| Previous changeset 2:5b01e6df25a0 (2019-03-28) |
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Commit message:
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit b1b74e91a242f2de250761a79b17d77e68b1045f" |
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modified:
macros.xml test-data/solv_ions.gro test-data/top_output.top test-data/topol.top test-data/topol_solv.top |
| b |
| diff -r 5b01e6df25a0 -r 511b084adf53 macros.xml --- a/macros.xml Thu Mar 28 10:13:01 2019 -0400 +++ b/macros.xml Fri Aug 30 15:04:51 2019 -0400 |
| b |
| @@ -1,5 +1,5 @@ <macros> - <token name="@VERSION@">2018.2</token> + <token name="@VERSION@">2019.1</token> <xml name="requirements"> <requirements> <requirement type="package" version="@VERSION@">gromacs</requirement> |
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| diff -r 5b01e6df25a0 -r 511b084adf53 test-data/solv_ions.gro --- a/test-data/solv_ions.gro Thu Mar 28 10:13:01 2019 -0400 +++ b/test-data/solv_ions.gro Fri Aug 30 15:04:51 2019 -0400 |
| b |
| b'@@ -4774,5934 +4774,5934 @@\n 1067SOL OW 4772 0.809 1.866 0.502\n 1067SOL HW1 4773 0.849 1.957 0.493\n 1067SOL HW2 4774 0.709 1.874 0.508\n- 1068SOL OW 4775 1.525 2.861 0.190\n- 1068SOL HW1 4776 1.462 2.785 0.203\n- 1068SOL HW2 4777 1.573 2.879 0.276\n- 1069SOL OW 4778 1.187 3.654 1.616\n- 1069SOL HW1 4779 1.211 3.714 1.540\n- 1069SOL HW2 4780 1.194 3.559 1.586\n- 1070SOL OW 4781 0.317 2.113 1.801\n- 1070SOL HW1 4782 0.388 2.184 1.807\n- 1070SOL HW2 4783 0.229 2.152 1.829\n- 1071SOL OW 4784 1.466 3.279 0.953\n- 1071SOL HW1 4785 1.407 3.285 1.033\n- 1071SOL HW2 4786 1.451 3.191 0.907\n- 1072SOL OW 4787 1.667 3.576 0.572\n- 1072SOL HW1 4788 1.626 3.553 0.484\n- 1072SOL HW2 4789 1.649 3.502 0.637\n- 1073SOL OW 4790 0.598 2.591 0.270\n- 1073SOL HW1 4791 0.622 2.660 0.202\n- 1073SOL HW2 4792 0.520 2.624 0.324\n- 1074SOL OW 4793 1.281 2.207 0.944\n- 1074SOL HW1 4794 1.195 2.157 0.931\n- 1074SOL HW2 4795 1.343 2.153 1.000\n- 1075SOL OW 4796 1.576 3.524 0.307\n- 1075SOL HW1 4797 1.665 3.570 0.310\n- 1075SOL HW2 4798 1.555 3.500 0.212\n- 1076SOL OW 4799 0.807 2.467 1.465\n- 1076SOL HW1 4800 0.760 2.464 1.554\n- 1076SOL HW2 4801 0.756 2.412 1.399\n- 1077SOL OW 4802 1.394 2.331 1.674\n- 1077SOL HW1 4803 1.374 2.374 1.762\n- 1077SOL HW2 4804 1.472 2.269 1.683\n- 1078SOL OW 4805 0.973 2.752 1.572\n- 1078SOL HW1 4806 1.019 2.668 1.543\n- 1078SOL HW2 4807 0.917 2.786 1.497\n- 1079SOL OW 4808 0.991 2.272 1.242\n- 1079SOL HW1 4809 0.914 2.306 1.296\n- 1079SOL HW2 4810 0.957 2.221 1.163\n- 1080SOL OW 4811 1.041 2.563 0.429\n- 1080SOL HW1 4812 1.067 2.559 0.525\n- 1080SOL HW2 4813 0.956 2.512 0.415\n- 1081SOL OW 4814 0.076 2.673 0.789\n- 1081SOL