| Previous changeset 13:2c349b027a01 (2020-11-23) Next changeset 15:8ad46f918541 (2021-10-27) |
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Commit message:
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 2f3d14b4f200100881e362b0f3b97f0e8a36d1f3" |
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modified:
macros.xml setup.xml test-data/minim.mdp test-data/newbox.pdb test-data/outp.xvg test-data/topol.top test-data/topol_solv.top |
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added:
test-data/frame7.pdb test-data/minim.edr test-data/minim.gro test-data/topol_md.top |
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removed:
test-data/solv.gro |
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| diff -r 2c349b027a01 -r 1d4dd4f908d4 macros.xml --- a/macros.xml Mon Nov 23 10:46:34 2020 +0000 +++ b/macros.xml Wed Sep 29 07:42:14 2021 +0000 |
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| @@ -1,5 +1,5 @@ <macros> - <token name="@TOOL_VERSION@">2020.4</token> + <token name="@TOOL_VERSION@">2021.3</token> <xml name="requirements"> <requirements> <requirement type="package" version="@TOOL_VERSION@">gromacs</requirement> @@ -62,7 +62,7 @@ </xml> <xml name="log_outputs"> - <data name="report" format="txt" from_work_dir="verbose.txt"> + <data name="report" format="txt" from_work_dir="verbose.txt" label="GROMACS log file on ${on_string}"> <filter>capture_log</filter> </data> </xml> |
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| diff -r 2c349b027a01 -r 1d4dd4f908d4 setup.xml --- a/setup.xml Mon Nov 23 10:46:34 2020 +0000 +++ b/setup.xml Wed Sep 29 07:42:14 2021 +0000 |
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| @@ -50,9 +50,9 @@ </inputs> <outputs> - <data name="output1" format="top" from_work_dir="topol.top"/> - <data name="output2" format="gro" from_work_dir="processed.gro"/> - <data name="output3" format="itp" from_work_dir="posres.itp"/> + <data name="output1" format="top" from_work_dir="topol.top" label="GROMACS setup (TOP) on ${on_string}"/> + <data name="output2" format="gro" from_work_dir="processed.gro" label="GROMACS setup (GRO) on ${on_string}"/> + <data name="output3" format="itp" from_work_dir="posres.itp" label="GROMACS setup (ITP) on ${on_string}"/> <expand macro="log_outputs" /> </outputs> <tests> |
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| diff -r 2c349b027a01 -r 1d4dd4f908d4 test-data/frame7.pdb --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/frame7.pdb Wed Sep 29 07:42:14 2021 +0000 |
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| @@ -0,0 +1,101 @@ +REMARK GENERATED BY TRJCONV +TITLE TEST in water t= 0.70000 step= 350 +REMARK THIS IS A SIMULATION BOX +CRYST1 40.912 40.912 40.912 90.00 90.00 90.00 P 1 1 +MODEL 8 +ATOM 1 N LYS 1 20.430 26.480 14.890 1.00 0.00 N +ATOM 2 H1 LYS 1 21.000 27.280 14.660 1.00 0.00 H +ATOM 3 H2 LYS 1 19.800 26.230 14.130 1.00 0.00 H +ATOM 4 H3 LYS 1 19.780 26.690 15.640 1.00 0.00 H +ATOM 5 CA LYS 1 21.140 25.300 15.400 1.00 0.00 