| Previous changeset 7:8ddd75c21cbd (2020-01-21) Next changeset 9:d1d0efda35c0 (2020-05-08) |
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Commit message:
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 71a3084d6e402b31563b1662bb629d5a959ce7b7" |
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modified:
merge_top.py merge_top.xml |
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added:
test-data/complex.gro test-data/complex.top test-data/lig.gro test-data/lig.itp |
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removed:
test-data/top_output.top |
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| diff -r 8ddd75c21cbd -r 06ea4e040d45 merge_top.py --- a/merge_top.py Tue Jan 21 07:30:45 2020 -0500 +++ b/merge_top.py Wed Apr 15 14:35:17 2020 -0400 |
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| @@ -1,38 +1,65 @@ -import re -import sys +import argparse + +import parmed as pmd -def combine_tops(top_text, itp_texts): - """ - Search through parent topology top_text and replace - #include lines with the relevant child topologies - from the dictionary itp_texts - """ - for itp in itp_texts: - # split on include string, then rejoin around itp file - spl = re.split('#include ".*{}"\n'.format(itp), top_text) - top_text = itp_texts[itp].join(spl) - return top_text +def merge_gro_files(prot_gro, lig_gro, cmplx_gro): + prot = pmd.load_file(prot_gro) + lig = pmd.load_file(lig_gro) + cmplx = prot + lig + cmplx.save(cmplx_gro) -top = sys.argv[1] # parent topology file -itps_file = sys.argv[2] # file with list of child topologies (.itp files) +def merge_top_files(prot_top, lig_top, cmplx_top): + with open(lig_top, 'r') as f: + lig_top_sections = f.read().split('\n[') -with open(itps_file) as f: - itps = f.read().split() - -with open(top, 'r') as f: - top_text = f.read() + # open ligand topology + for n in range(len(lig_top_sections)): + if 'atomtypes' in lig_top_sections[n][:10]: + lig_atomtypes = lig_top_sections[n] + del lig_top_sections[n] + break + else: + lig_atomtypes = None + lig_top_updated = '\n['.join(lig_top_sections) -itp_texts = {} # create dictionary of child topologies -for itp in itps: - with open(itp, 'r') as f: - itp_texts[itp] = f.read() + # open protein topology + with open(prot_top, 'r') as f: + prot_top_combined = f.read() + if lig_atomtypes: + prot_top_sections = prot_top_combined.split('[ moleculetype ]\n') + prot_top_combined = (prot_top_sections[0] + + '; Include ligand atomtypes\n[' + + lig_atomtypes + + '\n[ moleculetype ]\n' + + prot_top_sections[1]) + prot_top_sections = prot_top_combined.split('; Include water topology') + prot_top_combined = (prot_top_sections[0] + + '; Include ligand topology\n' + + lig_top_updated + + '\n; Include water topology' + + prot_top_sections[1]) + prot_top_combined += 'base 1\n' -for itp in itp_texts: - # child tops may also refer to each other; we need to check this - itp_texts[itp] = combine_tops(itp_texts[itp], itp_texts) + # save complex topology + with open(cmplx_top, 'w') as f: + f.write(prot_top_combined) + -with open('top_output.top', 'w') as f: - # now combine all children into the parent - f.write(combine_tops(top_text, itp_texts)) +def main(): + parser = argparse.ArgumentParser( + description='Perform SMD runs for dynamic undocking') + parser.add_argument('--lig-top', help='Ligand TOP file.') + parser.add_argument('--prot-top', help='Protein TOP file.') + parser.add_argument('--lig-gro', help='Ligand GRO file.') + parser.add_argument('--prot-gro', help='Protein GRO file.') + parser.add_argument('--complex-top', help='Complex TOP file.') + parser.add_argument('--complex-gro', help='Complex GRO file.') + args = parser.parse_args() + merge_gro_files(args.prot_gro, args.lig_gro, args.complex_gro) + merge_top_files(args.prot_top, args.lig_top, args.complex_top) + + +if __name__ == "__main__": + main() |
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| diff -r 8ddd75c21cbd -r 06ea4e040d45 merge_top.xml --- a/merge_top.xml Tue Jan 21 07:30:45 2020 -0500 +++ b/merge_top.xml Wed Apr 15 14:35:17 2020 -0400 |