HW1 4815 0.175 2.661 0.798\n- 1081SOL HW2 4816 0.052 2.768 0.810\n- 1082SOL OW 4817 0.130 3.683 1.571\n- 1082SOL HW1 4818 0.120 3.668 1.670\n- 1082SOL HW2 4819 0.044 3.719 1.535\n- 1083SOL OW 4820 0.865 2.210 0.195\n- 1083SOL HW1 4821 0.924 2.273 0.146\n- 1083SOL HW2 4822 0.884 2.116 0.166\n- 1084SOL OW 4823 1.719 2.447 1.831\n- 1084SOL HW1 4824 1.693 2.536 1.795\n- 1084SOL HW2 4825 1.717 2.379 1.758\n- 1085SOL OW 4826 1.362 3.006 0.545\n- 1085SOL HW1 4827 1.445 2.977 0.497\n- 1085SOL HW2 4828 1.313 3.073 0.489\n- 1086SOL OW 4829 0.550 2.058 0.885\n- 1086SOL HW1 4830 0.545 2.053 0.985\n- 1086SOL HW2 4831 0.552 2.154 0.856\n- 1087SOL OW 4832 1.008 3.318 0.477\n- 1087SOL HW1 4833 0.962 3.390 0.425\n- 1087SOL HW2 4834 1.004 3.338 0.575\n- 1088SOL OW 4835 0.351 3.663 0.853\n- 1088SOL HW1 4836 0.401 3.577 0.859\n- 1088SOL HW2 4837 0.416 3.740 0.850\n- 1089SOL OW 4838 1.795 2.928 0.873\n- 1089SOL HW1 4839 1.733 2.913 0.797\n- 1089SOL HW2 4840 1.743 2.939 0.958\n- 1090SOL OW 4841 1.227 3.412 1.506\n- 1090SOL HW1 4842 1.233 3.335 1.570\n- 1090SOL HW2 4843 1.175 3.386 1.426\n- 1091SOL OW 4844 0.321 2.805 0.242\n- 1091SOL HW1 4845 0.403 2.844 0.200\n- 1091SOL HW2 4846 0.294 2.723 0.193\n- 1092SOL OW 4847 1.458 2.597 0.728\n- 1092SOL HW1 4848 1.453 2.532 0.803\n- 1092SOL HW2 4849 1.538 2.656 0.741\n- 1093SOL OW 4850 0.461 3.128 1.727\n- 1093SOL HW1 4851 0.411 3.129 1.641\n- 1093SOL HW2 4852 0.398 3.110 1.803\n- 1094SOL OW 4853 1.111 3.638 0.237\n- 1094SOL HW1 4854 1.051 3.576 0.287\n- 1094SOL HW2 4855 1.142 3.594 0.152\n- 1095SOL OW 4856 0.202 2.147 1.498\n- 1095SOL HW1 4857 0.122 2.207 1.485\n- 1095SOL HW'..b'237879 5.577 5.881 6.170\n+12103SOL OW37880 6.155 6.861 6.751\n+12103SOL HW137881 6.062 6.854 6.714\n+12103SOL HW237882 6.166 6.950 6.795\n+12104SOL OW37883 7.141 7.097 6.289\n+12104SOL HW137884 7.084 7.081 6.370\n+12104SOL HW237885 7.082 7.107 6.209\n+12105SOL OW37886 6.721 6.289 6.303\n+12105SOL HW137887 6.778 6.367 6.278\n+12105SOL HW237888 6.661 6.315 6.379\n+12106SOL OW37889 7.341 6.193 5.817\n+12106SOL HW137890 7.329 6.180 5.718\n+12106SOL HW237891 7.311 6.112 5.866\n+12107SOL OW37892 6.354 6.730 6.609\n+12107SOL HW137893 6.276 6.747 6.669\n+12107SOL HW237894 6.388 6.817 6.573\n+12108SOL OW37895 6.436 6.384 7.409\n+12108SOL HW137896 6.432 6.460 7.474\n+12108SOL HW237897 6.458 6.420 7.318\n+12109SOL OW37898 6.271 6.598 6.251\n+12109SOL HW137899 6.340 6.582 6.321\n+12109SOL HW237900 6.198 6.655 6.289\n+12110SOL OW37901 5.921 7.021 6.647\n+12110SOL HW137902 5.843 6.990 6.594\n+12110SOL HW237903 5.979 7.079 6.590\n+12111SOL OW37904 7.046 7.091 6.925\n+12111SOL HW137905 7.070 7.185 6.951\n+12111SOL HW237906 7.030 7.037 7.007\n+12112SOL