C +ATOM 6 HA LYS 1 21.560 24.750 14.560 1.00 0.00 H +ATOM 7 CB LYS 1 22.170 25.650 16.480 1.00 0.00 C +ATOM 8 HB1 LYS 1 22.790 26.470 16.110 1.00 0.00 H +ATOM 9 HB2 LYS 1 21.660 26.080 17.340 1.00 0.00 H +ATOM 10 CG LYS 1 23.090 24.530 16.960 1.00 0.00 C +ATOM 11 HG1 LYS 1 22.450 23.800 17.450 1.00 0.00 H +ATOM 12 HG2 LYS 1 23.530 24.000 16.110 1.00 0.00 H +ATOM 13 CD LYS 1 24.170 24.930 17.970 1.00 0.00 C +ATOM 14 HD1 LYS 1 24.950 25.550 17.520 1.00 0.00 H +ATOM 15 HD2 LYS 1 23.650 25.500 18.730 1.00 0.00 H +ATOM 16 CE LYS 1 24.790 23.700 18.630 1.00 0.00 C +ATOM 17 HE1 LYS 1 24.010 22.970 18.830 1.00 0.00 H +ATOM 18 HE2 LYS 1 25.560 23.240 18.000 1.00 0.00 H +ATOM 19 NZ LYS 1 25.370 24.050 19.940 1.00 0.00 N +ATOM 20 HZ1 LYS 1 25.980 23.300 20.230 1.00 0.00 H +ATOM 21 HZ2 LYS 1 25.880 24.910 19.870 1.00 0.00 H +ATOM 22 HZ3 LYS 1 24.620 24.150 20.600 1.00 0.00 H +ATOM 23 C LYS 1 20.020 24.530 16.080 1.00 0.00 C +ATOM 24 O LYS 1 19.190 25.210 16.670 1.00 0.00 O +ATOM 25 N VAL 2 20.070 23.200 16.050 1.00 0.00 N +ATOM 26 H VAL 2 20.860 22.710 15.640 1.00 0.00 H +ATOM 27 CA VAL 2 19.250 22.280 16.810 1.00 0.00 C +ATOM 28 HA VAL 2 18.490 22.810 17.380 1.00 0.00 H +ATOM 29 CB VAL 2 18.670 21.290 15.800 1.00 0.00 C +ATOM 30 HB VAL 2 19.470 20.890 15.170 1.00 0.00 H +ATOM 31 CG1 VAL 2 17.930 20.120 16.440 1.00 0.00 C +ATOM 32 HG11 VAL 2 17.880 19.250 15.790 1.00 0.00 H +ATOM 33 HG12 VAL 2 18.450 19.770 17.330 1.00 0.00 H +ATOM 34 HG13 VAL 2 16.900 20.300 16.750 1.00 0.00 H +ATOM 35 CG2 VAL 2 17.620 21.940 14.900 1.00 0.00 C +ATOM 36 HG21 VAL 2 17.150 21.180 14.270 1.00 0.00 H +ATOM 37 HG22 VAL 2 16.820 22.410 15.460 1.00 0.00 H +ATOM 38 HG23 VAL 2 18.070 22.690 14.240 1.00 0.00 H +ATOM 39 C VAL 2 20.210 21.630 17.800 1.00 0.00 C +ATOM 40 O VAL 2 21.370 21.400 17.460 1.00 0.00 O +ATOM 41 N PHE 3 19.760 21.420 19.030 1.00 0.00 N +ATOM 42 H PHE 3 18.750 21.300 19.050 1.00 0.00 H +ATOM 43 CA PHE 3 20.500 20.910 20.170 1.00 0.00 C +ATOM 44 HA PHE 3 21.560 20.880 19.900 1.00 0.00 H +ATOM 45 CB PHE 3 20.300 21.680 21.470 1.00 0.00 C +ATOM 46 HB1 PHE 3 19.330 22.160 21.560 1.00 0.00 H +ATOM 47 HB2 PHE 3 20.410 20.990 22.320 1.00 0.00 H +ATOM 48 CG PHE 3 21.310 22.780 21.700 1.00 0.00 C +ATOM 49 CD1 PHE 3 21.120 23.940 20.940 1.00 0.00 C +ATOM 50 HD1 PHE 3 20.240 24.000 20.310 1.00 0.00 H +ATOM 51 CD2 PHE 3 22.380 22.720 22.600 1.00 0.00 C +ATOM 52 HD2 PHE 3 22.550 21.860 23.230 1.00 0.00 H +ATOM 53 CE1 PHE 3 21.890 25.090 21.170 1.00 0.00 C +ATOM 54 HE1 PHE 3 21.670 26.000 20.640 1.00 0.00 H +ATOM 55 CE2 PHE 3 23.210 23.830 22.790 1.00 0.00 C +ATOM 56 HE2 PHE 3 23.990 23.790 23.530 1.00 0.00 H +ATOM 57 CZ PHE 3 22.950 25.010 22.090 1.00 0.00 C +ATOM 58 HZ PHE 3 23.450 25.920 22.360 1.00 0.00 H +ATOM 59 C PHE 3 20.120 19.440 20.290 1.00 0.00 C +ATOM 60 O PHE 3 19.090 18.930 19.840 1.00 0.00 O +ATOM 61 N GLY 4 20.900 18.680 21.060 1.00 0.00 N +ATOM 62 H GLY 4 21.560 19.090 21.710 1.00 0.00 H +ATOM 63 CA GLY 4 20.680 17.300 21.460 1.00 0.00 C +ATOM 64 HA1 GLY 4 19.840 