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| @@ -1,29 +1,38 @@ <tool id="gmx_merge_topology_files" name="Merge GROMACS topologies" version="@VERSION@"> - <description>for example, for protein and ligand files</description> + <description>and GRO files</description> <macros> - <import>macros.xml</import> + <token name="@VERSION@">3.2.0</token> </macros> + <requirements> + <requirement type="package" version="@VERSION@">parmed</requirement> + </requirements> <command detect_errors="exit_code"><![CDATA[ - ln -s '$top_input' ./top_input.top && - #for $itp_input in $itp_inputs - ln -s '$itp_input' ./$itp_input.element_identifier && - echo '$itp_input.element_identifier' >> ./itps.txt && - #end for - - python '$__tool_directory__/merge_top.py' top_input.top itps.txt + python '$__tool_directory__/merge_top.py' + --lig-top $lig_top + --prot-top $prot_top + --lig-gro $lig_gro + --prot-gro $prot_gro + --complex-top complex.top + --complex-gro complex.gro ]]></command> <inputs> - <param name="top_input" type="data" format='top' label="Topology (TOP) file" help="'Master' topology into which subordinate topologies will be added."/> - <param name="itp_inputs" type="data" format='top,itp' multiple="true" label="Topologies (TOP or ITP)" help="One or more topologies for insertion into the main topology. Either TOP or ITP format. Can include position restraint files."/> + <param name="prot_top" type="data" format='top' label="Protein topology (TOP) file" help="Protein topology into which a ligand topology will be added."/> + <param name="lig_top" type="data" format='top,itp' label="Ligand topology (TOP or ITP) file" help="Ligand topology for insertion into the protein topology. Either TOP or ITP format."/> + <param name="prot_gro" type="data" format='gro' label="Protein structure (GRO) file" help="Protein structure in GRO format."/> + <param name="lig_gro" type="data" format='gro' label="Ligand structure (GRO) file" help="Ligand structure in GRO format."/> </inputs> <outputs> - <data name="output" format="top" from_work_dir="top_output.top"/> + <data name="complex_top" format="top" from_work_dir="complex.top"/> + <data name="complex_gro" format="gro" from_work_dir="complex.gro"/> </outputs> <tests> <test> - <param name="top_input" value="topol.top" /> - <param name="itp_inputs" value="posres.itp" /> - <output name="output" file="top_output.top" ftype="top" /> + <param name="prot_top" value="topol.top" /> + <param name="lig_top" value="lig.itp" /> + <param name="prot_gro" value="newbox.gro" /> + <param name="lig_gro" value="lig.gro" /> + <output name="complex_top" file="complex.top" ftype="top" compare="diff" lines_diff="20"/> + <output name="complex_gro" file="complex.gro" ftype="gro"/> </test> </tests> <help><![CDATA[ @@ -32,7 +41,9 @@ **What it does** -This tool merges GROMACS topologies - for example, the topology files for a ligand and protein. TOP files contain references to other subordinate TOP files using the `#include` tag. In Galaxy, these tags need to be replaced directly with the contents of the topology files they refer to. +This tool merges GROMACS topologies and structure (GRO) files, calculated separately for a protein and ligand, into combined topology and GRO files for the resulting complex. + +The tool will work best if used with the outputs of the 'acpype' and 'GROMACS initial setup' tools. If the input files are formatted unusually or incorrectly, it will probably fail. _____ @@ -40,8 +51,10 @@ **Input** - - TOP file for the main topology - - One or more subordinate topologies (TOP or ITP) which can be inserted into the main topology if specified by an `#include` tag. + - TOP file for the protein topology + - A TOP or ITP file for the ligand topology + - GRO file for the protein structure + - GRO file for the ligand structure _____ @@ -50,8 +63,20 @@ **Output** - - TOP file. + - TOP file for the protein-ligand complex. + - GRO file for the protein-ligand complex. ]]></help> - <expand macro="citations" /> + <citations> + <citation type="bibtex"> +@misc{parmed_2020, +author = {Jason Swails and other contributors}, +title = {ParmEd}, +url={https://github.com/ParmEd/ParmEd}, +abstract = {Parameter/topology editor and molecular simulator.}, +urldate = {2020-04-03}, +publisher = {GitHub}, +year = {2020}, +month = mar, }</citation> + </citations> </tool> |
