1.08841798E+01 -1.03484442E+01 -7.57501011E+00  4.95464337E+00 -4.53735270E-01
+  1.53613989E+00  3.85766091E+00  6.41424960E-01  6.41424960E-01 -1.19283176E+01
+  7.79003325E+00  1.08841798E+01 -1.03484442E+01 -7.57501011E+00  4.95464337E+00
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+%FLAG MASS                                                                      
+%FORMAT(5E16.8)                                                                 
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+%FLAG ATOM_TYPE_INDEX                                                           
+%FORMAT(10I8)                                                                   
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+       8       8       3       8       8       1       3       8       8       3
+       5       5       3       5       5       3       5       5       3       8
+       8
+%FLAG NUMBER_EXCLUDED_ATOMS                                                     
+%FORMAT(10I8)                                                                   
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+       1       1       7       3      10       4      13       7      11       6
+       5       6       4       3       2       1       1       7       3      10
+       4      12       7      11       5       4       8       6       5       3
+       3       2       1       1       7       3      10       4      13       7
+      15       6       5      10       8       7       3       2       1       3
+       2       1       1       7       3      10       4      12       7      12
+       5       4      10       8       4       7       3       6       4       1
+       3       2       1       1       7       3      10       4      11       7
+       7       4       3       2       1       7       3      10       4      13
+       7      10       6       5       8       3       2       4       3       2
+       1       1       7       3      10       4      13       7      12       6
+       5      10       5       4       9       5       4       6       5       4
+       3       2       1       1       7       3      10       4      11       7
+       7       4       3       2       1       7       3      10       4      13
+       7      12       6       5      10       5       4       9       5       4
+       6       5       4       3       2       1       1       7       3      10
+       4      12       7      10       5       4       5       3       2       1
+       1       7       3      10       4      16       7      12       9       8
+       3       2       1       4       2       1       1       7       3      10
+       4      16       7      12       9       8       3       2       1       4
+       2       1       1      10       3      14      11       6       5       8
+       5       4       7       4       3       6       3       7       3      10
+       4      12       7      12       5       4      10       8       4       7
+       3       6       4       1       3       2       1       1       7       3
+      10       4      12       7       8       5       4       3       1       1
+       7       3      10       4      13       7      15       6       5      10
+       8       7       3       2       1       3       2       1       1       7
+       3      10       4      13       7      15       6       5      10       8
+       7       3       2       1       3       2       1       1       7       3
+      10       4      13       7      15       6       5      10       8       7
+       3       2       1       3       2       1       1       7       3      10
