| Previous changeset 0:52e64e8cf203 (2020-02-28) Next changeset 2:51023da731c0 (2021-01-25) |
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Commit message:
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373" |
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modified:
mmpbsa_mmgbsa.xml |
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added:
template_parmconv.j2 test-data/solv_ions.gro test-data/topol_solv.top |
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| diff -r 52e64e8cf203 -r d09f116dfca5 mmpbsa_mmgbsa.xml --- a/mmpbsa_mmgbsa.xml Fri Feb 28 03:47:30 2020 -0500 +++ b/mmpbsa_mmgbsa.xml Tue Apr 07 07:59:06 2020 -0400 |
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| @@ -1,4 +1,4 @@ -<tool id="mmpbsa_mmgbsa" name="mmpbsa mmgbsa" version="@VERSION@"> +<tool id="mmpbsa_mmgbsa" name="mmpbsa mmgbsa" version="@VERSION@.1"> <description>- estimate ligand binding affinities </description> <macros> @@ -10,7 +10,8 @@ <command detect_errors="exit_code"> <![CDATA[ python '$mmpbsa_script' '$inputs' && - export AMBERHOME=\$CONDA_PREFIX && + PATH_TO_MMPBSA=\$(dirname `which MMPBSA.py`) && + export AMBERHOME=\$(dirname \$PATH_TO_MMPBSA) && #if $input.simulation.solvatedcomplex: MMPBSA.py -O -i '$parameteroutfile' -sp '$input.simulation.solvatedcomplex' -cp '$input.simulation.complex' -rp '$input.simulation.receptor' -lp '$input.simulation.ligand' -y '$input.simulation.trajcomplex' -o '$resultoutfile' -do '$decompoutfile' #else: |
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| diff -r 52e64e8cf203 -r d09f116dfca5 template_parmconv.j2 --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/template_parmconv.j2 Tue Apr 07 07:59:06 2020 -0400 |
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| @@ -0,0 +1,14 @@ +# Template for parmconv in Galaxy +{% if fmt == 'AMBER' %} +parm {{ top_in }} +{% elif fmt == 'GROMACS' %} +gromber {{ top_in }} {{gro_in}} +{% elif fmt == 'CHARMM' %} +chamber {{ top_in }} {{gro_in}} +{% else %} +parm {{ top_in }} +{% endif %} +strip {{ stripmask }} +summary +outparm {{ prmtop_out }} +quit |
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| diff -r 52e64e8cf203 -r d09f116dfca5 test-data/solv_ions.gro --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/solv_ions.gro Tue Apr 07 07:59:06 2020 -0400 |
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| b'@@ -0,0 +1,38379 @@\n+LYSOZYME in water\n+38376\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 86 4.234 1.937 3.8'..b'36 5.798\n+12240SOL OW38291 6.199 6.428 7.017\n+12240SOL HW138292 6.255 6.509 7.000\n+12240SOL HW238293 6.258 6.348 7.020\n+12241SOL OW38294 7.079 7.353 6.545\n+12241SOL HW138295 7.112 7.417 6.476\n+12241SOL HW238296 7.145 7.347 6.620\n+12242SOL OW38297 6.302 6.151 7.294\n+12242SOL HW138298 6.321 6.216 7.368\n+12242SOL HW238299 6.362 6.071 7.303\n+12243SOL OW38300 5.976 7.327 7.146\n+12243SOL HW138301 5.885 7.368 7.144\n+12243SOL HW238302 5.969 7.233 7.178\n+12244SOL OW38303 7.260 6.469 6.840\n+12244SOL HW138304 7.233 6.380 6.803\n+12244SOL HW238305 7.261 6.537 