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| diff -r 8ddd75c21cbd -r 06ea4e040d45 test-data/complex.gro --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/complex.gro Wed Apr 15 14:35:17 2020 -0400 |
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| b'@@ -0,0 +1,2218 @@\n+GROningen MAchine for Chemical Simulation\n+ 2215\n+ 1LYS N 1 4.434 3.396 2.469\n+ 1LYS H1 2 4.510 3.450 2.431\n+ 1LYS H2 3 4.368 3.376 2.397\n+ 1LYS H3 4 4.390 3.448 2.542\n+ 1LYS CA 5 4.487 3.269 2.524\n+ 1LYS HA 6 4.531 3.217 2.451\n+ 1LYS CB 7 4.585 3.306 2.636\n+ 1LYS HB1 8 4.661 3.357 2.597\n+ 1LYS HB2 9 4.537 3.363 2.703\n+ 1LYS CG 10 4.643 3.187 2.711\n+ 1LYS HG1 11 4.574 3.151 2.773\n+ 1LYS HG2 12 4.668 3.116 2.644\n+ 1LYS CD 13 4.767 3.227 2.790\n+ 1LYS HD1 14 4.843 3.245 2.727\n+ 1LYS HD2 15 4.747 3.309 2.843\n+ 1LYS CE 16 4.804 3.113 2.883\n+ 1LYS HE1 17 4.739 3.108 2.959\n+ 1LYS HE2 18 4.804 3.026 2.834\n+ 1LYS NZ 19 4.940 3.139 2.937\n+ 1LYS HZ1 20 4.967 3.065 2.999\n+ 1LYS HZ2 21 5.006 3.144 2.861\n+ 1LYS HZ3 22 4.940 3.226 2.987\n+ 1LYS C 23 4.372 3.188 2.583\n+ 1LYS O 24 4.293 3.243 2.659\n+ 2VAL N 25 4.372 3.058 2.563\n+ 2VAL H 26 4.434 3.022 2.493\n+ 2VAL CA 27 4.288 2.962 2.634\n+ 2VAL HA 28 4.215 3.014 2.677\n+ 2VAL CB 29 4.212 2.865 2.544\n+ 2VAL HB 30 4.284 2.814 2.497\n+ 2VAL CG1 31 4.123 2.770 2.624\n+ 2VAL HG11 32 4.075 2.709 2.561\n+ 2VAL HG12 33 4.180 2.717 2.686\n+ 2VAL HG13 34 4.056 2.823 2.676\n+ 2VAL CG2 35 4.127 2.933 2.438\n+ 2VAL HG21 36 4.081 2.864 2.383\n+ 2VAL HG22 37 4.060 2.992 2.482\n+ 2VAL HG23 38 4.186 2.989 2.379\n+ 2VAL C 39 4.378 2.893 2.738\n+ 2VAL O 40 4.474 2.823 2.701\n+ 3PHE N 41 4.347 2.917 2.863\n+ 3PHE H 42 4.273 2.981 2.883\n+ 3PHE CA 43 4.417 2.852 2.975\n+ 3PHE HA 44 4.513 2.859 2.950\n+ 3PHE CB 45 4.395 2.925 3.108\n+ 3PHE HB1 46 4.303 2.964 3.109\n+ 3PHE HB2 47 4.404 2.860 3.183\n+ 3PHE CG 48 4.492 3.036 3.129\n+ 3PHE CD1 49 4.465 3.167 3.087\n+ 3PHE HD1 50 4.379 3.187 3.040\n+ 3PHE CD2 51 4.598 3.018 3.220\n+ 3PHE HD2 52 4.611 2.928 3.262\n+ 3PHE CE1 53 4.556 3.270 3.110\n+ 3PHE HE1 54 4.546 3.357 3.063\n+ 3PHE CE2 55 4.685 3.121 3.251\n+ 3PHE HE2 56 4.764 3.104 3.310\n+ 3PHE CZ 57 4.662 3.249 3.200\n+ 3PHE HZ 58 4.720 3.326 3.228\n+ 3PHE C 59 4.372 2.706 2.990\n+ 3PHE O 60 4.250 2.678 2.981\n+ 4GLY N 61 4.470 2.626 3.034\n+ 4GLY H 62 4.565 2.657 3.035\n+ 4GLY CA 63 4.435 2.490 3.080\n+ 4GLY HA1 64 4.360 2.454 3.024\n+ 4GLY HA2 65 4.514 2.430 3.073\n+ 4GLY C 66 4.390 2.504 3.225\n+ 4GLY O 67 4.428 2.602 3.289\n+ 5ARG N 68 4.303 2.416 3.270\n+ 5ARG H 69 4.269 2.346 3.207\n+ 5ARG CA 70 4.254 2.416 3.408\n+ 5ARG HA 71 4.196 2.496 3.415\n+ 5ARG CB 72 4.174 2.288 3.434\n+ 5ARG HB1 73 4.098 2.284 3.370\n+ 5ARG HB2 74 4.234 2.209 3.420\n+ 5ARG CG 75 4.119 2.282 3.575\n+ 5ARG HG1 76 4.195 2.279 3.640\n+ 5ARG HG2 77 4.063 2.363 3.592\n+ 5ARG CD 78 4.036 2.162 3.595\n+ 5ARG HD1 79 4.002 2.161 3.689\n+ 5ARG HD2 80 3.958 2.167 3.532\n+ 5ARG NE 81 4.104 2.037 3.571\n+ 5ARG HE 82 4.100 2.002 3.478\n+ 5ARG CZ 83 4.171 1.963 3.657\n+ 5ARG NH1 84 4.182 1.995 3.786\n+ 5ARG HH11 85 4.137 2.078 3.820\n+ 5ARG HH12 8'..b'73 4.351\n+ 186HOH HW1 2130 4.376 4.473 4.408\n+ 186HOH HW2 2131 4.295 4.392 4.293\n+ 187HOH OW 2132 2.855 3.704 3.525\n+ 187HOH HW1 2133 2.774 3.704 3.583\n+ 187HOH HW2 2134 2.855 3.786 3.467\n+ 188HOH OW 2135 2.377 2.729 4.393\n+ 188HOH HW1 2136 2.295 2.729 4.451\n+ 188HOH HW2 2137 2.377 2.648 4.335\n+ 189HOH OW 2138 2.809 3.964 2.202\n+ 189HOH HW1 2139 2.809 4.046 2.145\n+ 189HOH HW2 2140 2.809 3.883 2.145\n+ 190HOH OW 2141 2.628 5.068 2.422\n+ 190HOH HW1 2142 2.710 5.068 2.479\n+ 190HOH HW2 2143 2.547 5.068 2.479\n+ 191HOH OW 2144 2.518 2.612 4.225\n+ 191HOH HW1 2145 2.599 2.612 4.282\n+ 191HOH HW2 2146 2.518 2.694 