+       4      13       7      11       6       5       6       4       3       2
+       1       1       7       3      10       4      13       7      10       6
+       5       8       3       2       4       3       2       1       1       7
+       3      10       4      13       7      15       6       5      10       8
+       7       3       2       1       3       2       1       1       7       3
+      10       4      12       7       8       5       4       3       1       1
+       7       3      10       4      10       7       6       3       2       1
+       7       3      10       4      10       7      11       5       4       8
+       6       5       3       3       2       1       1       2       1       1
+       8       3       9       8       9       4       2       5       3       5
+       2       6       9       8      10       9       4       7       4       1
+       5       3       4       2       4       5       8       3       9       8
+       8       4       2       5       3       4       2       5       7       8
+       5       4      11       4       3      13      12       6       5       9
+       5       4       8       5       4       5       4       3       2       1
+       1
+%FLAG NONBONDED_PARM_INDEX                                                      
+%FORMAT(10I8)                                                                   
+       1       2       4       7      11      16      22      29      37      46
+      56      67      79      92     106       2       3       5       8      12
+      17      23      30      38      47      57      68      80      93     107
+       4       5       6       9      13      18      24      31      39      48
+      58      69      81      94     108       7       8       9      10      14
+      19      25      32      40      49      59      70      82      95     109
+      11      12      13      14      15      20      26      33      41      50
+      60      71      83      96     110      16      17      18      19      20
+      21      27      34      42      51      61      72      84      97     111
+      22      23      24      25      26      27      28      35      43      52
+      62      73      85      98     112      29      30      31      32      33
+      34      35      36      44      53      63      74      86      99     113
+      37      38      39      40      41      42      43      44      45      54
+      64      75      87     100     114      46      47      48      49      50
+      51      52      53      54      55      65      76      88     101     115
+      56      57      58      59      60      61      62      63      64      65
+      66      77      89     102     116      67      68      69      70      71
+      72      73      74      75      76      77      78      90     103     117
+      79      80      81      82      83      84      85      86      87      88
+      89      90      91     104     118      92      93      94      95      96
+      97      98      99     100     101     102     103     104     105     119
+     106     107     108     109     110     111     112     113     114     115
+     116     117     118     119     120
+%FLAG RESIDUE_LABEL                                                             
+%FORMAT(20a4)                                                                   
+ALA LEU SER LEU THR ALA ASP GLN MET VAL SER ALA LEU LEU ASP ALA GLU PRO PRO ILE 
+LEU TYR SER GLU TYR ASP PRO THR ARG PRO PHE SER GLU ALA SER MET MET GLY LEU LEU 