OW37907 6.024 5.978 7.085\n+12112SOL HW137908 6.106 5.922 7.094\n+12112SOL HW237909 5.943 5.920 7.089\n+12113SOL OW37910 5.816 7.020 6.124\n+12113SOL HW137911 5.790 7.116 6.124\n+12113SOL HW237912 5.745 6.966 6.169\n+12114SOL OW37913 5.826 6.677 6.472\n+12114SOL HW137914 5.840 6.593 6.524\n+12114SOL HW237915 5.771 6.741 6.527\n+12115SOL OW37916 6.192 6.550 5.709\n+12115SOL HW137917 6.199 6.634 5.655\n+12115SOL HW237918 6.238 6.563 5.797\n+12116SOL OW37919 7.180 5.700 7.066\n+12116SOL HW137920 7.162 5.767 6.994\n+12116SOL HW237921 7.177 5.746 7.155\n+12117SOL OW37922 5.708 6.229 6.149\n+12117SOL HW137923 5.663 6.141 6.166\n+12117SOL HW237924 5.707 6.283 6.233\n+12118SOL OW37925 5.613 7.182 5.703\n+12118SOL HW137926 5.594 7.086 5.724\n+12118SOL HW237927 5.580 7.240 5.778\n+12119SOL OW37928 7.275 6.508 6.198\n+12119SOL HW137929 7.370 6.479 6.206\n+12119SOL HW237930 7.267 6.573 6.123\n+12120SOL OW37931 5.699 6.323 7.183\n+12120SOL HW137932 5.787 6.310 7.228\n+12120SOL HW237933 5.686 6.420 7.161\n+12121SOL OW37934 6.199 6.951 6.312\n+12121SOL HW137935 6.150 6.864 6.321\n+12121SOL HW237936 6.176 6.994 6.225\n+12122SOL OW37937 6.879 6.814 7.009\n+12122SOL HW137938 6.916 6.741 6.951\n+12122SOL HW237939 6.931 6.819 7.094\n+12123SOL OW37940 6.395 5.590 6.088\n+12123SOL HW137941 6.435 5.681 6.079\n+12123SOL HW237942 6.295 5.598 6.094\n 12124SOL OW37943 5.783 6.562 6.850\n 12124SOL HW137944 5.872 6.517 6.836\n 12124SOL HW237945 5.710 6.497 6.831\n@@ -38368,12 +38368,12 @@\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 0.197 2.838 1.264\n-12267CL CL38370 1.709 2.247 3.243\n-12268CL CL38371 1.576 7.248 4.031\n-12269CL CL38372 1.302 6.441 5.895\n-12270CL CL38373 3.133 3.659 6.177\n-12271CL CL38374 2.875 3.829 1.770\n-12272CL CL38375 7.275 0.922 0.612\n-12273CL CL38376 6.395 5.590 6.088\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' |
| b |
| diff -r 5b01e6df25a0 -r 511b084adf53 test-data/top_output.top --- a/test-data/top_output.top Thu Mar 28 10:13:01 2019 -0400 +++ b/test-data/top_output.top Fri Aug 30 15:04:51 2019 -0400 |
| [ |
| b"@@ -1,19 +1,19 @@\n ;\n ;\tFile 'topol.top' was generated\n ;\tBy user: unknown (1000)\n-;\tOn host: simon-laptop\n-;\tAt date: Thu Aug 16 20:54:28 2018\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, 2018.2 (-:\n+;\t :-) GROMACS - gmx pdb2gmx, 2019.1 (-:\n ;\t\n-;\tExecutable: /home/simon/miniconda3/envs/gromacs2/bin/gmx\n-;\tData prefix: /home/simon/miniconda3/envs/gromacs2\n-;\tWorking dir: /home/simon/moldyn-galaxy/protein/test-data\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 1AKI.pdb -o processed.gro -p topol.top -i posres.itp -water spce -ff oplsaa -noignh\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@@ -27,2093 +27,2093 @@\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 ; qtot -0.3\n- 2 opls_290 1 LYS H1 1 0.33 1.008 ; qtot 0.03\n- 3 opls_290 1 LYS H2 1 0.33 1.008 ; qtot 0.36\n- 4 opls_290 1 LYS H3 1 0.33 1.008 ; qtot 0.69\n- 5 opls_293B 1 LYS CA 1 0.25 12.011 ; qtot 0.94\n- 6 opls_140 1 LYS HA 1 0.06 1.008 ; qtot 1\n- 7 opls_136 1 LYS CB 2 -0.12 12.011 ; qtot 0.88\n- 8 opls_140 1 LYS HB1 2 0.06 1.008 ; qtot 0.94\n- 9 opls_140 1 LYS HB2 2 0.06 1.008 ; qtot 1\n- 10 opls_136 1 LYS CG 3 -0.12 12.011 ; qtot 0.88\n- 11 opls_140 1 LYS HG1 3 0.06 1.008 ; qtot 0.94\n- 12 opls_140 1 LYS HG2 3 0.06 1.008 ; qtot 1\n- 13 opls_136 1 LYS CD 4 -0.12 12.011 ; qtot 0.88\n- 14 opls_140 1 LYS HD1 4 0.06 1.008 ; qtot 0.94\n- 15 opls_140 1 LYS HD2 4 0.06 1.008 ; qtot 1\n- 16 opls_292 1 LYS CE 5 0.19 12.011 ; qtot 1.19\n- 17 opls_140 1 LYS HE1 5 0.06 1.008 ; qtot 1.25\n- 18 opls_140 1 LYS HE2 5 0.06 1.008 ; qtot 1.31\n- 19 opls_287 1 LYS NZ 6 -0.3 14.0067 ; qtot 1.01\n- 20 opls_290 1 LYS HZ1 6 0.33 1.008 ; qtot 1.34\n- 21 opls_290 1 LYS HZ2 6 0.33 1.008 ; qtot 1.67\n- 22 opls_290 1 LYS HZ3 6 0.33 1.008 ; qtot 2\n- 23 opls_235 1 LYS C 7 0.5 12.011 ; qtot 2.5\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 -0.1"..b'.06 1.008\n+ 1927 opls_307 128 ARG CD 672 0.19 12.011\n+ 1928 opls_140 128 ARG HD1 672 0.06 1.008\n+ 1929 opls_140 128 ARG HD2 672 0.06 1.008\n+ 1930 opls_303 128 ARG NE 673 -0.7 14.0067\n+ 1931 opls_304 128 ARG HE 673 0.44 1.008\n+ 1932 opls_302 128 ARG CZ 673 0.64 12.011\n+ 1933 opls_300 128 ARG NH1 674 -0.8 14.0067\n+ 1934 opls_301 128 ARG HH11 674 0.46 1.008\n+ 1935 opls_301 128 ARG HH12 674 0.46 1.008\n+ 1936 opls_300 128 ARG NH2 675 -0.8 14.0067\n+ 1937 opls_301 128 ARG HH21 675 0.46 1.008\n+ 1938 opls_301 128 ARG HH22 675 0.46 1.008\n+ 1939 opls_235 128 ARG C 676 0.5 12.011\n 1940 opls_236 128 ARG O 676 -0.5 15.9994 ; qtot 9\n ; residue 129 LEU rtp LEU q -1.0\n- 1941 opls_238 129 LEU N 677 -0.5 14.0067 ; qtot 8.5\n- 1942 opls_241 129 LEU H 677 0.3 1.008 ; qtot 8.8\n- 1943 opls_283 129 LEU CA 677 0.04 12.011 ; qtot 8.84\n- 1944 opls_140 129 LEU HA 677 0.06 1.008 ; qtot 8.9\n- 1945 opls_136 129 LEU CB 678 -0.12 12.011 ; qtot 8.78\n- 1946 opls_140 129 LEU HB1 678 0.06 1.008 ; qtot 8.84\n- 1947 opls_140 129 LEU HB2 678 0.06 1.008 ; qtot 8.9\n- 1948 opls_137 129 LEU CG 679 -0.06 12.011 ; qtot 8.84\n- 1949 opls_140 129 LEU HG 679 0.06 1.008 ; qtot 8.9\n- 1950 opls_135 129 LEU CD1 680 -0.18 12.011 ; qtot 8.72\n- 1951 opls_140 129 LEU HD11 680 0.06 1.008 ; qtot 8.78\n- 1952 opls_140 129 LEU HD12 680 0.06 1.008 ; qtot 8.84\n- 1953 opls_140 129 LEU HD13 680 0.06 1.008 ; qtot 8.9\n- 1954 opls_135 