| Previous changeset 5:27ee142314a9 (2021-01-25) Next changeset 7:c8cdde00b105 (2021-03-12) |
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Commit message:
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3c440a43396b4d815ef35f45ed562e22bf37c028" |
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modified:
acpype.xml |
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added:
test-data/LigA_output.top |
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| diff -r 27ee142314a9 -r 2417677038b2 acpype.xml --- a/acpype.xml Mon Jan 25 11:15:57 2021 +0000 +++ b/acpype.xml Tue Feb 16 21:55:56 2021 +0000 |
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| @@ -2,7 +2,7 @@ <description>using acpype</description> <macros> <import>macros.xml</import> - <token name="@GALAXY_VERSION@">0</token> + <token name="@GALAXY_VERSION@">1</token> </macros> <expand macro="requirements"> <requirement type="package" version="2020.10.24.12.16">acpype</requirement> @@ -14,6 +14,7 @@ -b base -m '$multiplicity' -a '$atomtype' + -c '$charge_method' -o gmx ]]></command> <inputs> @@ -26,6 +27,11 @@ <option value="gaff2">gaff2</option> <option value="amber2">AMBER14SB + gaff2</option> </param> + <param name="charge_method" type="select" value="bcc" label="Charge method"> + <option value="bcc">bcc (default)</option> + <option value="gas">gas</option> + <option value="user">charges provided by user in mol2 file</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> @@ -38,6 +44,7 @@ <test> <param name="input1" value="JZ4.mol2"/> <param name="save_gro" value="True"/> + <param name="charge_method" value="bcc"/> <output name="output"> <assert_contents> <has_line line="[ atoms ]"/> @@ -47,6 +54,12 @@ </output> <output name="gro_output" file="base_GMX.gro" lines_diff="2"/> </test> + <test> + <param name="input1" value="LigA_output.mol2"/> + <param name="save_gro" value="false"/> + <param name="charge_method" value="user"/> + <output name="output" file="LigA_output.top" lines_diff="26"/> + </test> </tests> <help><![CDATA[ Tool to produce GROMACS topologies for small molecules using the acpype interface to AmberTools. |
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| diff -r 27ee142314a9 -r 2417677038b2 test-data/LigA_output.top --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/LigA_output.top Tue Feb 16 21:55:56 2021 +0000 |