+THR ASN LEU ALA ASP ARG GLU LEU VAL HIE MET ILE ASN TRP ALA LYS ARG VAL PRO GLY 
+PHE VAL ASP LEU THR LEU HIE ASP GLN VAL HIE LEU LEU GLU CYS ALA TRP LEU GLU ILE 
+LEU MET ILE GLY LEU VAL TRP ARG SER MET GLU HIE PRO GLY LYS LEU LEU PHE ALA PRO 
+ASN LEU LEU LEU ASP ARG ASN GLN GLY LYS CYS VAL GLU GLY MET VAL GLU ILE PHE ASP 
+MET LEU LEU ALA THR SER SER ARG PHE ARG MET MET ASN LEU GLN GLY GLU GLU PHE VAL 
+CYS LEU LYS SER ILE ILE LEU LEU ASN SER GLY VAL TYR THR PHE LEU SER SER THR LEU 
+LYS SER LEU GLU GLU LYS ASP HIE ILE HIE ARG VAL LEU ASP LYS ILE THR ASP THR LEU 
+ILE HIE LEU MET ALA LYS ALA GLY LEU THR LEU GLN GLN GLN HIE GLN ARG LEU ALA GLN 
+LEU LEU LEU ILE LEU SER HIE ILE ARG HIE MET SER ASN LYS GLY MET GLU HIE LEU TYR 
+SER MET LYS CYS LYS ASN VAL VAL PRO TYR ASP LEU LEU LEU GLU MET LEU ASP ALA HIE 
+RAL 
+%FLAG RESIDUE_POINTER                                                           
+%FORMAT(10I8)                                                                   
+       1      13      32      43      62      76      86      98     115     132
+     148     159     169     188     207     219     229     244     258     272
+     291     310     331     342     357     378     390     404     418     442
+     456     476     487     502     512     523     540     557     564     583
+     602     616     630     649     659     671     695     710     729     745
+     762     779     798     812     836     846     868     892     908     922
+     929     949     965     977     996    1010    1029    1046    1058    1075
+    1091    1108    1127    1146    1161    1172    1182    1206    1225    1240
+    1259    1278    1295    1314    1321    1340    1356    1380    1404    1415
+    1432    1447    1464    1478    1485    1507    1526    1545    1565    1575
+    1589    1603    1622    1641    1660    1672    1696    1710    1727    1734
+    1756    1767    1783    1798    1805    1822    1838    1853    1872    1892
+    1904    1921    1940    1959    1969    1983    1994    2005    2029    2049
+    2073    2090    2107    2121    2140    2157    2164    2179    2194    2214
+    2230    2241    2260    2282    2293    2312    2331    2350    2369    2383
+    2394    2401    2417    2438    2452    2472    2491    2502    2513    2527
+    2546    2568    2579    2598    2613    2628    2650    2662    2679    2698
+    2715    2739    2755    2774    2786    2808    2827    2841    2853    2867
+    2886    2905    2922    2941    2958    2968    2990    3000    3007    3026
+    3040    3059    3076    3093    3110    3127    3144    3168    3187    3197
+    3214    3233    3252    3271    3290    3309    3320    3337    3356    3380
+    3397    3414    3425    3439    3461    3468    3485    3500    3517    3536
+    3557    3568    3585    3607    3618    3640    3654    3670    3686    3700
+    3721    3733    3752    3771    3790    3805    3822    3841    3853    3863
+    3881
+%FLAG BOND_FORCE_CONSTANT                                                       
+%FORMAT(5E16.8)                                                                 
+  5.70000000E+02  4.90000000E+02  3.40000000E+02  3.40000000E+02  3.10000000E+02
+  3.17000000E+02  4.34000000E+02  3.67000000E+02  3.40000000E+02  4.34000000E+02
+  3.37000000E+02  5.53000000E+02  3.20000000E+02  6.56000000E+02  2.27000000E+02
+  3.67000000E+02  4.69000000E+02  4.50000000E+02  4.69000000E+02  3.17000000E+02
+  4.34000000E+02  4.81000000E+02  3.37000000E+02  3.67000000E+02  4.34000000E+02
+  4.27000000E+02  3.67000000E+02  4.77000000E+02  4.88000000E+02  4.10000000E+02
+  5.18000000E+02  3.17000000E+02  4.69000000E+02  4.69000000E+02  4.47000000E+02