129 LEU CD2 681 -0.18 12.011 ; qtot 8.72\n- 1955 opls_140 129 LEU HD21 681 0.06 1.008 ; qtot 8.78\n- 1956 opls_140 129 LEU HD22 681 0.06 1.008 ; qtot 8.84\n- 1957 opls_140 129 LEU HD23 681 0.06 1.008 ; qtot 8.9\n- 1958 opls_271 129 LEU C 682 0.7 12.011 ; qtot 9.6\n- 1959 opls_272 129 LEU O1 682 -0.8 15.9994 ; qtot 8.8\n+ 1941 opls_238 129 LEU N 677 -0.5 14.0067\n+ 1942 opls_241 129 LEU H 677 0.3 1.008\n+ 1943 opls_283 129 LEU CA 677 0.04 12.011\n+ 1944 opls_140 129 LEU HA 677 0.06 1.008\n+ 1945 opls_136 129 LEU CB 678 -0.12 12.011\n+ 1946 opls_140 129 LEU HB1 678 0.06 1.008\n+ 1947 opls_140 129 LEU HB2 678 0.06 1.008\n+ 1948 opls_137 129 LEU CG 679 -0.06 12.011\n+ 1949 opls_140 129 LEU HG 679 0.06 1.008\n+ 1950 opls_135 129 LEU CD1 680 -0.18 12.011\n+ 1951 opls_140 129 LEU HD11 680 0.06 1.008\n+ 1952 opls_140 129 LEU HD12 680 0.06 1.008\n+ 1953 opls_140 129 LEU HD13 680 0.06 1.008\n+ 1954 opls_135 129 LEU CD2 681 -0.18 12.011\n+ 1955 opls_140 129 LEU HD21 681 0.06 1.008\n+ 1956 opls_140 129 LEU HD22 681 0.06 1.008\n+ 1957 opls_140 129 LEU HD23 681 0.06 1.008\n+ 1958 opls_271 129 LEU C 682 0.7 12.011\n+ 1959 opls_272 129 LEU O1 682 -0.8 15.9994\n 1960 opls_272 129 LEU O2 682 -0.8 15.9994 ; qtot 8\n \n [ bonds ]\n' |
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| diff -r 5b01e6df25a0 -r 511b084adf53 test-data/topol.top --- a/test-data/topol.top Thu Mar 28 10:13:01 2019 -0400 +++ b/test-data/topol.top Fri Aug 30 15:04:51 2019 -0400 |
| [ |
| b"@@ -1,19 +1,19 @@\n ;\n ;\tFile 'topol.top' was generated\n ;\tBy user: unknown (1000)\n-;\tOn host: simon-laptop\n-;\tAt date: Thu Aug 16 20:54:28 2018\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, 2018.2 (-:\n+;\t :-) GROMACS - gmx pdb2gmx, 2019.1 (-:\n ;\t\n-;\tExecutable: /home/simon/miniconda3/envs/gromacs2/bin/gmx\n-;\tData prefix: /home/simon/miniconda3/envs/gromacs2\n-;\tWorking dir: /home/simon/moldyn-galaxy/protein/test-data\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 1AKI.pdb -o processed.gro -p topol.top -i posres.itp -water spce -ff oplsaa -noignh\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@@ -27,2093 +27,2093 @@\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 ; qtot -0.3\n- 2 opls_290 1 LYS H1 1 0.33 1.008 ; qtot 0.03\n- 3 opls_290 1 LYS H2 1 0.33 1.008 ; qtot 0.36\n- 4 opls_290 1 LYS H3 1 0.33 1.008 ; qtot 0.69\n- 5 opls_293B 1 LYS CA 1 0.25 12.011 ; qtot 0.94\n- 6 opls_140 1 LYS HA 1 0.06 1.008 ; qtot 1\n- 7 opls_136 1 LYS CB 2 -0.12 12.011 ; qtot 0.88\n- 8 opls_140 1 LYS HB1 2 0.06 1.008 ; qtot 0.94\n- 9 opls_140 1 LYS HB2 2 0.06 1.008 ; qtot 1\n- 10 opls_136 1 LYS CG 3 -0.12 12.011 ; qtot 0.88\n- 11 opls_140 1 LYS HG1 3 0.06 1.008 ; qtot 