16.840 20.940 1.00 0.00 H +ATOM 65 HA2 GLY 4 21.560 16.710 21.210 1.00 0.00 H +ATOM 66 C GLY 4 20.450 17.340 22.960 1.00 0.00 C +ATOM 67 O GLY 4 21.000 18.090 23.760 1.00 0.00 O +ATOM 68 N ARG 5 19.240 16.900 23.300 1.00 0.00 N +ATOM 69 H ARG 5 18.980 16.100 22.740 1.00 0.00 H +ATOM 70 CA ARG 5 18.620 16.900 24.610 1.00 0.00 C +ATOM 71 HA ARG 5 18.270 17.920 24.790 1.00 0.00 H +ATOM 72 CB ARG 5 17.400 16.040 24.290 1.00 0.00 C +ATOM 73 HB1 ARG 5 16.840 16.530 23.490 1.00 0.00 H +ATOM 74 HB2 ARG 5 17.690 15.100 23.810 1.00 0.00 H +ATOM 75 CG ARG 5 16.410 15.710 25.410 1.00 0.00 C +ATOM 76 HG1 ARG 5 16.240 16.690 25.850 1.00 0.00 H +ATOM 77 HG2 ARG 5 15.560 15.120 25.040 1.00 0.00 H +ATOM 78 CD ARG 5 16.930 14.710 26.430 1.00 0.00 C +ATOM 79 HD1 ARG 5 17.590 15.260 27.110 1.00 0.00 H +ATOM 80 HD2 ARG 5 15.990 14.290 26.780 1.00 0.00 H +ATOM 81 NE ARG 5 17.690 13.540 25.980 1.00 0.00 N +ATOM 82 HE ARG 5 17.230 13.190 25.150 1.00 0.00 H +ATOM 83 CZ ARG 5 18.860 13.110 26.480 1.00 0.00 C +ATOM 84 NH1 ARG 5 19.290 13.590 27.650 1.00 0.00 N +ATOM 85 HH11 ARG 5 18.960 14.520 27.870 1.00 0.00 H +ATOM 86 HH12 ARG 5 20.280 13.620 27.810 1.00 0.00 H +ATOM 87 NH2 ARG 5 19.550 12.120 25.890 1.00 0.00 N +ATOM 88 HH21 ARG 5 19.090 11.700 25.090 1.00 0.00 H +ATOM 89 HH22 ARG 5 20.490 11.840 26.130 1.00 0.00 H +ATOM 90 C ARG 5 19.520 16.150 25.580 1.00 0.00 C +ATOM 91 O1 ARG 5 19.500 16.540 26.770 1.00 0.00 O +ATOM 92 O2 ARG 5 20.150 15.090 25.350 1.00 0.00 O +ATOM 93 CL CL 6 12.830 22.520 18.690 1.00 0.00 Cl +ATOM 94 CL CL 7 26.880 35.300 23.940 1.00 0.00 Cl +TER +ENDMDL |
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| diff -r 2c349b027a01 -r 1d4dd4f908d4 test-data/minim.edr |
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| Binary file test-data/minim.edr has changed |
| b |
| diff -r 2c349b027a01 -r 1d4dd4f908d4 test-data/minim.gro --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/minim.gro Wed Sep 29 07:42:14 2021 +0000 |
| b |
| @@ -0,0 +1,97 @@ +TEST in water + 94 + 1LYS N 1 2.079 2.649 1.485 + 1LYS H1 2 2.153 2.706 1.447 + 1LYS H2 3 2.010 2.628 1.414 + 1LYS H3 4 2.032 2.698 1.561 + 1LYS CA 5 2.132 2.525 1.541 + 1LYS HA 6 2.182 2.467 1.463 + 1LYS CB 7 2.233 2.560 1.653 + 1LYS HB1 8 2.315 2.618 1.610 + 1LYS HB2 9 2.185 2.625 1.726 + 1LYS CG 10 2.291 2.440 1.728 + 1LYS HG1 11 2.215 2.399 1.795 + 1LYS HG2 12 2.317 2.360 1.658 + 1LYS CD 13 2.414 2.478 1.808 + 1LYS HD1 14 2.495 2.502 1.739 + 1LYS HD2 15 2.394 2.569 1.866 + 1LYS CE 16 2.455 2.366 1.903 + 1LYS HE1 17 2.383 2.357 1.984 + 1LYS HE2 18 2.455 2.270 1.850 + 1LYS NZ 19 2.589 2.391 1.958 + 1LYS HZ1 20 2.615 2.316 2.021 + 1LYS HZ2 21 2.656 2.396 1.883 + 1LYS HZ3 22 2.589 2.478 2.009 + 1LYS C 23 2.018 2.443 1.600 + 1LYS O 24 1.939 2.502 1.673 + 2VAL N 25 2.015 2.312 1.576 + 2VAL H 26 2.082 2.267 1.515 + 2VAL CA 27 1.931 2.220 1.653 + 2VAL HA 28 1.853 2.273 1.707 + 2VAL CB 29 1.862 2.117 1.561 + 2VAL HB 30 1.938 2.057 1.509 + 2VAL CG1 31 1.772 2.022 1.641 + 2VAL HG11 32 1.718 1.954 1.575 + 