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| b'@@ -0,0 +1,239 @@\n+; base_GMX.itp created by acpype (v: 2020-10-24T12:16:34CEST) on Tue Feb 16 21:55:09 2021\n+\n+[ atomtypes ]\n+;name bond_type mass charge ptype sigma epsilon Amb\n+ c2 c2 0.00000 0.00000 A 3.39967e-01 3.59824e-01 ; 1.91 0.0860\n+ ha ha 0.00000 0.00000 A 2.59964e-01 6.27600e-02 ; 1.46 0.0150\n+ ce ce 0.00000 0.00000 A 3.39967e-01 3.59824e-01 ; 1.91 0.0860\n+ c c 0.00000 0.00000 A 3.39967e-01 3.59824e-01 ; 1.91 0.0860\n+ o o 0.00000 0.00000 A 2.95992e-01 8.78640e-01 ; 1.66 0.2100\n+ os os 0.00000 0.00000 A 3.00001e-01 7.11280e-01 ; 1.68 0.1700\n+ c3 c3 0.00000 0.00000 A 3.39967e-01 4.57730e-01 ; 1.91 0.1094\n+ h1 h1 0.00000 0.00000 A 2.47135e-01 6.56888e-02 ; 1.39 0.0157\n+ oh oh 0.00000 0.00000 A 3.06647e-01 8.80314e-01 ; 1.72 0.2104\n+ ho ho 0.00000 0.00000 A 0.00000e+00 0.00000e+00 ; 0.00 0.0000\n+\n+[ moleculetype ]\n+;name nrexcl\n+ base 3\n+\n+[ atoms ]\n+; nr type resi res atom cgnr charge mass ; qtot bond_type\n+ 1 c2 1 MOL C 1 -0.311000 12.01000 ; qtot -0.311\n+ 2 ha 1 MOL H 2 0.109500 1.00800 ; qtot -0.202\n+ 3 ha 1 MOL H1 3 0.109500 1.00800 ; qtot -0.092\n+ 4 ce 1 MOL C1 4 0.022900 12.01000 ; qtot -0.069\n+ 5 c 1 MOL C2 5 0.384200 12.01000 ; qtot 0.315\n+ 6 o 1 MOL O 6 -0.575500 16.00000 ; qtot -0.260\n+ 7 o 1 MOL O1 7 -0.575500 16.00000 ; qtot -0.836\n+ 8 os 1 MOL O2 8 -0.351900 16.00000 ; qtot -1.188\n+ 9 c3 1 MOL C3 9 0.157300 12.01000 ; qtot -1.031\n+ 10 h1 1 MOL H2 10 0.051700 1.00800 ; qtot -0.979\n+ 11 c2 1 MOL C4 11 -0.174200 12.01000 ; qtot -1.153\n+ 12 ha 1 MOL H3 12 0.141000 1.00800 ; qtot -1.012\n+ 13 ce 1 MOL C5 13 -0.149200 12.01000 ; qtot -1.161\n+ 14 ce 1 MOL C6 14 -0.081000 12.01000 ; qtot -1.242\n+ 15 ha 1 MOL H4 15 0.142000 1.00800 ; qtot -1.100\n+ 16 c2 1 MOL C7 16 -0.248200 12.01000 ; qtot -1.348\n+ 17 ha 1 MOL H5 17 0.104000 1.00800 ; qtot -1.244\n+ 18 c3 1 MOL C8 18 0.131300 12.01000 ; qtot -1.113\n+ 19 h1 1 MOL H6 19 0.151700 1.00800 ; qtot -0.961\n+ 20 oh 1 MOL O3 20 -0.614800 16.00000 ; qtot -1.576\n+ 21 ho 1 MOL H7 21 0.374000 1.00800 ; qtot -1.202\n+ 22 c 1 MOL C9 22 0.376200 12.01000 ; qtot -0.826\n+ 23 o 1 MOL O4 23 -0.587000 16.00000 ; qtot -1.413\n+ 24 o 1 MOL O5 24 -0.587000 16.00000 ; qtot -2.000\n+\n+[ bonds ]\n+; ai aj funct r k\n+ 1 2 1 1.0879e-01 2.8711e+05 ; C - H \n+ 1 3 1 1.0879e-01 2.8711e+05 ; C - H1 \n+ 1 4 1 1.3461e-01 4.5798e+05 ; C - C1 \n+ 4 5 1 1.4825e-01 2.9665e+05 ; C1 - C2 \n+ 4 8 1 1.3710e-01 3.1372e+05 ; C1 - O2 \n+ 5 6 1 1.2183e-01 5.3363e+05 ; C2 - O \n+ 5 7 1 1.2183e-01 5.3363e+05 ; C2 - O1 \n+ 8 9 1 1.4316e-01 2.5824e+05 ; O2 - C3 \n+ 9 10 