+  4.28000000E+02  5.46000000E+02  3.88000000E+02  3.17000000E+02  2.74000000E+02
+  2.37000000E+02  3.35900000E+02  3.37300000E+02  3.03100000E+02  3.20600000E+02
+  3.01500000E+02  3.72400000E+02  3.44300000E+02  4.78400000E+02  6.48000000E+02
+  3.49700000E+02  3.77400000E+02  4.11700000E+02  3.69600000E+02  3.86100000E+02
+  2.56600000E+02  2.79300000E+02  5.04000000E+02  4.11700000E+02
+%FLAG BOND_EQUIL_VALUE                                                          
+%FORMAT(5E16.8)                                                                 
+  1.22900000E+00  1.33500000E+00  1.09000000E+00  1.09000000E+00  1.52600000E+00
+  1.52200000E+00  1.01000000E+00  1.47100000E+00  1.09000000E+00  1.01000000E+00
+  1.44900000E+00  9.60000000E-01  1.41000000E+00  1.25000000E+00  1.81000000E+00
+  1.08000000E+00  1.40000000E+00  1.36400000E+00  1.40900000E+00  1.51000000E+00
+  1.01000000E+00  1.34000000E+00  1.46300000E+00  1.08000000E+00  1.01000000E+00
+  1.38100000E+00  1.08000000E+00  1.34300000E+00  1.33500000E+00  1.39400000E+00
+  1.37100000E+00  1.50400000E+00  1.40400000E+00  1.40000000E+00  1.41900000E+00
+  1.38000000E+00  1.35200000E+00  1.45900000E+00  1.49500000E+00  1.33600000E+00
+  1.81000000E+00  1.09300000E+00  1.09200000E+00  1.53500000E+00  1.47000000E+00
+  1.43900000E+00  1.37300000E+00  1.08700000E+00  1.38700000E+00  1.21400000E+00
+  1.48700000E+00  1.46200000E+00  1.43400000E+00  9.74000000E-01  1.36200000E+00
+  1.77000000E+00  1.73700000E+00  1.37100000E+00  1.43400000E+00
+%FLAG ANGLE_FORCE_CONSTANT                                                      
+%FORMAT(5E16.8)                                                                 
+  8.00000000E+01  5.00000000E+01  5.00000000E+01  3.50000000E+01  6.30000000E+01
+  5.00000000E+01  5.00000000E+01  5.00000000E+01  8.00000000E+01  7.00000000E+01
+  5.00000000E+01  3.50000000E+01  5.00000000E+01  8.00000000E+01  8.00000000E+01
+  4.00000000E+01  5.00000000E+01  5.00000000E+01  5.00000000E+01  5.00000000E+01
+  8.00000000E+01  6.30000000E+01  5.00000000E+01  3.50000000E+01  5.50000000E+01
+  5.00000000E+01  8.00000000E+01  5.00000000E+01  7.00000000E+01  3.50000000E+01
+  5.00000000E+01  6.20000000E+01  5.00000000E+01  5.00000000E+01  5.00000000E+01
+  7.00000000E+01  5.00000000E+01  5.00000000E+01  6.30000000E+01  6.30000000E+01
+  6.30000000E+01  5.00000000E+01  7.00000000E+01  6.30000000E+01  3.50000000E+01
+  7.00000000E+01  5.00000000E+01  5.00000000E+01  5.00000000E+01  5.00000000E+01
+  8.00000000E+01  5.00000000E+01  5.00000000E+01  5.00000000E+01  5.00000000E+01
+  7.00000000E+01  7.00000000E+01  5.00000000E+01  7.00000000E+01  7.00000000E+01
+  7.00000000E+01  5.00000000E+01  5.00000000E+01  7.00000000E+01  7.00000000E+01
+  6.30000000E+01  5.00000000E+01  6.30000000E+01  6.30000000E+01  5.00000000E+01
+  6.30000000E+01  6.30000000E+01  5.00000000E+01  7.00000000E+01  7.00000000E+01
+  6.30000000E+01  7.00000000E+01  5.00000000E+01  7.00000000E+01  6.30000000E+01
+  6.30000000E+01  5.00000000E+01  7.00000000E+01  7.00000000E+01  6.30000000E+01
+  3.50000000E+01  5.00000000E+01  4.30000000E+01  5.00000000E+01  3.92000000E+01
+  4.64000000E+01  3.94000000E+01  4.64000000E+01  6.32000000E+01  6.40000000E+01
+  4.94000000E+01  6.62000000E+01  5.08000000E+01  6.78000000E+01  6.24000000E+01
+  4.85000000E+01  6.98000000E+01  6.72000000E+01  6.87000000E+01  6.46000000E+01
+  6.89000000E+01  6.48000000E+01  6.36000000E+01  6.60000000E+01  6.98000000E+01
+  4.89000000E+01  6.36000000E+01  6.20000000E+01  6.39000000E+01  6.82000000E+01