2VAL HG12 33 1.829 1.961 1.711 + 2VAL HG13 34 1.698 2.078 1.699 + 2VAL CG2 35 1.776 2.187 1.455 + 2VAL HG21 36 1.724 2.114 1.394 + 2VAL HG22 37 1.701 2.251 1.502 + 2VAL HG23 38 1.836 2.249 1.388 + 2VAL C 39 2.024 2.151 1.754 + 2VAL O 40 2.122 2.086 1.715 + 3PHE N 41 1.997 2.173 1.882 + 3PHE H 42 1.916 2.228 1.905 + 3PHE CA 43 2.067 2.107 1.991 + 3PHE HA 44 2.174 2.107 1.970 + 3PHE CB 45 2.039 2.179 2.125 + 3PHE HB1 46 1.937 2.217 2.130 + 3PHE HB2 47 2.048 2.109 2.208 + 3PHE CG 48 2.136 2.292 2.153 + 3PHE CD1 49 2.113 2.421 2.101 + 3PHE HD1 50 2.023 2.440 2.044 + 3PHE CD2 51 2.247 2.269 2.237 + 3PHE HD2 52 2.262 2.171 2.282 + 3PHE CE1 53 2.203 2.525 2.128 + 3PHE HE1 54 2.186 2.623 2.086 + 3PHE CE2 55 2.335 2.375 2.269 + 3PHE HE2 56 2.416 2.357 2.338 + 3PHE CZ 57 2.312 2.503 2.215 + 3PHE HZ 58 2.375 2.585 2.244 + 3PHE C 59 2.020 1.962 2.005 + 3PHE O 60 1.901 1.933 1.991 + 4GLY N 61 2.113 1.874 2.043 + 4GLY H 62 2.207 1.908 2.060 + 4GLY CA 63 2.079 1.744 2.097 + 4GLY HA1 64 1.999 1.698 2.039 + 4GLY HA2 65 2.167 1.679 2.091 + 4GLY C 66 2.043 1.761 2.245 + 4GLY O 67 2.087 1.860 2.302 + 5ARG N 68 1.960 1.672 2.299 + 5ARG H 69 1.921 1.604 2.236 + 5ARG CA 70 1.906 1.670 2.437 + 5ARG HA 71 1.835 1.752 2.434 + 5ARG CB 72 1.823 1.541 2.455 + 5ARG HB1 73 1.743 1.539 2.379 + 5ARG HB2 74 1.887 1.455 2.435 + 5ARG CG 75 1.758 1.529 2.593 + 5ARG HG1 76 1.830 1.514 2.672 + 5ARG HG2 77 1.704 1.621 2.616 + 5ARG CD 78 1.671 1.408 2.613 + 5ARG HD1 79 1.635 1.411 2.715 + 5ARG HD2 80 1.586 1.415 2.545 + 5ARG NE 81 1.746 1.284 2.587 + 5ARG HE 82 1.746 1.259 2.489 + 5ARG CZ 83 1.815 1.210 2.676 + 5ARG NH1 84 1.827 1.246 2.804 + 5ARG HH11 85 1.789 1.335 2.836 + 5ARG HH12 86 1.882 1.195 2.871 + 5ARG NH2 87 1.871 1.097 2.633 + 5ARG HH21 88 1.861 1.067 2.538 + 5ARG HH22 89 1.925 1.037 2.695 + 5ARG C 90 1.994 1.715 2.560 + 5ARG O1 91 2.032 1.834 2.565 + 5ARG O2 92 2.013 1.637 2.654 + 6CL CL 93 0.867 2.210 2.056 + 7CL CL 94 2.878 3.762 2.614 + 4.09123 4.09123 4.09123 |
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| diff -r 2c349b027a01 -r 1d4dd4f908d4 test-data/minim.mdp --- a/test-data/minim.mdp Mon Nov 23 10:46:34 2020 +0000 +++ b/test-data/minim.mdp Wed Sep 29 07:42:14 2021 +0000 |
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| @@ -11,4 +11,5 @@ rcoulomb = 1.0 ; Short-range electrostatic cut-off rlist = 1.0 ; Cut-off distance for the short-range neighbor list. rvdw = 1.0 ; Short-range Van der Waals cut-off -pbc = xyz ; Periodic Boundary Conditions (yes/no) \ No newline at end of file +pbc = xyz ; Periodic Boundary Conditions (yes/no) +gen-seed = 1 |
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| diff -r 2c349b027a01 -r 1d4dd4f908d4 test-data/newbox.pdb --- a/test-data/newbox.pdb Mon Nov 23 10:46:34 2020 +0000 +++ b/test-data/newbox.pdb Wed Sep 29 07:42:14 2021 +0000 |
| b |