0.94\n- 12 opls_140 1 LYS HG2 3 0.06 1.008 ; qtot 1\n- 13 opls_136 1 LYS CD 4 -0.12 12.011 ; qtot 0.88\n- 14 opls_140 1 LYS HD1 4 0.06 1.008 ; qtot 0.94\n- 15 opls_140 1 LYS HD2 4 0.06 1.008 ; qtot 1\n- 16 opls_292 1 LYS CE 5 0.19 12.011 ; qtot 1.19\n- 17 opls_140 1 LYS HE1 5 0.06 1.008 ; qtot 1.25\n- 18 opls_140 1 LYS HE2 5 0.06 1.008 ; qtot 1.31\n- 19 opls_287 1 LYS NZ 6 -0.3 14.0067 ; qtot 1.01\n- 20 opls_290 1 LYS HZ1 6 0.33 1.008 ; qtot 1.34\n- 21 opls_290 1 LYS HZ2 6 0.33 1.008 ; qtot 1.67\n- 22 opls_290 1 LYS HZ3 6 0.33 1.008 ; qtot 2\n- 23 opls_235 1 LYS C 7 0.5 12.011 ; qtot 2.5\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 -0.1"..b'.06 1.008\n+ 1927 opls_307 128 ARG CD 672 0.19 12.011\n+ 1928 opls_140 128 ARG HD1 672 0.06 1.008\n+ 1929 opls_140 128 ARG HD2 672 0.06 1.008\n+ 1930 opls_303 128 ARG NE 673 -0.7 14.0067\n+ 1931 opls_304 128 ARG HE 673 0.44 1.008\n+ 1932 opls_302 128 ARG CZ 673 0.64 12.011\n+ 1933 opls_300 128 ARG NH1 674 -0.8 14.0067\n+ 1934 opls_301 128 ARG HH11 674 0.46 1.008\n+ 1935 opls_301 128 ARG HH12 674 0.46 1.008\n+ 1936 opls_300 128 ARG NH2 675 -0.8 14.0067\n+ 1937 opls_301 128 ARG HH21 675 0.46 1.008\n+ 1938 opls_301 128 ARG HH22 675 0.46 1.008\n+ 1939 opls_235 128 ARG C 676 0.5 12.011\n 1940 opls_236 128 ARG O 676 -0.5 15.9994 ; qtot 9\n ; residue 129 LEU rtp LEU q -1.0\n- 1941 opls_238 129 LEU N 677 -0.5 14.0067 ; qtot 8.5\n- 1942 opls_241 129 LEU H 677 0.3 1.008 ; qtot 8.8\n- 1943 opls_283 129 LEU CA 677 0.04 12.011 ; qtot 8.84\n- 1944 opls_140 129 LEU HA 677 0.06 1.008 ; qtot 8.9\n- 1945 opls_136 129 LEU CB 678 -0.12 12.011 ; qtot 8.78\n- 1946 opls_140 129 LEU HB1 678 0.06 1.008 ; qtot 8.84\n- 1947 opls_140 129 LEU HB2 678 0.06 1.008 ; qtot 8.9\n- 1948 opls_137 129 LEU CG 679 -0.06 12.011 ; qtot 8.84\n- 1949 opls_140 129 LEU HG 679 0.06 1.008 ; qtot 8.9\n- 1950 opls_135 129 LEU CD1 680 -0.18 12.011 ; qtot 8.72\n- 1951 opls_140 129 LEU HD11 680 0.06 1.008 ; qtot 8.78\n- 1952 opls_140 129 LEU HD12 680 0.06 1.008 ; qtot 8.84\n- 1953 opls_140 129 LEU HD13 680 0.06 1.008 ; qtot 8.9\n- 1954 opls_135 129 LEU CD2 681 -0.18 12.011 ; qtot 8.72\n- 1955 opls_140 129 LEU HD21 681 0.06 1.008 ; qtot 8.78\n- 1956 opls_140 129 LEU HD22 681 0.06 1.008 ; qtot 8.84\n- 1957 opls_140 129 LEU HD23 681 0.06 1.008 ; qtot 8.9\n- 1958 opls_271 129 LEU C 682 0.7 12.011 ; qtot 9.6\n- 1959 opls_272 129 LEU O1 682 -0.8 15.9994 ; qtot 8.8\n+ 1941 opls_238 129 LEU N 677 -0.5 14.0067\n+ 1942 opls_241 129 LEU H 677 0.3 1.008\n+ 1943 opls_283 129 LEU CA 677 0.04 12.011\n+ 1944 opls_140 129 LEU HA 677 0.06 1.008\n+ 1945 opls_136 129 LEU CB 678 -0.12 12.011\n+ 1946 opls_140 129 LEU HB1 678 0.06 1.008\n+ 1947 opls_140 129 