| Previous changeset 1:e9cc595562b8 (2020-02-13) Next changeset 3:6ac5f450ad31 (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 |
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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 |
| b |
| diff -r e9cc595562b8 -r b2acdbff8dfb merge_top.py --- a/merge_top.py Thu Feb 13 03:51:40 2020 -0500 +++ b/merge_top.py Wed Apr 15 14:14:07 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() |
| b |
| diff -r e9cc595562b8 -r b2acdbff8dfb test-data/complex.gro --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/complex.gro Wed Apr 15 14:14:07 2020 -0400 |
| b |
| 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' |
| b |
| diff -r e9cc595562b8 -r b2acdbff8dfb test-data/complex.top --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/complex.top Wed Apr 15 14:14:07 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 e9cc595562b8 -r b2acdbff8dfb test-data/lig.gro --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/lig.gro Wed Apr 15 14:14:07 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 e9cc595562b8 -r b2acdbff8dfb test-data/lig.itp --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/lig.itp Wed Apr 15 14:14:07 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 e9cc595562b8 -r b2acdbff8dfb test-data/top_output.top --- a/test-data/top_output.top Thu Feb 13 03:51:40 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' |