4.167\n+ 192HOH OW 2147 2.633 5.797 2.959\n+ 192HOH HW1 2148 2.714 5.797 3.017\n+ 192HOH HW2 2149 2.633 5.715 2.901\n+ 193HOH OW 2150 2.397 4.292 3.243\n+ 193HOH HW1 2151 2.316 4.292 3.301\n+ 193HOH HW2 2152 2.397 4.374 3.185\n+ 194HOH OW 2153 3.718 5.639 3.352\n+ 194HOH HW1 2154 3.636 5.639 3.410\n+ 194HOH HW2 2155 3.718 5.558 3.294\n+ 195HOH OW 2156 3.846 2.548 2.756\n+ 195HOH HW1 2157 3.846 2.630 2.699\n+ 195HOH HW2 2158 3.846 2.467 2.699\n+ 196HOH OW 2159 3.259 5.643 3.928\n+ 196HOH HW1 2160 3.341 5.643 3.986\n+ 196HOH HW2 2161 3.178 5.643 3.986\n+ 197HOH OW 2162 4.955 3.380 3.031\n+ 197HOH HW1 2163 5.037 3.380 3.089\n+ 197HOH HW2 2164 4.955 3.462 2.973\n+ 198HOH OW 2165 2.145 4.348 3.044\n+ 198HOH HW1 2166 2.227 4.348 3.102\n+ 198HOH HW2 2167 2.145 4.266 2.987\n+ 199HOH OW 2168 2.566 2.521 3.084\n+ 199HOH HW1 2169 2.485 2.521 3.142\n+ 199HOH HW2 2170 2.566 2.603 3.026\n+ 200HOH OW 2171 3.651 4.968 2.381\n+ 200HOH HW1 2172 3.570 4.968 2.439\n+ 200HOH HW2 2173 3.651 4.886 2.323\n+ 201HOH OW 2174 3.487 4.759 4.823\n+ 201HOH HW1 2175 3.487 4.841 4.766\n+ 201HOH HW2 2176 3.487 4.678 4.766\n+ 202HOH OW 2177 3.377 3.680 5.273\n+ 202HOH HW1 2178 3.459 3.680 5.331\n+ 202HOH HW2 2179 3.295 3.680 5.331\n+ 203HOH OW 2180 2.156 3.283 4.168\n+ 203HOH HW1 2181 2.238 3.283 4.225\n+ 203HOH HW2 2182 2.156 3.365 4.110\n+ 204HOH OW 2183 2.867 3.537 3.182\n+ 204HOH HW1 2184 2.948 3.537 3.240\n+ 204HOH HW2 2185 2.867 3.455 3.124\n+ 205HOH OW 2186 3.608 4.758 2.431\n+ 205HOH HW1 2187 3.526 4.758 2.489\n+ 205HOH HW2 2188 3.608 4.839 2.373\n+ 206HOH OW 2189 4.624 2.125 4.667\n+ 206HOH HW1 2190 4.542 2.125 4.725\n+ 206HOH HW2 2191 4.624 2.044 4.609\n+ 207HOH OW 2192 5.274 3.546 4.471\n+ 207HOH HW1 2193 5.274 3.628 4.413\n+ 207HOH HW2 2194 5.274 3.465 4.413\n+ 208G5E C1 2195 6.456 3.250 2.707\n+ 208G5E C2 2196 6.330 3.283 2.656\n+ 208G5E C3 2197 6.321 3.361 2.541\n+ 208G5E C7 2198 6.426 3.498 2.362\n+ 208G5E C10 2199 6.449 3.677 2.236\n+ 208G5E C12 2200 6.570 3.684 2.448\n+ 208G5E C13 2201 6.707 3.692 2.422\n+ 208G5E C14 2202 6.793 3.751 2.516\n+ 208G5E C15 2203 6.742 3.801 2.635\n+ 208G5E C16 2204 6.605 3.793 2.661\n+ 208G5E C4 2205 6.438 3.406 2.478\n+ 208G5E C5 2206 6.564 3.375 2.531\n+ 208G5E C6 2207 6.572 3.297 2.645\n+ 208G5E N8 2208 6.353 3.478 2.256\n+ 208G5E N9 2209 6.368 3.590 2.173\n+ 208G5E N11 2210 6.485 3.623 2.353\n+ 208G5E C17 2211 6.519 3.734 2.568\n+ 208G5E S18 2212 6.498 3.829 2.176\n+ 208G5E F19 2213 6.755 3.642 2.306\n+ 208G5E O20 2214 6.199 3.392 2.489\n+ 208G5E O21 2215 6.465 3.175 2.819\n+ 7.33925 7.33925 7.33925\n' |
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| diff -r 8ddd75c21cbd -r 06ea4e040d45 test-data/complex.top --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/complex.top Wed Apr 15 14:35:17 2020 -0400 |
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| b'@@ -0,0 +1,18615 @@\n+;\n+;\tFile \'topol.top\' was generated\n+;\tBy user: unknown (1000)\n+;\tOn host: simon-notebook\n+;\tAt date: Wed Aug 28 14:35:18 2019\n+;\n+;\tThis is a standalone topology file\n+;\n+;\tCreated by:\n+;\t :-) GROMACS - gmx pdb2gmx, 2019.1 (-:\n+;\t\n+;\tExecutable: /home/simon/miniconda3/envs/gmx/bin/gmx\n+;\tData prefix: /home/simon/miniconda3/envs/gmx\n+;\tWorking dir: /home/simon/Repos/galaxy-tools-compchem/tools/gromacs\n+;\tCommand line:\n+;\t gmx pdb2gmx -f test-data/1AKI.pdb -o processed.gro -p topol.top -i posres.itp -water spce -ff oplsaa -noignh\n+;\tForce field was read from the standard GROMACS share directory.