Mercurial > repos > chemteam > ambertools_acpype
changeset 0:2e202f6c3034 draft
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit f1620d2eb7fd3ea43bb4dfe6cee5b45015fd13a3
| author | chemteam |
|---|---|
| date | Thu, 13 Jun 2019 06:16:34 -0400 |
| parents | |
| children | 597ee2f97479 |
| files | acpype.xml macros.xml 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.txt test-data/LigA_prmchk.mol2 test-data/base_GMX.gro test-data/base_GMX.itp |
| diffstat | 11 files changed, 638 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/acpype.xml Thu Jun 13 06:16:34 2019 -0400 @@ -0,0 +1,73 @@ +<tool id="ambertools_acpype" name="Generate MD topologies for small molecules" version="@VERSION@"> + <description>using acpype</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements"> + <requirement type="package" version="0.1.0">acpype</requirement> + </expand> + <command detect_errors="exit_code"><![CDATA[ + ln -s '$input1' ./input1.${input1.ext} && + acpype -i './input1.${input1.ext}' + -n '$charge' + -b base + -m '$multiplicity' + -a '$atomtype' + -o gmx + ]]></command> + <inputs> + <param name="input1" type="data" format="pdb,mol2" label="Input file" help="Structure of the compound in pdb or mol2 format"/> + <param name="charge" type="integer" value="0" label="Charge of the molecule"/> + <param name="multiplicity" type="integer" value="1" label="Multiplicity" help="Default value is 1, which is correct for almost all organic molecules."/> + <param name="atomtype" type="select" value="gaff" label="Force field to use for parameterization"> + <option value="gaff">gaff</option> + <option value="amber">AMBER14SB</option> + <option value="gaff2">gaff2</option> + <option value="amber2">AMBER14SB + gaff2</option> + </param> + <param name="save_gro" type="boolean" value="false" label="Save GRO file?" help="Save atomic coordinates of ligand in GRO format."/> + </inputs> + <outputs> + <data format="itp" name="output" label="Topology" from_work_dir='base.acpype/base_GMX.itp'/> + <data format="gro" name="gro_output" label="Structure file (GRO format, optional)" from_work_dir="base.acpype/base_GMX.gro"> + <filter>save_gro</filter> + </data> + </outputs> + <tests> + <test> + <param name="input1" value="JZ4.mol2"/> + <param name="save_gro" value="True"/> + <output name="output"> + <assert_contents> + <has_line line="[ atoms ]"/> + <has_text text=" 15 ha 1 JZ4 H4 15 0.13"/> + <has_text text=" 18 hc 1 JZ4 H7 18 0.05"/> + </assert_contents> + </output> + <output name="gro_output" file="base_GMX.gro" lines_diff="2"/> + </test> + </tests> + <help><![CDATA[ +Tool to produce GROMACS topologies for small molecules using the acpype interface to AmberTools. + +.. class:: infomark + +**Input** + +Either a mol2 file (more appropriate for small structures) or a +pdb file. If you want to parameterize a large macromolecule +(which is more likely to be stored in PDB format, e.g. a protein) +consider using a tool such as 'GROMACS initial setup' instead. + +.. class:: infomark + +**Outputs** + +GROMACS topology for the ligand, in itp format. Optional: structure file, in gro format. + + + ]]></help> + <expand macro="citations"> + <citation type="doi">doi:10.1186/1756-0500-5-367</citation> + </expand> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Thu Jun 13 06:16:34 2019 -0400 @@ -0,0 +1,20 @@ +<macros> + <token name="@VERSION@">19.0</token> + <xml name="requirements"> + <requirements> + <requirement type="package" version="19.0">ambertools</requirement> + <yield/> + </requirements> + </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> +</macros>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/JZ4.mol2 Thu Jun 13 06:16:34 2019 -0400 @@ -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 Jun 13 06:16:34 2019 -0400 @@ -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 Jun 13 06:16:34 2019 -0400 @@ -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 Jun 13 06:16:34 2019 -0400 @@ -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 Jun 13 06:16:34 2019 -0400 @@ -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.txt Thu Jun 13 06:16:34 2019 -0400 @@ -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 Jun 13 06:16:34 2019 -0400 @@ -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/base_GMX.gro Thu Jun 13 06:16:34 2019 -0400 @@ -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 Jun 13 06:16:34 2019 -0400 @@ -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