+  6.57000000E+01  6.49000000E+01  6.82000000E+01  6.60000000E+01
+%FLAG ANGLE_EQUIL_VALUE                                                         
+%FORMAT(5E16.8)                                                                 
+  2.14501057E+00  2.09439600E+00  2.12755727E+00  1.91113635E+00  1.93906163E+00
+  1.91113635E+00  1.91113635E+00  1.91113635E+00  2.10137732E+00  2.03505478E+00
+  1.91113635E+00  1.91113635E+00  1.91113635E+00  1.94080696E+00  1.94080696E+00
+  1.91113635E+00  1.91113635E+00  1.91113635E+00  2.06018753E+00  1.91113635E+00
+  1.91462701E+00  1.92160833E+00  1.91113635E+00  1.91113635E+00  1.89368305E+00
+  1.91113635E+00  2.19911580E+00  1.91113635E+00  2.04203610E+00  2.09439600E+00
+  1.91113635E+00  1.72613137E+00  2.00189351E+00  2.05948940E+00  2.09439600E+00
+  2.09439600E+00  1.97222290E+00  2.09439600E+00  2.09439600E+00  2.09439600E+00
+  2.09439600E+00  1.91113635E+00  2.09439600E+00  1.98967620E+00  2.09439600E+00
+  2.09439600E+00  2.09439600E+00  1.91113635E+00  2.06647072E+00  2.15024656E+00
+  1.94080696E+00  2.09439600E+00  2.09439600E+00  2.09439600E+00  2.09439600E+00
+  2.09439600E+00  2.09439600E+00  2.09439600E+00  2.09439600E+00  2.04203610E+00
+  2.09439600E+00  2.09439600E+00  1.91113635E+00  2.09439600E+00  2.09439600E+00
+  1.97396823E+00  2.09439600E+00  2.09439600E+00  2.14151991E+00  2.09439600E+00
+  2.09439600E+00  2.02807346E+00  2.14850123E+00  2.31779824E+00  1.82212452E+00
+  1.85703112E+00  1.94778828E+00  2.09439600E+00  1.89717371E+00  1.89891904E+00
+  2.35445017E+00  1.91113635E+00  2.18166250E+00  2.24449438E+00  2.01760148E+00
+  1.91113635E+00  1.91113635E+00  1.67551680E+00  1.89542838E+00  1.91200902E+00
+  1.92073567E+00  1.89106506E+00  1.92108473E+00  1.93085858E+00  1.93557097E+00
+  1.91846674E+00  1.92649525E+00  1.89926811E+00  1.89228679E+00  2.05250808E+00
+  2.09457053E+00  2.08043336E+00  2.09387240E+00  2.15443535E+00  2.09683946E+00
+  2.19405434E+00  1.99124700E+00  2.14588324E+00  2.09614133E+00  2.09334880E+00
+  1.91061275E+00  2.06245646E+00  2.09317427E+00  1.69262103E+00  1.98112408E+00
+  2.09299974E+00  1.93888710E+00  1.98112408E+00  2.09614133E+00
+%FLAG DIHEDRAL_FORCE_CONSTANT                                                   
+%FORMAT(5E16.8)                                                                 
+  2.00000000E+00  2.50000000E+00  0.00000000E+00  2.00000000E+00  4.00000000E-01
+  0.00000000E+00  0.00000000E+00  2.70000000E-01  4.20000000E-01  1.55555556E-01
+  2.00000000E-01  2.00000000E-01  1.60000000E-01  1.50000000E-01  8.00000000E-01
+  8.00000000E-02  2.00000000E-01  2.50000000E-01  1.80000000E-01  4.50000000E-01
+  1.58000000E+00  5.50000000E-01  1.66666667E-01  2.50000000E-01  0.00000000E+00
+  3.33333333E-01  3.62500000E+00  2.30000000E+00  2.40000000E+00  1.50000000E+00
+  2.32500000E+00  5.37500000E+00  5.00000000E+00  3.00000000E+00  3.50000000E+00
+  1.52500000E+00  6.52500000E+00  1.67500000E+00  2.50000000E-01  4.80000000E-01
+  3.00000000E-01  3.83333333E-01  9.00000000E-01  2.87500000E+00  2.55000000E+00
+  1.10000000E+00  4.00000000E+00  4.00000000E-01  1.05000000E+01  1.10000000E+00
+  1.00000000E+00
+%FLAG DIHEDRAL_PERIODICITY                                                      
+%FORMAT(5E16.8)                                                                 
+  1.00000000E+00  2.00000000E+00  2.00000000E+00  2.00000000E+00  3.00000000E+00
+  4.00000000E+00  1.00000000E+00  2.00000000E+00  3.00000000E+00  3.00000000E+00
+  1.00000000E+00  2.00000000E+00  3.00000000E+00  3.00000000E+00  1.00000000E+00
+  3.00000000E+00  1.00000000E+00  2.00000000E+00  3.00000000E+00  1.00000000E+00