\n+;\n+\n+; Include forcefield parameters\n+#include "oplsaa.ff/forcefield.itp"\n+\n+; Include ligand atomtypes\n+[ atomtypes ]\n+;name bond_type mass charge ptype sigma epsilon Amb\n+ C C 0.00000 0.00000 A 3.39967e-01 3.59824e-01 ; 1.91 0.0860\n+ CZ CZ 0.00000 0.00000 A 3.39967e-01 3.59824e-01 ; 1.91 0.0860\n+ CK CK 0.00000 0.00000 A 3.39967e-01 3.59824e-01 ; 1.91 0.0860\n+ CM CM 0.00000 0.00000 A 3.39967e-01 3.59824e-01 ; 1.91 0.0860\n+ CD CD 0.00000 0.00000 A 3.39967e-01 3.59824e-01 ; 1.91 0.0860\n+ NB NB 0.00000 0.00000 A 3.25000e-01 7.11280e-01 ; 1.82 0.1700\n+ N* N* 0.00000 0.00000 A 3.25000e-01 7.11280e-01 ; 1.82 0.1700\n+ DU DU 0.00000 0.00000 A 0.00000e+00 0.00000e+00 ; 0.00 0.0000\n+ F F 0.00000 0.00000 A 3.11815e-01 2.55224e-01 ; 1.75 0.0610\n+ O O 0.00000 0.00000 A 2.95992e-01 8.78640e-01 ; 1.66 0.2100\n+\n+[ moleculetype ]\n+; Name nrexcl\n+Protein_chain_A 3\n+\n+[ atoms ]\n+; nr type resnr residue atom cgnr charge mass typeB chargeB massB\n+; residue 1 LYS rtp LYSH q +2.0\n+ 1 opls_287 1 LYS N 1 -0.3 14.0027\n+ 2 opls_290 1 LYS H1 1 0.33 1.008\n+ 3 opls_290 1 LYS H2 1 0.33 1.008\n+ 4 opls_290 1 LYS H3 1 0.33 1.008\n+ 5 opls_293B 1 LYS CA 1 0.25 12.011\n+ 6 opls_140 1 LYS HA 1 0.06 1.008\n+ 7 opls_136 1 LYS CB 2 -0.12 12.011\n+ 8 opls_140 1 LYS HB1 2 0.06 1.008\n+ 9 opls_140 1 LYS HB2 2 0.06 1.008\n+ 10 opls_136 1 LYS CG 3 -0.12 12.011\n+ 11 opls_140 1 LYS HG1 3 0.06 1.008\n+ 12 opls_140 1 LYS HG2 3 0.06 1.008\n+ 13 opls_136 1 LYS CD 4 -0.12 12.011\n+ 14 opls_140 1 LYS HD1 4 0.06 1.008\n+ 15 opls_140 1 LYS HD2 4 0.06 1.008\n+ 16 opls_292 1 LYS CE 5 0.19 12.011\n+ 17 opls_140 1 LYS HE1 5 0.06 1.008\n+ 18 opls_140 1 LYS HE2 5 0.06 1.008\n+ 19 opls_287 1 LYS NZ 6 -0.3 14.0067\n+ 20 opls_290 1 LYS HZ1 6 0.33 1.008\n+ 21 opls_290 1 LYS HZ2 6 0.33 1.008\n+ 22 opls_290 1 LYS HZ3 6 0.33 1.008\n+ 23 opls_235 1 LYS C 7 0.5 12.011\n+ 24 opls_236 1 LYS O 7 -0.5 15.9994 ; qtot 2\n+; residue 2 VAL rtp VAL q 0.0\n+ 25 opls_238 2 VAL N 8 -0.5 14.0067\n+ 26 opls_241 2 VAL H 8 0.3 1.008\n+ 27 opls_224B 2 VAL CA 8 0.14 12.011\n+ 28 opls_140 2 VAL HA 8 0.06 1.008\n+ 29 opls_137 2 VAL CB 9 -0.06 12.011'..b' C12- C13\n+ 4 16 6 17 9 180.00 7.74040 2 ; C7- N11- C12- C17\n+ 5 16 4 11 9 180.00 7.11280 2 ; C10- N11- C7- C4\n+ 5 16 4 14 9 180.00 7.11280 2 ; C10- N11- C7- N8\n+ 5 16 6 7 9 180.00 7.74040 2 ; C10- N11- C12- C13\n+ 5 16 6 17 9 180.00 7.74040 2 ; C10- N11- C12- C17\n+ 6 7 8 9 9 180.00 0.00000 2 ; C12- C13- C14- C15\n+ 6 16 4 11 9 180.00 7.11280 2 ; C12- N11- C7- C4\n+ 6 16 4 14 9 180.00 7.11280 2 ; C12- N11- C7- N8\n+ 6 16 5 15 9 180.00 6.06680 2 ; C12- N11- C10- N9\n+ 6 16 5 18 9 180.00 6.06680 2 ; C12- N11- C10- S18\n+ 6 17 10 9 9 180.00 0.00000 2 ; C12- C17- C16- C15\n+ 7 6 17 10 9 180.00 0.00000 2 ; C13- C12- C17- C16\n+ 7 8 9 10 9 180.00 0.00000 2 ; C13- C14- C15- C16\n+ 8 7 6 16 9 180.00 27.82360 2 ; C14- C13- C12- N11\n+ 8 7 6 17 9 180.00 27.82360 2 ; C14- C13- C12- C17\n+ 8 9 10 17 9 180.00 0.00000 2 ; C14- C15- C16- C17\n+ 9 8 7 19 9 180.00 0.00000 2 ; C15- C14- C13- F19\n+ 10 17 6 16 9 180.00 0.00000 2 ; C16- C17- C12- N11\n+ 11 4 14 15 9 180.00 41.84000 2 ; C4- C7- N8- N9\n+ 12 11 3 20 9 180.00 12.02900 2 ; C5- C4- C3- O20\n+ 12 11 4 14 9 180.00 16.73600 2 ; C5- C4- C7- N8\n+ 12 11 4 16 9 180.00 16.73600 2 ; C5- C4- C7- N11\n+ 13 1 2 3 9 180.00 0.00000 2 ; C6- C1- C2- C3\n+ 14 15 5 16 9 180.00 16.73600 2 ; N8- N9- C10- N11\n+ 14 15 5 18 9 180.00 16.73600 2 ; N8- N9- C10- S18\n+ 15 14 4 16 9 180.00 41.84000 2 ; N9- N8- C7- N11\n+ 16 6 7 19 9 180.00 27.82360 2 ; N11- C12- C13- F19\n+ 17 6 7 19 9 180.00 27.82360 2 ; C17- C12- C13- F19\n+ 21 1 2 3 9 180.00 0.00000 2 ; O21- C1- C2- C3\n+ 21 1 13 12 9 180.00 0.00000 2 ; O21- C1- C6- C5\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 4 11 12 4 180.00 4.60240 2 ; C3- C7- C4- C5\n+ 5 4 16 6 4 180.00 4.60240 2 ; C10- C7- N11- C12\n+ 6 8 7 19 4 180.00 4.60240 2 ; C12- C14- C13- F19\n+ 7 17 6 16 4 180.00 4.60240 2 ; C13- C17- C12- N11\n+ 11 2 3 20 4 180.00 43.93200 2 ; C4- C2- C3- O20\n+ 11 16 4 14 4 180.00 4.60240 2 ; C4- N11- C7- N8\n+ 18 16 5 15 4 180.00 4.60240 2 ; S18- N11- C10- N9\n+ 21 1 13 2 4 180.00 43.93200 2 ; O21- C1- C6- C2\n+\n+; Include water topology\n+#include "oplsaa.ff/spce.itp"\n+\n+#ifdef POSRES_WATER\n+; Position restraint for each water oxygen\n+[ position_restraints ]\n+; i funct fcx fcy fcz\n+ 1 1 1000 1000 1000\n+#endif\n+\n+; Include topology for ions\n+#include "oplsaa.ff/ions.itp"\n+\n+[ system ]\n+; Name\n+LYSOZYME\n+\n+[ molecules ]\n+; Compound #mols\n+Protein_chain_A 1\n+SOL 78\n+base 1\n' |
| b |