6.767\n+12245SOL OW38306 6.811 5.911 6.035\n+12245SOL HW138307 6.876 5.837 6.024\n+12245SOL HW238308 6.831 5.961 6.119\n+12246SOL OW38309 6.180 6.331 6.238\n+12246SOL HW138310 6.230 6.416 6.219\n+12246SOL HW238311 6.092 6.333 6.190\n+12247SOL OW38312 7.316 6.520 7.103\n+12247SOL HW138313 7.354 6.611 7.118\n+12247SOL HW238314 7.308 6.503 7.004\n+12248SOL OW38315 6.445 6.960 5.602\n+12248SOL HW138316 6.399 6.975 5.690\n+12248SOL HW238317 6.489 7.045 5.572\n+12249SOL OW38318 6.445 6.542 6.447\n+12249SOL HW138319 6.499 6.473 6.495\n+12249SOL HW238320 6.413 6.611 6.513\n+12250SOL OW38321 6.669 6.570 5.673\n+12250SOL HW138322 6.646 6.623 5.591\n+12250SOL HW238323 6.750 6.514 5.654\n+12251SOL OW38324 7.447 7.155 6.437\n+12251SOL HW138325 7.376 7.143 6.367\n+12251SOL HW238326 7.448 7.076 6.497\n+12252SOL OW38327 5.665 6.826 6.239\n+12252SOL HW138328 5.664 6.779 6.327\n+12252SOL HW238329 5.747 6.798 6.188\n+12253SOL OW38330 6.258 6.977 7.210\n+12253SOL HW138331 6.180 6.927 7.248\n+12253SOL HW238332 6.255 7.072 7.241\n+12254SOL OW38333 7.410 5.778 6.813\n+12254SOL HW138334 7.406 5.688 6.857\n+12254SOL HW238335 7.413 5.767 6.714\n+12255SOL OW38336 6.014 6.010 6.106\n+12255SOL HW138337 6.044 5.938 6.044\n+12255SOL HW238338 5.975 5.970 6.189\n+12256SOL OW38339 5.903 6.133 6.866\n+12256SOL HW138340 5.941 6.074 6.938\n+12256SOL HW238341 5.943 6.107 6.778\n+12257SOL OW38342 6.398 7.172 6.273\n+12257SOL HW138343 6.430 7.182 6.179\n+12257SOL HW238344 6.319 7.110 6.275\n+12258SOL OW38345 7.010 5.800 6.698\n+12258SOL HW138346 7.062 5.735 6.753\n+12258SOL HW238347 6.961 5.863 6.759\n+12259SOL OW38348 6.587 5.620 6.740\n+12259SOL HW138349 6.524 5.548 6.709\n+12259SOL HW238350 6.680 5.584 6.740\n+12260SOL OW38351 6.356 6.916 5.887\n+12260SOL HW138352 6.310 6.829 5.904\n+12260SOL HW238353 6.447 6.913 5.928\n+12261SOL OW38354 6.204 7.153 6.870\n+12261SOL HW138355 6.199 7.235 6.927\n+12261SOL HW238356 6.293 7.150 6.825\n+12262SOL OW38357 6.938 5.638 5.754\n+12262SOL HW138358 6.973 5.597 5.670\n+12262SOL HW238359 6.848 5.600 5.774\n+12263SOL OW38360 6.886 6.039 6.277\n+12263SOL HW138361 6.827 6.119 6.281\n+12263SOL HW238362 6.901 6.004 6.370\n+12264SOL OW38363 7.179 5.807 6.468\n+12264SOL HW138364 7.095 5.806 6.522\n+12264SOL HW238365 7.181 5.890 6.412\n+12265SOL OW38366 5.625 6.663 5.886\n+12265SOL HW138367 5.724 6.652 5.877\n+12265SOL HW238368 5.585 6.577 5.918\n+12266CL CL38369 1.638 2.961 6.665\n+12267CL CL38370 1.014 5.822 2.833\n+12268CL CL38371 4.539 0.572 5.911\n+12269CL CL38372 4.031 3.787 0.618\n+12270CL CL38373 4.492 4.868 4.747\n+12271CL CL38374 5.835 5.509 4.965\n+12272CL CL38375 6.974 7.159 0.477\n+12273CL CL38376 7.044 6.321 2.590\n+ 7.33925 7.33925 7.33925\n' |
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| diff -r 52e64e8cf203 -r d09f116dfca5 test-data/topol_solv.top --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/topol_solv.top Tue Apr 07 07:59:06 2020 -0400 |