| @@ -33,13 +33,13 @@ ATOM 29 CB VAL 2 18.590 21.180 15.620 1.00 0.00 ATOM 30 HB VAL 2 19.310 20.670 15.150 1.00 0.00 ATOM 31 CG1 VAL 2 17.700 20.230 16.420 1.00 0.00 -ATOM 32 1HG1 VAL 2 17.220 19.620 15.790 1.00 0.00 -ATOM 33 2HG1 VAL 2 18.270 19.700 17.040 1.00 0.00 -ATOM 34 3HG1 VAL 2 17.030 20.760 16.940 1.00 0.00 +ATOM 32 HG11 VAL 2 17.220 19.620 15.790 1.00 0.00 +ATOM 33 HG12 VAL 2 18.270 19.700 17.040 1.00 0.00 +ATOM 34 HG13 VAL 2 17.030 20.760 16.940 1.00 0.00 ATOM 35 CG2 VAL 2 17.740 21.860 14.560 1.00 0.00 -ATOM 36 1HG2 VAL 2 17.280 21.170 14.010 1.00 0.00 -ATOM 37 2HG2 VAL 2 17.070 22.450 15.000 1.00 0.00 -ATOM 38 3HG2 VAL 2 18.330 22.420 13.970 1.00 0.00 +ATOM 36 HG21 VAL 2 17.280 21.170 14.010 1.00 0.00 +ATOM 37 HG22 VAL 2 17.070 22.450 15.000 1.00 0.00 +ATOM 38 HG23 VAL 2 18.330 22.420 13.970 1.00 0.00 ATOM 39 C VAL 2 20.250 21.460 17.560 1.00 0.00 ATOM 40 O VAL 2 21.210 20.760 17.190 1.00 0.00 ATOM 41 N PHE 3 19.940 21.700 18.810 1.00 0.00 @@ -86,11 +86,11 @@ ATOM 82 HE ARG 5 17.470 12.550 24.960 1.00 0.00 ATOM 83 CZ ARG 5 18.180 12.160 26.750 1.00 0.00 ATOM 84 NH1 ARG 5 18.290 12.480 28.040 1.00 0.00 -ATOM 85 1HH1 ARG 5 17.840 13.310 28.380 1.00 0.00 -ATOM 86 2HH1 ARG 5 18.810 11.900 28.660 1.00 0.00 +ATOM 85 HH11 ARG 5 17.840 13.310 28.380 1.00 0.00 +ATOM 86 HH12 ARG 5 18.810 11.900 28.660 1.00 0.00 ATOM 87 NH2 ARG 5 18.700 10.990 26.320 1.00 0.00 -ATOM 88 1HH2 ARG 5 18.560 10.700 25.380 1.00 0.00 -ATOM 89 2HH2 ARG 5 19.210 10.410 26.950 1.00 0.00 +ATOM 88 HH21 ARG 5 18.560 10.700 25.380 1.00 0.00 +ATOM 89 HH22 ARG 5 19.210 10.410 26.950 1.00 0.00 ATOM 90 C ARG 5 20.120 16.880 25.290 1.00 0.00 ATOM 91 O1 ARG 5 20.120 17.800 26.150 1.00 0.00 ATOM 92 O2 ARG 5 19.750 16.890 26.600 1.00 0.00 |
| b |
| diff -r 2c349b027a01 -r 1d4dd4f908d4 test-data/outp.xvg --- a/test-data/outp.xvg Mon Nov 23 10:46:34 2020 +0000 +++ b/test-data/outp.xvg Wed Sep 29 07:42:14 2021 +0000 |
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| @@ -1,15 +1,15 @@ -# This file was created Tue May 19 15:42:53 2020 +# This file was created Mon Jun 7 09:13:14 2021 # Created by: -# :-) GROMACS - gmx energy, 2019.1 (-: +# :-) GROMACS - gmx energy, 2021.1-MODIFIED (-: # -# Executable: /home/simon/miniconda3/envs/__gromacs@2019.1/bin/gmx -# Data prefix: /home/simon/miniconda3/envs/__gromacs@2019.1 -# Working dir: /tmp/tmprwcs9m2t/job_working_directory/000/17/working +# Executable: /home/runner/miniconda3/envs/__gromacs@2021.1/bin.AVX2_256/gmx +# Data prefix: /home/runner/miniconda3/envs/__gromacs@2021.1 +# Working dir: /tmp/tmpc3_9dc8m/job_working_directory/000/13/working # Command line: # gmx energy -f ./edr_input.edr -o ./energy.xvg # gmx energy is part of G R O M A C S: # -# GROningen Mixture of Alchemy and Childrens' Stories +# Glycine aRginine prOline Methionine Alanine Cystine Serine # @ title "GROMACS Energies" @ xaxis label "Time (ps)" |