| diff -r 8ddd75c21cbd -r 06ea4e040d45 test-data/lig.gro --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/lig.gro Wed Apr 15 14:35:17 2020 -0400 |
| b |
| @@ -0,0 +1,24 @@ +base_GMX.gro created by acpype (v: 2019-11-07T23:16:00CET) on Fri Mar 20 14:38:01 2020 + 21 + 1 G5E C1 1 6.456 3.250 2.707 + 1 G5E C2 2 6.330 3.283 2.656 + 1 G5E C3 3 6.321 3.361 2.541 + 1 G5E C7 4 6.426 3.498 2.362 + 1 G5E C10 5 6.449 3.677 2.236 + 1 G5E C12 6 6.570 3.684 2.448 + 1 G5E C13 7 6.707 3.692 2.422 + 1 G5E C14 8 6.793 3.751 2.516 + 1 G5E C15 9 6.742 3.801 2.635 + 1 G5E C16 10 6.605 3.793 2.661 + 1 G5E C4 11 6.438 3.406 2.478 + 1 G5E C5 12 6.564 3.375 2.531 + 1 G5E C6 13 6.572 3.297 2.645 + 1 G5E N8 14 6.353 3.478 2.256 + 1 G5E N9 15 6.368 3.590 2.173 + 1 G5E N11 16 6.485 3.623 2.353 + 1 G5E C17 17 6.519 3.734 2.568 + 1 G5E S18 18 6.498 3.829 2.176 + 1 G5E F19 19 6.755 3.642 2.306 + 1 G5E O20 20 6.199 3.392 2.489 + 1 G5E O21 21 6.465 3.175 2.819 + 11.88000 13.08400 12.91800 |
| b |
| diff -r 8ddd75c21cbd -r 06ea4e040d45 test-data/lig.itp --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/lig.itp Wed Apr 15 14:35:17 2020 -0400 |
| [ |
| b'@@ -0,0 +1,202 @@\n+; base_GMX.itp created by acpype (v: 2019-11-07T23:16:00CET) on Fri Mar 20 14:38:01 2020\n+\n+[ atomtypes ]\n+;name bond_type mass charge ptype sigma epsilon Amb\n+ C C 0.00000 0.00000 A 3.39967e-01 3.59824e-01 ; 1.91 0.0860\n+ CZ CZ 0.00000 0.00000 A 3.39967e-01 3.59824e-01 ; 1.91 0.0860\n+ CK CK 0.00000 0.00000 A 3.39967e-01 3.59824e-01 ; 1.91 0.0860\n+ CM CM 0.00000 0.00000 A 3.39967e-01 3.59824e-01 ; 1.91 0.0860\n+ CD CD 0.00000 0.00000 A 3.39967e-01 3.59824e-01 ; 1.91 0.0860\n+ NB NB 0.00000 0.00000 A 3.25000e-01 7.11280e-01 ; 1.82 0.1700\n+ N* N* 0.00000 0.00000 A 3.25000e-01 7.11280e-01 ; 1.82 0.1700\n+ DU DU 0.00000 0.00000 A 0.00000e+00 0.00000e+00 ; 0.00 0.0000\n+ F F 0.00000 0.00000 A 3.11815e-01 2.55224e-01 ; 1.75 0.0610\n+ O O 0.00000 0.00000 A 2.95992e-01 8.78640e-01 ; 1.66 0.2100\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 C 1 G5E C1 1 0.545501 12.01000 ; qtot 0.546\n+ 2 CZ 1 G5E C2 2 0.075000 12.01000 ; qtot 0.621\n+ 3 C 1 G5E C3 3 0.508501 12.01000 ; qtot 1.129\n+ 4 CK 1 G5E C7 4 0.208200 12.01000 ; qtot 1.337\n+ 5 C 1 G5E C10 5 0.352800 12.01000 ; qtot 1.690\n+ 6 CM 1 G5E C12 6 0.002500 12.01000 ; qtot 1.693\n+ 7 CM 1 G5E C13 7 0.233400 12.01000 ; qtot 1.926\n+ 8 CZ 1 G5E C14 8 -0.087900 12.01000 ; qtot 1.838\n+ 9 CZ 1 G5E C15 9 0.072000 12.01000 ; qtot 1.910\n+ 10 CZ 1 G5E C16 10 0.028000 12.01000 ; qtot 1.938\n+ 11 CD 1 G5E C4 11 -0.048900 12.01000 ; qtot 1.889\n+ 12 CZ 1 G5E C5 12 -0.123300 12.01000 ; qtot 1.766\n+ 13 CZ 1 G5E C6 13 -0.161200 12.01000 ; qtot 1.605\n+ 14 NB 1 G5E N8 14 -0.082600 14.01000 ; qtot 1.522\n+ 15 NB 1 G5E N9 15 -0.125400 14.01000 ; qtot 1.397\n+ 16 N* 1 G5E N11 16 -0.261200 14.01000 ; qtot 1.135\n+ 17 CZ 1 G5E C17 17 -0.043900 12.01000 ; qtot 1.092\n+ 18 DU 1 G5E S18 18 -0.081400 0.00000 ; qtot 1.010\n+ 19 F 1 G5E F19 19 -0.100500 19.00000 ; qtot 0.910\n+ 20 O 1 G5E O20 20 -0.460300 16.00000 ; qtot 0.449\n+ 21 O 1 G5E O21 21 -0.449300 16.00000 ; qtot -0.000\n+\n+[ bonds ]\n+; ai aj funct r k\n+ 1 2 1 1.4600e-01 3.1782e+05 ; C1 - C2 \n+ 1 13 1 1.4600e-01 3.1782e+05 ; C1 - C6 \n+ 1 21 1 1.2290e-01 4.7698e+05 ; C1 - O21 \n+ 2 3 1 1.4600e-01 3.1782e+05 ; C2 - C3 \n+ 3 11 1 1.4680e-01 3.1045e+05 ; C3 - C4 \n+ 3 20 1 1.2290e-01 4.7698e+05 ; C3 - O20 \n+ 4 11 1 1.4280e-01 3.5129e+05 ; C7 - C4 \n+ 4 14 1 1.3040e-01 4.4267e+05 ; C7 - N8 \n+ 4 16 1 1.3710e-01 3.6819e+05 ; C7 - N11 \n+ 5 15 1 1.3870e-01 3.4886e+05 ; C10 - N9 \n+ 5 16 1 1.3830e-01 3.5480e+05 ; C10 - N11 \n+ 5 18 1 0.0000e+00 0.0000e+00 ; C10 - S18 \n+ 6 7 1 1.3500e-01 4.5940e+05 ; C12 - C13 \n+ 6 16 1 1.3650e-01 3.7489e+05 ; C12 - N11 \n+ 6 17 1 1.4400e-01 3.3815e+05 ; C12 - C17 \n+ 7 8 1 1.4400e-01 3.3815e+05 ; C13 - C14 \n+ 7 19 1 1.3490e-01 2.9941e+05 ; C13 - F19 \n+ 8 '..b'C3- O20\n+ 4 11 12 13 9 180.00 0.00000 2 ; C7- C4- C5- C6\n+ 4 14 15 5 9 180.00 16.73600 2 ; C7- N8- N9- C10\n+ 4 16 5 15 9 180.00 6.06680 2 ; C7- N11- C10- N9\n+ 4 16 5 18 9 180.00 6.06680 