+  2.00000000E+00  3.00000000E+00  3.00000000E+00  1.00000000E+00  3.00000000E+00
+  3.00000000E+00  2.00000000E+00  2.00000000E+00  2.00000000E+00  2.00000000E+00
+  2.00000000E+00  2.00000000E+00  2.00000000E+00  2.00000000E+00  2.00000000E+00
+  2.00000000E+00  2.00000000E+00  2.00000000E+00  3.00000000E+00  2.00000000E+00
+  3.00000000E+00  3.00000000E+00  2.00000000E+00  2.00000000E+00  2.00000000E+00
+  2.00000000E+00  2.00000000E+00  2.00000000E+00  2.00000000E+00  2.00000000E+00
+  2.00000000E+00
+%FLAG DIHEDRAL_PHASE                                                            
+%FORMAT(5E16.8)                                                                 
+  0.00000000E+00  3.14159400E+00  0.00000000E+00  0.00000000E+00  0.00000000E+00
+  0.00000000E+00  0.00000000E+00  0.00000000E+00  0.00000000E+00  0.00000000E+00
+  0.00000000E+00  0.00000000E+00  0.00000000E+00  0.00000000E+00  0.00000000E+00
+  3.14159400E+00  3.14159400E+00  3.14159400E+00  0.00000000E+00  3.14159400E+00
+  3.14159400E+00  3.14159400E+00  0.00000000E+00  0.00000000E+00  0.00000000E+00
+  0.00000000E+00  3.14159400E+00  3.14159400E+00  3.14159400E+00  3.14159400E+00
+  3.14159400E+00  3.14159400E+00  3.14159400E+00  3.14159400E+00  3.14159400E+00
+  3.14159400E+00  3.14159400E+00  3.14159400E+00  0.00000000E+00  3.14159400E+00
+  0.00000000E+00  0.00000000E+00  3.14159400E+00  3.14159400E+00  3.14159400E+00
+  3.14159400E+00  3.14159400E+00  3.14159400E+00  3.14159400E+00  3.14159400E+00
+  3.14159400E+00
+%FLAG SOLTY                                                                     
+%FORMAT(5E16.8)                                                                 
+  0.00000000E+00  0.00000000E+00  0.00000000E+00  0.00000000E+00  0.00000000E+00
+  0.00000000E+00  0.00000000E+00  0.00000000E+00  0.00000000E+00  0.00000000E+00
+  0.00000000E+00  0.00000000E+00  0.00000000E+00  0.00000000E+00  0.00000000E+00
+  0.00000000E+00  0.00000000E+00  0.00000000E+00  0.00000000E+00  0.00000000E+00
+  0.00000000E+00  0.00000000E+00  0.00000000E+00  0.00000000E+00  0.00000000E+00
+  0.00000000E+00  0.00000000E+00  0.00000000E+00  0.00000000E+00  0.00000000E+00
+  0.00000000E+00  0.00000000E+00  0.00000000E+00  0.00000000E+00  0.00000000E+00
+  0.00000000E+00  0.00000000E+00  0.00000000E+00  0.00000000E+00  0.00000000E+00
+  0.00000000E+00  0.00000000E+00
+%FLAG LENNARD_JONES_ACOEF                                                       
+%FORMAT(5E16.8)                                                                 
+  9.44293233E+05  2.12601181E+03  1.39982777E-01  9.95480466E+05  2.56678134E+03
+  1.04308023E+06  2.01791425E+04  9.14716912E+00  2.27401052E+04  2.01823541E+02
+  8.96776989E+04  1.07193646E+02  9.71708117E+04  1.41077189E+03  7.51607703E+03
+  8.82619071E+05  2.27577561E+03  9.24822270E+05  2.01619733E+04  8.61541883E+04
+  8.19971662E+05  6.06829342E+05  1.02595236E+03  6.47841731E+05  1.12780457E+04
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+%FLAG LENNARD_JONES_BCOEF                                                       
+%FORMAT(5E16.8)                                                                 
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+%FLAG BONDS_INC_HYDROGEN                                                        
+%FORMAT(10I8)                                                                   
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+      48   11661   11664      48   11652   11655      48   11649   11658      48
+   11640   11643      54
+%FLAG BONDS_WITHOUT_HYDROGEN                                                    
+%FORMAT(10I8)