1 1.0969e-01 2.7665e+05 ; C3 - H2 \n+ 9 11 1 1.5095e-01 2.7347e+05 ; C3 - C4 \n+ 9 18 1 1.5375e-01 2.5179e+05 ; C3 - C8 \n+ 11 12 1 1.0879e-01 2.8711e+05 ; C4 - H3 \n+ 11 13 1 1.3461e-01 4.5798e+05 ; C4 - C5 \n+ 13 14 1 '..b'C5- C9\n+ 9 18 16 14 9 0.00 0.00000 0 ; C3- C8- C7- C6\n+ 9 18 16 17 9 0.00 0.00000 0 ; C3- C8- C7- H5\n+ 9 18 20 21 9 0.00 0.66944 3 ; C3- C8- O3- H7\n+ 9 18 20 21 9 0.00 1.04600 1 ; C3- C8- O3- H7\n+ 10 9 11 12 9 0.00 0.00000 0 ; H2- C3- C4- H3\n+ 10 9 11 13 9 0.00 0.00000 0 ; H2- C3- C4- C5\n+ 10 9 18 16 9 0.00 0.65084 3 ; H2- C3- C8- C7\n+ 10 9 18 19 9 0.00 0.65084 3 ; H2- C3- C8- H6\n+ 10 9 18 20 9 0.00 0.00000 0 ; H2- C3- C8- O3\n+ 10 9 18 20 9 0.00 1.04600 1 ; H2- C3- C8- O3\n+ 11 9 18 16 9 0.00 0.65084 3 ; C4- C3- C8- C7\n+ 11 9 18 19 9 0.00 0.65084 3 ; C4- C3- C8- H6\n+ 11 9 18 20 9 0.00 0.65084 3 ; C4- C3- C8- O3\n+ 11 13 14 15 9 180.00 4.18400 2 ; C4- C5- C6- H4\n+ 11 13 14 16 9 180.00 4.18400 2 ; C4- C5- C6- C7\n+ 11 13 22 23 9 180.00 9.10020 2 ; C4- C5- C9- O4\n+ 11 13 22 24 9 180.00 9.10020 2 ; C4- C5- C9- O5\n+ 12 11 9 18 9 0.00 0.00000 0 ; H3- C4- C3- C8\n+ 12 11 13 14 9 180.00 27.82360 2 ; H3- C4- C5- C6\n+ 12 11 13 22 9 180.00 27.82360 2 ; H3- C4- C5- C9\n+ 13 11 9 18 9 0.00 0.00000 0 ; C5- C4- C3- C8\n+ 13 14 16 17 9 180.00 27.82360 2 ; C5- C6- C7- H5\n+ 13 14 16 18 9 180.00 27.82360 2 ; C5- C6- C7- C8\n+ 14 13 22 23 9 180.00 9.10020 2 ; C6- C5- C9- O4\n+ 14 13 22 24 9 180.00 9.10020 2 ; C6- C5- C9- O5\n+ 14 16 18 19 9 0.00 0.00000 0 ; C6- C7- C8- H6\n+ 14 16 18 20 9 0.00 0.00000 0 ; C6- C7- C8- O3\n+ 15 14 13 22 9 180.00 4.18400 2 ; H4- C6- C5- C9\n+ 15 14 16 17 9 180.00 27.82360 2 ; H4- C6- C7- H5\n+ 15 14 16 18 9 180.00 27.82360 2 ; H4- C6- C7- C8\n+ 16 14 13 22 9 180.00 4.18400 2 ; C7- C6- C5- C9\n+ 16 18 20 21 9 0.00 0.69733 3 ; C7- C8- O3- H7\n+ 17 16 18 19 9 0.00 0.00000 0 ; H5- C7- C8- H6\n+ 17 16 18 20 9 0.00 0.00000 0 ; H5- C7- C8- O3\n+ 19 18 20 21 9 0.00 0.69733 3 ; H6- C8- O3- H7\n+\n+[ dihedrals ] ; impropers\n+; treated as propers in GROMACS to use correct AMBER analytical function\n+; i j k l func phase kd pn\n+ 3 1 2 4 4 180.00 4.60240 2 ; H1- C- H- C1\n+ 4 6 5 7 4 180.00 4.60240 2 ; C1- O- C2- O1\n+ 5 1 4 8 4 180.00 4.60240 2 ; C2- C- C1- O2\n+ 9 13 11 12 4 180.00 4.60240 2 ; C3- C5- C4- H3\n+ 13 23 22 24 4 180.00 4.60240 2 ; C5- O4- C9- O5\n+ 16 13 14 15 4 180.00 4.60240 2 ; C7- C5- C6- H4\n+ 18 14 16 17 4 180.00 4.60240 2 ; C8- C6- C7- H5\n+ 22 11 13 14 4 180.00 4.60240 2 ; C9- C4- C5- C6\n' |