LEU HB2 678 0.06 1.008\n+ 1948 opls_137 129 LEU CG 679 -0.06 12.011\n+ 1949 opls_140 129 LEU HG 679 0.06 1.008\n+ 1950 opls_135 129 LEU CD1 680 -0.18 12.011\n+ 1951 opls_140 129 LEU HD11 680 0.06 1.008\n+ 1952 opls_140 129 LEU HD12 680 0.06 1.008\n+ 1953 opls_140 129 LEU HD13 680 0.06 1.008\n+ 1954 opls_135 129 LEU CD2 681 -0.18 12.011\n+ 1955 opls_140 129 LEU HD21 681 0.06 1.008\n+ 1956 opls_140 129 LEU HD22 681 0.06 1.008\n+ 1957 opls_140 129 LEU HD23 681 0.06 1.008\n+ 1958 opls_271 129 LEU C 682 0.7 12.011\n+ 1959 opls_272 129 LEU O1 682 -0.8 15.9994\n 1960 opls_272 129 LEU O2 682 -0.8 15.9994 ; qtot 8\n \n [ bonds ]\n' |
| b |
| diff -r 5b01e6df25a0 -r 511b084adf53 test-data/topol_solv.top --- a/test-data/topol_solv.top Thu Mar 28 10:13:01 2019 -0400 +++ b/test-data/topol_solv.top Fri Aug 30 15:04:51 2019 -0400 |
| [ |
| b"@@ -1,19 +1,19 @@\n ;\n ;\tFile 'topol.top' was generated\n ;\tBy user: unknown (1000)\n-;\tOn host: simon-laptop\n-;\tAt date: Thu Aug 16 20:54:28 2018\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, 2018.2 (-:\n+;\t :-) GROMACS - gmx pdb2gmx, 2019.1 (-:\n ;\t\n-;\tExecutable: /home/simon/miniconda3/envs/gromacs2/bin/gmx\n-;\tData prefix: /home/simon/miniconda3/envs/gromacs2\n-;\tWorking dir: /home/simon/moldyn-galaxy/protein/test-data\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 1AKI.pdb -o processed.gro -p topol.top -i posres.itp -water spce -ff oplsaa -noignh\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@@ -27,2093 +27,2093 @@\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 ; qtot -0.3\n- 2 opls_290 1 LYS H1 1 0.33 1.008 ; qtot 0.03\n- 3 opls_290 1 LYS H2 1 0.33 1.008 ; qtot 0.36\n- 4 opls_290 1 LYS H3 1 0.33 1.008 ; qtot 0.69\n- 5 opls_293B 1 LYS CA 1 0.25 12.011 ; qtot 0.94\n- 6 opls_140 1 LYS HA 1 0.06 1.008 ; qtot 1\n- 7 opls_136 1 LYS CB 2 -0.12 12.011 ; qtot 0.88\n- 8 opls_140 1 LYS HB1 2 0.06 1.008 ; qtot 0.94\n- 9 opls_140 1 LYS HB2 2 0.06 1.008 ; qtot 1\n- 10 opls_136 1 LYS CG 3 -0.12 12.011 ; qtot 0.88\n- 11 opls_140 1 LYS HG1 3 0.06 1.008 ; qtot 0.94\n- 12 opls_140 1 LYS HG2 3 0.06 1.008 ; qtot 1\n- 13 opls_136 1 LYS CD 4 -0.12 12.011 ; qtot 0.88\n- 14 opls_140 1 LYS HD1 4 0.06 1.008 ; qtot 0.94\n- 15 opls_140 1 LYS HD2 4 0.06 1.008 ; qtot 1\n- 16 opls_292 1 LYS CE 5 0.19 12.011 ; qtot 1.19\n- 17 opls_140 1 LYS HE1 5 0.06 1.008 ; qtot 1.25\n- 18 opls_140 1 LYS HE2 5 0.06 1.008 ; qtot 1.31\n- 19 opls_287 1 LYS NZ 6 -0.3 14.0067 ; qtot 1.01\n- 20 opls_290 1 LYS HZ1 6 0.33 1.008 ; qtot 1.34\n- 21 opls_290 1 LYS HZ2 6 0.33 1.008 ; qtot 1.67\n- 22 opls_290 1 LYS HZ3 6 0.33 1.008 ; qtot 2\n- 23 opls_235 1 LYS C 7 0.5 12.011 ; qtot 2.5\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 -0.1"..b'.06 1.008\n+ 1927 opls_307 128 ARG CD 672 0.19 12.011\n+ 1928 opls_140 128 ARG HD1 672 0.06 1.008\n+ 1929 opls_140 128 ARG HD2 672 0.06 1.008\n+ 1930 opls_303 128 ARG NE 673 -0.7 14.0067\n+ 1931 opls_304 128 ARG HE 673 0.44 1.008\n+ 1932 opls_302 128 ARG CZ 673 0.64 12.011\n+ 1933 opls_300 128 ARG NH1 674 -0.8 14.0067\n+ 1934 opls_301 128 ARG HH11 674 0.46 1.008\n+ 1935 opls_301 128 ARG HH12 674 0.46 1.008\n+ 1936 opls_300 128 ARG NH2 675 -0.8 14.0067\n+ 1937 opls_301 128 ARG HH21 675 0.46 1.008\n+ 1938 opls_301 128 ARG HH22 675 0.46 1.008\n+ 1939 opls_235 128 ARG C 676 0.5 12.011\n 1940 opls_236 128 ARG O 676 -0.5 15.9994 ; qtot 9\n ; residue 129 LEU rtp LEU q -1.0\n- 1941 opls_238 129 LEU N 677 -0.5 14.0067 ; qtot 8.5\n- 1942 opls_241 129 LEU H 677 0.3 1.008 ; qtot 8.8\n- 1943 opls_283 129 LEU CA 677 0.04 12.011 ; qtot 8.84\n- 1944 opls_140 129 LEU HA 677 0.06 1.008 ; qtot 8.9\n- 1945 opls_136 129 LEU CB 678 -0.12 12.011 ; qtot 8.78\n- 1946 opls_140 129 LEU HB1 678 0.06 1.008 ; qtot 8.84\n- 1947 opls_140 129 LEU HB2 678 0.06 1.008 ; qtot 8.9\n- 1948 opls_137 129 LEU CG 679 -0.06 12.011 ; qtot 8.84\n- 1949 opls_140 129 LEU HG 679 0.06 1.008 ; qtot 8.9\n- 1950 opls_135 129 LEU CD1 680 -0.18 12.011 ; qtot 8.72\n- 1951 opls_140 129 LEU HD11 680 0.06 1.008 ; qtot 8.78\n- 1952 opls_140 129 LEU HD12 680 0.06 1.008 ; qtot 8.84\n- 1953 opls_140 129 LEU HD13 680 0.06 1.008 ; qtot 8.9\n- 1954 opls_135 129 LEU CD2 681 -0.18 12.011 ; qtot 8.72\n- 1955 opls_140 129 LEU HD21 681 0.06 1.008 ; qtot 8.78\n- 1956 opls_140 129 LEU HD22 681 0.06 1.008 ; qtot 8.84\n- 1957 opls_140 129 LEU HD23 681 0.06 1.008 ; qtot 8.9\n- 1958 opls_271 129 LEU C 682 0.7 12.011 ; qtot 9.6\n- 1959 opls_272 129 LEU O1 682 -0.8 15.9994 ; qtot 8.8\n+ 1941 opls_238 129 LEU N 677 -0.5 14.0067\n+ 1942 opls_241 129 LEU H 677 0.3 1.008\n+ 1943 opls_283 129 LEU CA 677 0.04 12.011\n+ 1944 opls_140 129 LEU HA 677 0.06 1.008\n+ 1945 opls_136 129 LEU CB 678 -0.12 12.011\n+ 1946 opls_140 129 LEU HB1 678 0.06 1.008\n+ 1947 opls_140 129 LEU HB2 678 0.06 1.008\n+ 1948 opls_137 129 LEU CG 679 -0.06 12.011\n+ 1949 opls_140 129 LEU HG 679 0.06 1.008\n+ 1950 opls_135 129 LEU CD1 680 -0.18 12.011\n+ 1951 opls_140 129 LEU HD11 680 0.06 1.008\n+ 1952 opls_140 129 LEU HD12 680 0.06 1.008\n+ 1953 opls_140 129 LEU HD13 680 0.06 1.008\n+ 1954 opls_135 129 LEU CD2 681 -0.18 12.011\n+ 1955 opls_140 129 LEU HD21 681 0.06 1.008\n+ 1956 opls_140 129 LEU HD22 681 0.06 1.008\n+ 1957 opls_140 129 LEU HD23 681 0.06 1.008\n+ 1958 opls_271 129 LEU C 682 0.7 12.011\n+ 1959 opls_272 129 LEU O1 682 -0.8 15.9994\n 1960 opls_272 129 LEU O2 682 -0.8 15.9994 ; qtot 8\n \n [ bonds ]\n' |