Mercurial > repos > chemteam > tleap
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> + 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+ <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
--- /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 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--- /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 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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 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--- /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 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