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| diff -r 2c349b027a01 -r 1d4dd4f908d4 test-data/solv.gro --- a/test-data/solv.gro Mon Nov 23 10:46:34 2020 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b'@@ -1,6733 +0,0 @@\n-TEST in water\n- 6730\n- 1LYS N 1 2.081 2.649 1.487\n- 1LYS H1 2 2.157 2.703 1.449\n- 1LYS H2 3 2.015 2.629 1.415\n- 1LYS H3 4 2.037 2.701 1.560\n- 1LYS CA 5 2.134 2.522 1.542\n- 1LYS HA 6 2.178 2.470 1.469\n- 1LYS CB 7 2.232 2.559 1.654\n- 1LYS HB1 8 2.308 2.610 1.615\n- 1LYS HB2 9 2.184 2.616 1.721\n- 1LYS CG 10 2.290 2.440 1.729\n- 1LYS HG1 11 2.221 2.404 1.791\n- 1LYS HG2 12 2.315 2.369 1.662\n- 1LYS CD 13 2.414 2.480 1.808\n- 1LYS HD1 14 2.490 2.498 1.745\n- 1LYS HD2 15 2.394 2.562 1.861\n- 1LYS CE 16 2.451 2.366 1.901\n- 1LYS HE1 17 2.386 2.361 1.977\n- 1LYS HE2 18 2.451 2.279 1.852\n- 1LYS NZ 19 2.587 2.392 1.955\n- 1LYS HZ1 20 2.614 2.318 2.017\n- 1LYS HZ2 21 2.653 2.397 1.879\n- 1LYS HZ3 22 2.587 2.479 2.005\n- 1LYS C 23 2.019 2.441 1.601\n- 1LYS O 24 1.940 2.496 1.677\n- 2VAL N 25 2.019 2.311 1.581\n- 2VAL H 26 2.081 2.275 1.511\n- 2VAL CA 27 1.935 2.215 1.652\n- 2VAL HA 28 1.862 2.267 1.695\n- 2VAL CB 29 1.859 2.118 1.562\n- 2VAL HB 30 1.931 2.067 1.515\n- 2VAL CG1 31 1.770 2.023 1.642\n- 2VAL HG11 32 1.722 1.962 1.579\n- 2VAL HG12 33 1.827 1.970 1.704\n- 2VAL HG13 34 1.703 2.076 1.694\n- 2VAL CG2 35 1.774 2.186 1.456\n- 2VAL HG21 36 1.728 2.117 1.401\n- 2VAL HG22 37 1.707 2.245 1.500\n- 2VAL HG23 38 1.833 2.242 1.397\n- 2VAL C 39 2.025 2.146 1.756\n- 2VAL O 40 2.121 2.076 1.719\n- 3PHE N 41 1.994 2.170 1.881\n- 3PHE H 42 1.920 2.234 1.901\n- 3PHE CA 43 2.064 2.105 1.993\n- 3PHE HA 44 2.160 2.112 1.968\n- 3PHE CB 45 2.042 2.178 2.126\n- 3PHE HB1 46 1.950 2.217 2.127\n- 3PHE HB2 47 2.051 2.113 2.201\n- 3PHE CG 48 2.139 2.289 2.147\n- 3PHE CD1 49 2.112 2.420 2.105\n- 3PHE HD1 50 2.026 2.440 2.058\n- 3PHE CD2 51 2.245 2.271 2.238\n- 3PHE HD2 52 2.258 2.181 2.280\n- 3PHE CE1 53 2.203 2.523 2.128\n- 3PHE HE1 54 2.193 2.610 2.081\n- 3PHE CE2 55 2.332 2.374 2.269\n- 3PHE HE2 56 2.411 2.357 2.328\n- 3PHE CZ 57 2.309 2.502 2.218\n- 3PHE HZ 58 2.367 2.579 2.246\n- 3PHE C 59 2.019 1.959 2.008\n- 3PHE O 60 1.897 1.931 1.999\n- 4GLY N 61 2.117 1.879 2.052\n- 4GLY H 62 2.212 1.910 2.053\n- 4GLY CA 63 2.082 1.743 2.098\n- 4GLY HA1 64 2.007 1.707 2.042\n- 4GLY HA2 65 2.161 1.683 2.091\n- 4GLY C 66 2.037 1.757 2.243\n- 4GLY O 67 2.075 1.855 2.307\n- 5ARG N 68 1.950 1.669 2.288\n- 5ARG H 69 1.916 1.599 2.225\n- 5ARG CA 70 1.901 1.669 2.426\n- 5ARG HA 71 1.843 1.749 2.433\n- 5ARG CB 72 1.821 1.541 2.452\n- 5ARG HB1 73 1.745 1.537 2.388\n- 5ARG HB2 74 1.881 1.462 2.438\n- 5ARG CG 75 1.766 1.535 2.593\n- 5ARG HG1 76 1.842 1.532 2.658\n- 5ARG HG2 77 1.710 1.616 2.610\n- 5ARG CD 78 1.683 1.415 2.613\n- 5ARG HD1 79 1.649 1.414 2.707\n- 5ARG HD2 80 1.605 1.420 2.550\n- 5ARG NE 81 1.751 1.290 2.589\n- 5ARG HE 82 1.747 1.255 2.496\n- 5ARG CZ 83 1.818 1.216 2.675\n- 5ARG NH1 84 1.829 1.248 2.804\n- 5ARG HH11 85 1.784 1.331 2.838\n- 5ARG HH12 86 1.881 1.190 2.866\n- '..b'51 3.745\n- 2190SOL OW 6645 3.955 3.575 4.207\n- 2190SOL HW1 6646 3.989 3.652 4.261\n- 2190SOL HW2 6647 3.999 3.575 4.117\n- 2191SOL OW 6648 3.751 3.458 3.841\n- 2191SOL HW1 6649 3.732 3.362 3.862\n- 2191SOL HW2 6650 3.718 3.516 3.916\n- 2192SOL OW 6651 4.021 1.897 3.895\n- 