2 ; C7- N11- C10- S18\n+ 4 16 6 7 9 180.00 7.74040 2 ; C7- N11- C12- C13\n+ 4 16 6 17 9 180.00 7.74040 2 ; C7- N11- C12- C17\n+ 5 16 4 11 9 180.00 7.11280 2 ; C10- N11- C7- C4\n+ 5 16 4 14 9 180.00 7.11280 2 ; C10- N11- C7- N8\n+ 5 16 6 7 9 180.00 7.74040 2 ; C10- N11- C12- C13\n+ 5 16 6 17 9 180.00 7.74040 2 ; C10- N11- C12- C17\n+ 6 7 8 9 9 180.00 0.00000 2 ; C12- C13- C14- C15\n+ 6 16 4 11 9 180.00 7.11280 2 ; C12- N11- C7- C4\n+ 6 16 4 14 9 180.00 7.11280 2 ; C12- N11- C7- N8\n+ 6 16 5 15 9 180.00 6.06680 2 ; C12- N11- C10- N9\n+ 6 16 5 18 9 180.00 6.06680 2 ; C12- N11- C10- S18\n+ 6 17 10 9 9 180.00 0.00000 2 ; C12- C17- C16- C15\n+ 7 6 17 10 9 180.00 0.00000 2 ; C13- C12- C17- C16\n+ 7 8 9 10 9 180.00 0.00000 2 ; C13- C14- C15- C16\n+ 8 7 6 16 9 180.00 27.82360 2 ; C14- C13- C12- N11\n+ 8 7 6 17 9 180.00 27.82360 2 ; C14- C13- C12- C17\n+ 8 9 10 17 9 180.00 0.00000 2 ; C14- C15- C16- C17\n+ 9 8 7 19 9 180.00 0.00000 2 ; C15- C14- C13- F19\n+ 10 17 6 16 9 180.00 0.00000 2 ; C16- C17- C12- N11\n+ 11 4 14 15 9 180.00 41.84000 2 ; C4- C7- N8- N9\n+ 12 11 3 20 9 180.00 12.02900 2 ; C5- C4- C3- O20\n+ 12 11 4 14 9 180.00 16.73600 2 ; C5- C4- C7- N8\n+ 12 11 4 16 9 180.00 16.73600 2 ; C5- C4- C7- N11\n+ 13 1 2 3 9 180.00 0.00000 2 ; C6- C1- C2- C3\n+ 14 15 5 16 9 180.00 16.73600 2 ; N8- N9- C10- N11\n+ 14 15 5 18 9 180.00 16.73600 2 ; N8- N9- C10- S18\n+ 15 14 4 16 9 180.00 41.84000 2 ; N9- N8- C7- N11\n+ 16 6 7 19 9 180.00 27.82360 2 ; N11- C12- C13- F19\n+ 17 6 7 19 9 180.00 27.82360 2 ; C17- C12- C13- F19\n+ 21 1 2 3 9 180.00 0.00000 2 ; O21- C1- C2- C3\n+ 21 1 13 12 9 180.00 0.00000 2 ; O21- C1- C6- C5\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 4 11 12 4 180.00 4.60240 2 ; C3- C7- C4- C5\n+ 5 4 16 6 4 180.00 4.60240 2 ; C10- C7- N11- C12\n+ 6 8 7 19 4 180.00 4.60240 2 ; C12- C14- C13- F19\n+ 7 17 6 16 4 180.00 4.60240 2 ; C13- C17- C12- N11\n+ 11 2 3 20 4 180.00 43.93200 2 ; C4- C2- C3- O20\n+ 11 16 4 14 4 180.00 4.60240 2 ; C4- N11- C7- N8\n+ 18 16 5 15 4 180.00 4.60240 2 ; S18- N11- C10- N9\n+ 21 1 13 2 4 180.00 43.93200 2 ; O21- C1- C6- C2\n' |
| b |
| diff -r 8ddd75c21cbd -r 06ea4e040d45 test-data/top_output.top --- a/test-data/top_output.top Tue Jan 21 07:30:45 2020 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| b'@@ -1,19416 +0,0 @@\n-;\n-;\tFile \'topol.top\' was generated\n-;\tBy user: unknown (1000)\n-;\tOn host: simon-notebook\n-;\tAt date: Wed Aug 28 14:35:18 2019\n-;\n-;\tThis is a standalone topology file\n-;\n-;\tCreated by:\n-;\t :-) GROMACS - gmx pdb2gmx, 2019.1 (-:\n-;\t\n-;\tExecutable: /home/simon/miniconda3/envs/gmx/bin/gmx\n-;\tData prefix: /home/simon/miniconda3/envs/gmx\n-;\tWorking dir: /home/simon/Repos/galaxy-tools-compchem/tools/gromacs\n-;\tCommand line:\n-;\t gmx pdb2gmx -f test-data/1AKI.pdb -o processed.gro -p topol.top -i posres.itp -water spce -ff oplsaa -noignh\n-;\tForce field was read from the standard GROMACS share directory.\n-;\n-\n-; Include forcefield parameters\n-#include "oplsaa.ff/forcefield.itp"\n-\n-[ moleculetype ]\n-; Name nrexcl\n-Protein_chain_A 3\n-\n-[ atoms ]\n-; nr type resnr residue atom cgnr charge mass typeB chargeB massB\n-; residue 1 LYS rtp LYSH q +2.0\n- 1 opls_287 1 LYS N 1 -0.3 14.0027\n- 2 opls_290 1 LYS H1 1 0.33 1.008\n- 3 opls_290 1 LYS H2 1 0.33 1.008\n- 4 opls_290 1 LYS H3 1 0.33 1.008\n- 5 opls_293B 1 LYS CA 1 0.25 12.011\n- 6 opls_140 1 LYS HA 1 0.06 1.008\n- 7 opls_136 1 LYS CB 2 -0.12 12.011\n- 8 opls_140 1 LYS HB1 2 0.06 1.008\n- 9 opls_140 1 LYS HB2 2 0.06 1.008\n- 10 opls_136 1 LYS CG 3 -0.12 12.011\n- 11 opls_140 1 LYS HG1 3 0.06 1.008\n- 12 opls_140 1 LYS HG2 3 0.06 1.008\n- 13 opls_136 1 LYS CD 4 -0.12 12.011\n- 14 opls_140 1 LYS HD1 4 0.06 1.008\n- 15 opls_140 1 LYS HD2 4 0.06 1.008\n- 16 opls_292 1 LYS CE 5 0.19 12.011\n- 17 opls_140 1 LYS HE1 5 0.06 1.008\n- 18 opls_140 1 LYS HE2 5 0.06 1.008\n- 19 opls_287 1 LYS NZ 6 -0.3 14.0067\n- 20 opls_290 1 LYS HZ1 6 0.33 1.008\n- 21 opls_290 1 LYS HZ2 6 0.33 1.008\n- 22 opls_290 1 LYS HZ3 6 0.33 1.008\n- 23 opls_235 1 LYS C 7 0.5 