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| b'@@ -0,0 +1,18411 @@\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'per_Z_CA_X_Y\n+ 1654 1653 1649 1657 1 improper_Z_CA_X_Y\n+ 1655 1657 1659 1660 1 improper_Z_CA_X_Y\n+ 1658 1657 1653 1659 1 improper_Z_CA_X_Y\n+ 1661 1665 1663 1664 1 improper_Z_N_X_Y\n+ 1665 1687 1685 1686 1 improper_O_C_X_Y\n+ 1673 1678 1676 1677 1 improper_Z_N_X_Y\n+ 1676 1679 1678 1682 1 improper_O_C_X_Y\n+ 1678 1680 1679 1681 1 improper_Z_N_X_Y\n+ 1678 1683 1682 1684 1 improper_Z_N_X_Y\n+ 1685 1689 1687 1688 1 improper_Z_N_X_Y\n+ 1689 1701 1699 1700 1 improper_O_C_X_Y\n+ 1691 1696 1694 1695 1 improper_O_C_X_Y\n+ 1694 1697 1696 1698 1 improper_Z_N_X_Y\n+ 1699 1703 1701 1702 1 improper_Z_N_X_Y\n+ 1703 1725 1723 1724 1 improper_O_C_X_Y\n+ 1711 1716 1714 1715 1 improper_Z_N_X_Y\n+ 1714 1717 1716 1720 1 improper_O_C_X_Y\n+ 1716 1718 1717 1719 1 improper_Z_N_X_Y\n+ 1716 1721 1720 1722 1 improper_Z_N_X_Y\n+ 1723 1727 1725 1726 1 improper_Z_N_X_Y\n+ 1727 1735 1733 1734 1 improper_O_C_X_Y\n+ 1733 1737 1735 1736 1 improper_Z_N_X_Y\n+ 1737 1757 1755 1756 1 improper_O_C_X_Y\n+ 1755 1759 1757 1758 1 improper_Z_N_X_Y\n+ 1759 1764 1762 1763 1 improper_O_C_X_Y\n+ 1762 1766 1764 1765 1 improper_Z_N_X_Y\n+ 1766 1778 1776 1777 1 improper_O_C_X_Y\n+ 1776 1780 1778 1779 1 improper_Z_N_X_Y\n+ 1780 1790 1788 1789 1 improper_O_C_X_Y\n+ 1782 1786 1785 1787 1 improper_O_C_X_Y\n+ 1788 1792 1790 1791 1 improper_Z_N_X_Y\n+ 1792 1806 1804 1805 1 improper_O_C_X_Y\n+ 1804 1808 1806 1807 1 improper_Z_N_X_Y\n+ 1808 1823 1821 1822 1 improper_O_C_X_Y\n+ 1813 1818 1816 1817 1 improper_O_C_X_Y\n+ 1816 1819 1818 1820 1 improper_Z_N_X_Y\n+ 1821 1825 1823 1824 1 improper_Z_N_X_Y\n+ 1825 1833 1831 1832 1 improper_O_C_X_Y\n+ 1831 1835 1833 1834 1 improper_Z_N_X_Y\n+ 1835 1857 1855 1856 1 improper_O_C_X_Y\n+ 1837 1840 1843 1841 1 improper_Z_CA_X_Y\n+ 1840 1844 1841 1842 1 improper_Z_CA_X_Y\n+ 1841 1846 1844 1845 1 improper_Z_N_X_Y\n+ 1846 1853 1849 1850 1 improper_Z_CA_X_Y\n+ 1848 1847 1843 1851 1 improper_Z_CA_X_Y\n+ 1849 1851 1853 1854 1 improper_Z_CA_X_Y\n+ 1852 1851 1847 1853 1 improper_Z_CA_X_Y\n+ 1855 1859 1857 1858 1 improper_Z_N_X_Y\n+ 1859 1876 1874 1875 1 improper_O_C_X_Y\n+ 1874 1878 1876 1877 1 improper_Z_N_X_Y\n+ 1878 1900 1898 1899 1 improper_O_C_X_Y\n+ 1886 1891 1889 1890 1 improper_Z_N_X_Y\n+ 1889 1892 1891 1895 1 improper_O_C_X_Y\n+ 1891 1893 1892 1894 1 improper_Z_N_X_Y\n+ 1891 1896 1895 1897 1 improper_Z_N_X_Y\n+ 1898 1902 1900 1901 1 improper_Z_N_X_Y\n+ 1902 1907 1905 1906 1 improper_O_C_X_Y\n+ 1905 1909 1907 1908 1 improper_Z_N_X_Y\n+ 1909 1917 1915 1916 1 improper_O_C_X_Y\n+ 1915 1919 1917 1918 1 improper_Z_N_X_Y\n+ 1919 1941 1939 1940 1 improper_O_C_X_Y\n+ 1927 1932 1930 1931 1 improper_Z_N_X_Y\n+ 1930 1933 1932 1936 1 improper_O_C_X_Y\n+ 1932 1934 1933 1935 1 improper_Z_N_X_Y\n+ 1932 1937 1936 1938 1 improper_Z_N_X_Y\n+ 1939 1943 1941 1942 1 improper_Z_N_X_Y\n+ 1943 1959 1958 1960 1 improper_O_C_X_Y\n+\n+; Include Position restraint file\n+#ifdef POSRES\n+#include "posres.itp"\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 in water\n+\n+[ molecules ]\n+; Compound #mols\n+Protein_chain_A 1\n+SOL 78\n+SOL 12058\n+CL 8\n' |