2192SOL HW1 6652 4.070 1.981 3.874\n- 2192SOL HW2 6653 4.083 1.832 3.940\n- 2193SOL OW 6654 3.732 3.188 3.924\n- 2193SOL HW1 6655 3.639 3.209 3.893\n- 2193SOL HW2 6656 3.742 3.089 3.937\n- 2194SOL OW 6657 3.799 2.207 3.757\n- 2194SOL HW1 6658 3.707 2.179 3.728\n- 2194SOL HW2 6659 3.830 2.284 3.701\n- 2195SOL OW 6660 3.796 2.028 4.042\n- 2195SOL HW1 6661 3.779 2.111 3.988\n- 2195SOL HW2 6662 3.886 1.991 4.020\n- 2196SOL OW 6663 3.763 2.939 4.024\n- 2196SOL HW1 6664 3.862 2.928 4.015\n- 2196SOL HW2 6665 3.723 2.853 4.056\n- 2197SOL OW 6666 3.954 4.352 0.113\n- 2197SOL HW1 6667 3.861 4.350 0.150\n- 2197SOL HW2 6668 3.955 4.313 0.021\n- 2198SOL OW 6669 3.949 3.999 0.996\n- 2198SOL HW1 6670 3.984 3.982 1.088\n- 2198SOL HW2 6671 3.861 3.954 0.984\n- 2199SOL OW 6672 3.743 4.092 0.647\n- 2199SOL HW1 6673 3.661 4.135 0.686\n- 2199SOL HW2 6674 3.715 4.019 0.584\n- 2200SOL OW 6675 3.926 4.009 1.498\n- 2200SOL HW1 6676 3.846 4.069 1.485\n- 2200SOL HW2 6677 3.916 3.960 1.584\n- 2201SOL OW 6678 4.031 3.937 1.231\n- 2201SOL HW1 6679 4.008 3.974 1.321\n- 2201SOL HW2 6680 4.001 3.842 1.225\n- 2202SOL OW 6681 4.031 3.787 0.618\n- 2202SOL HW1 6682 4.020 3.881 0.651\n- 2202SOL HW2 6683 4.026 3.724 0.695\n- 2203SOL OW 6684 3.796 3.890 0.318\n- 2203SOL HW1 6685 3.779 3.973 0.264\n- 2203SOL HW2 6686 3.886 3.853 0.296\n- 2204SOL OW 6687 3.954 4.352 1.975\n- 2204SOL HW1 6688 3.861 4.350 2.012\n- 2204SOL HW2 6689 3.955 4.313 1.883\n- 2205SOL OW 6690 3.949 3.999 2.858\n- 2205SOL HW1 6691 3.984 3.982 2.950\n- 2205SOL HW2 6692 3.861 3.954 2.846\n- 2206SOL OW 6693 3.743 4.092 2.509\n- 2206SOL HW1 6694 3.661 4.135 2.548\n- 2206SOL HW2 6695 3.715 4.019 2.446\n- 2207SOL OW 6696 3.926 4.009 3.360\n- 2207SOL HW1 6697 3.846 4.069 3.347\n- 2207SOL HW2 6698 3.916 3.960 3.446\n- 2208SOL OW 6699 4.021 3.759 2.033\n- 2208SOL HW1 6700 4.070 3.843 2.012\n- 2208SOL HW2 6701 4.083 3.694 2.078\n- 2209SOL OW 6702 4.031 3.937 3.093\n- 2209SOL HW1 6703 4.008 3.974 3.183\n- 2209SOL HW2 6704 4.001 3.842 3.087\n- 2210SOL OW 6705 4.031 3.787 2.480\n- 2210SOL HW1 6706 4.020 3.881 2.513\n- 2210SOL HW2 6707 4.026 3.724 2.557\n- 2211SOL OW 6708 3.799 4.069 1.895\n- 2211SOL HW1 6709 3.707 4.041 1.866\n- 2211SOL HW2 6710 3.830 4.146 1.839\n- 2212SOL OW 6711 3.796 3.890 2.180\n- 2212SOL HW1 6712 3.779 3.973 2.126\n- 2212SOL HW2 6713 3.886 3.853 2.158\n- 2213SOL OW 6714 3.954 4.352 3.837\n- 2213SOL HW1 6715 3.861 4.350 3.874\n- 2213SOL HW2 6716 3.955 4.313 3.745\n- 2214SOL OW 6717 4.021 3.759 3.895\n- 2214SOL HW1 6718 4.070 3.843 3.874\n- 2214SOL HW2 6719 4.083 3.694 3.940\n- 2215SOL OW 6720 3.799 4.069 3.757\n- 2215SOL HW1 6721 3.707 4.041 3.728\n- 2215SOL HW2 6722 3.830 4.146 3.701\n- 2216SOL OW 6723 3.796 3.890 4.042\n- 2216SOL HW1 6724 3.779 3.973 3.988\n- 2216SOL HW2 6725 3.886 3.853 4.020\n- 2217SOL OW 6726 4.152 4.148 4.244\n- 2217SOL HW1 6727 4.182 4.076 4.182\n- 2217SOL HW2 6728 4.113 4.108 4.327\n- 2218CL CL 6729 0.865 2.210 2.057\n- 2219CL CL 6730 2.879 3.763 2.615\n- 4.09123 4.09123 4.09123\n' |