12.011\n- 24 opls_236 1 LYS O 7 -0.5 15.9994 ; qtot 2\n-; residue 2 VAL rtp VAL q 0.0\n- 25 opls_238 2 VAL N 8 -0.5 14.0067\n- 26 opls_241 2 VAL H 8 0.3 1.008\n- 27 opls_224B 2 VAL CA 8 0.14 12.011\n- 28 opls_140 2 VAL HA 8 0.06 1.008\n- 29 opls_137 2 VAL CB 9 -0.06 12.011\n- 30 opls_140 2 VAL HB 9 0.06 1.008\n- 31 opls_135 2 VAL CG1 10 -0.18 12.011\n- 32 opls_140 2 VAL HG11 10 0.06 1.008\n- 33 opls_140 2 VAL HG12 10 0.06 1.008\n- 34 opls_140 2 VAL HG13 10 0.06 1.008\n- 35 opls_135 2 VAL CG2 11 -0.18 12.011\n- 36 opls_140 2 VAL HG21 11 0.06 1.008\n- 37 opls_140 2 VAL HG22 11 0.06 1.008\n- 38 opls_140 2 VAL HG23 11 0.06 1.008\n- 39 opls_235 2 VAL C 12 0.5 12.011\n- 40 opls_236 2 VAL O 12 -0.5 15.9994 ; qtot 2\n-; residue 3 PHE rtp PHE q 0.0\n- 41 opls_238 3 PHE N 13 -0.5 14.0067\n- 42 opls_241 3 PHE H 13 0.3 1.008\n- 43 opls_224B 3 PHE CA 13 0.14 12.011\n- '..b'000 1000\n- 1737 1 1000 1000 1000\n- 1739 1 1000 1000 1000\n- 1742 1 1000 1000 1000\n- 1745 1 1000 1000 1000\n- 1748 1 1000 1000 1000\n- 1751 1 1000 1000 1000\n- 1755 1 1000 1000 1000\n- 1756 1 1000 1000 1000\n- 1757 1 1000 1000 1000\n- 1759 1 1000 1000 1000\n- 1762 1 1000 1000 1000\n- 1763 1 1000 1000 1000\n- 1764 1 1000 1000 1000\n- 1766 1 1000 1000 1000\n- 1768 1 1000 1000 1000\n- 1770 1 1000 1000 1000\n- 1772 1 1000 1000 1000\n- 1776 1 1000 1000 1000\n- 1777 1 1000 1000 1000\n- 1778 1 1000 1000 1000\n- 1780 1 1000 1000 1000\n- 1782 1 1000 1000 1000\n- 1785 1 1000 1000 1000\n- 1786 1 1000 1000 1000\n- 1787 1 1000 1000 1000\n- 1788 1 1000 1000 1000\n- 1789 1 1000 1000 1000\n- 1790 1 1000 1000 1000\n- 1792 1 1000 1000 1000\n- 1794 1 1000 1000 1000\n- 1796 1 1000 1000 1000\n- 1800 1 1000 1000 1000\n- 1804 1 1000 1000 1000\n- 1805 1 1000 1000 1000\n- 1806 1 1000 1000 1000\n- 1808 1 1000 1000 1000\n- 1810 1 1000 1000 1000\n- 1813 1 1000 1000 1000\n- 1816 1 1000 1000 1000\n- 1817 1 1000 1000 1000\n- 1818 1 1000 1000 1000\n- 1821 1 1000 1000 1000\n- 1822 1 1000 1000 1000\n- 1823 1 1000 1000 1000\n- 1825 1 1000 1000 1000\n- 1827 1 1000 1000 1000\n- 1831 1 1000 1000 1000\n- 1832 1 1000 1000 1000\n- 1833 1 1000 1000 1000\n- 1835 1 1000 1000 1000\n- 1837 1 1000 1000 1000\n- 1840 1 1000 1000 1000\n- 1841 1 1000 1000 1000\n- 1843 1 1000 1000 1000\n- 1844 1 1000 1000 1000\n- 1846 1 1000 1000 1000\n- 1847 1 1000 1000 1000\n- 1849 1 1000 1000 1000\n- 1851 1 1000 1000 1000\n- 1853 1 1000 1000 1000\n- 1855 1 1000 1000 1000\n- 1856 1 1000 1000 1000\n- 1857 1 1000 1000 1000\n- 1859 1 1000 1000 1000\n- 1861 1 1000 1000 1000\n- 1863 1 1000 1000 1000\n- 1866 1 1000 1000 1000\n- 1870 1 1000 1000 1000\n- 1874 1 1000 1000 1000\n- 1875 1 1000 1000 1000\n- 1876 1 1000 1000 1000\n- 1878 1 1000 1000 1000\n- 1880 1 1000 1000 1000\n- 1883 1 1000 1000 1000\n- 1886 1 1000 1000 1000\n- 1889 1 1000 1000 1000\n- 1891 1 1000 1000 1000\n- 1892 1 1000 1000 1000\n- 1895 1 1000 1000 1000\n- 1898 1 1000 1000 1000\n- 1899 1 1000 1000 1000\n- 1900 1 1000 1000 1000\n- 1902 1 1000 1000 1000\n- 1905 1 1000 1000 1000\n- 1906 1 1000 1000 1000\n- 1907 1 1000 1000 1000\n- 1909 1 1000 1000 1000\n- 1911 1 1000 1000 1000\n- 1914 1 1000 1000 1000\n- 1915 1 1000 1000 1000\n- 1916 1 1000 1000 1000\n- 1917 1 1000 1000 1000\n- 1919 1 1000 1000 1000\n- 1921 1 1000 1000 1000\n- 1924 1 1000 1000 1000\n- 1927 1 1000 1000 1000\n- 1930 1 1000 1000 1000\n- 1932 1 1000 1000 1000\n- 1933 1 1000 1000 1000\n- 1936 1 1000 1000 1000\n- 1939 1 1000 1000 1000\n- 1940 1 1000 1000 1000\n- 1941 1 1000 1000 1000\n- 1943 1 1000 1000 1000\n- 1945 1 1000 1000 1000\n- 1948 1 1000 1000 1000\n- 1950 1 1000 1000 1000\n- 1954 1 1000 1000 1000\n- 1958 1 1000 1000 1000\n- 1959 1 1000 1000 1000\n- 1960 1 1000 1000 1000\n-#endif\n-\n-; Include water topology\n-#include "oplsaa.ff/spce.itp"\n-\n-#ifdef POSRES_WATER\n-; Position restraint for each water oxygen\n-[ position_restraints ]\n-; i funct fcx fcy fcz\n- 1 1 1000 1000 1000\n-#endif\n-\n-; Include topology for ions\n-#include "oplsaa.ff/ions.itp"\n-\n-[ system ]\n-; Name\n-LYSOZYME\n-\n-[ molecules ]\n-; Compound #mols\n-Protein_chain_A 1\n-SOL 78\n' |