| b |
| diff -r 2c349b027a01 -r 1d4dd4f908d4 test-data/topol.top --- a/test-data/topol.top Mon Nov 23 10:46:34 2020 +0000 +++ b/test-data/topol.top Wed Sep 29 07:42:14 2021 +0000 |
| b |
| @@ -1,17 +1,17 @@ ; ; File 'topol.top' was generated -; By user: unknown (1000) -; On host: simon-notebook -; At date: Tue May 12 12:59:21 2020 +; By user: unknown (1001) +; On host: fv-az99-468 +; At date: Mon Jun 7 09:15:15 2021 ; ; This is a standalone topology file ; ; Created by: -; :-) GROMACS - gmx pdb2gmx, 2019.1 (-: +; :-) GROMACS - gmx pdb2gmx, 2021.1-MODIFIED (-: ; -; Executable: /home/simon/miniconda3/envs/__gromacs@2019.1/bin/gmx -; Data prefix: /home/simon/miniconda3/envs/__gromacs@2019.1 -; Working dir: /tmp/tmpg0ncnt9q/job_working_directory/000/10/working +; Executable: /home/runner/miniconda3/envs/__gromacs@2021.1/bin.AVX2_256/gmx +; Data prefix: /home/runner/miniconda3/envs/__gromacs@2021.1 +; Working dir: /tmp/tmpc3_9dc8m/job_working_directory/000/27/working ; Command line: ; gmx pdb2gmx -f ./pdb_input.pdb -o processed.gro -p topol.top -i posres.itp -water spce -ff oplsaa -noignh -merge all ; Force field was read from the standard GROMACS share directory. |
| b |
| diff -r 2c349b027a01 -r 1d4dd4f908d4 test-data/topol_md.top --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/topol_md.top Wed Sep 29 07:42:14 2021 +0000 |
| [ |
| b'@@ -0,0 +1,910 @@\n+;\n+;\tFile \'topol.top\' was generated\n+;\tBy user: unknown (1000)\n+;\tOn host: simon-notebook\n+;\tAt date: Tue May 12 12:59:21 2020\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/__gromacs@2019.1/bin/gmx\n+;\tData prefix: /home/simon/miniconda3/envs/__gromacs@2019.1\n+;\tWorking dir: /tmp/tmpg0ncnt9q/job_working_directory/000/10/working\n+;\tCommand line:\n+;\t gmx pdb2gmx -f ./pdb_input.pdb -o processed.gro -p topol.top -i posres.itp -water spce -ff oplsaa -noignh -merge all\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 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 '..b' 59 61 63 3 \n+ 59 61 63 64 3 \n+ 59 61 63 65 3 \n+ 59 61 63 66 3 \n+ 62 61 63 64 3 \n+ 62 61 63 65 3 \n+ 62 61 63 66 3 \n+ 61 63 66 67 3 \n+ 61 63 66 68 3 \n+ 64 63 66 67 3 \n+ 64 63 66 68 3 \n+ 65 63 66 67 3 \n+ 65 63 66 68 3 \n+ 63 66 68 69 3 \n+ 63 66 68 70 3 \n+ 67 66 68 69 3 \n+ 67 66 68 70 3 \n+ 66 68 70 71 3 \n+ 66 68 70 72 3 \n+ 66 68 70 90 3 \n+ 69 68 70 71 3 \n+ 69 68 70 72 3 \n+ 69 68 70 90 3 \n+ 68 70 72 75 3 dih_ARG_chi1_N_C_C_C\n+ 90 70 72 75 3 dih_ARG_chi1_C_C_C_CO\n+ 68 70 72 73 3 \n+ 68 70 72 74 3 \n+ 71 70 72 73 3 \n+ 71 70 72 74 3 \n+ 71 70 72 75 3 \n+ 90 70 72 73 3 \n+ 90 70 72 74 3 \n+ 68 70 90 91 3 \n+ 68 70 90 92 3 \n+ 71 70 90 91 3 \n+ 71 70 90 92 3 \n+ 72 70 90 91 3 \n+ 72 70 90 92 3 \n+ 70 72 75 76 3 \n+ 70 72 75 77 3 \n+ 70 72 75 78 3 \n+ 73 72 75 76 3 \n+ 73 72 75 77 3 \n+ 73 72 75 78 3 \n+ 74 72 75 76 3 \n+ 74 72 75 77 3 \n+ 74 72 75 78 3 \n+ 72 75 78 79 3 \n+ 72 75 78 80 3 \n+ 72 75 78 81 3 \n+ 76 75 78 79 3 \n+ 76 75 78 80 3 \n+ 76 75 78 81 3 \n+ 77 75 78 79 3 \n+ 77 75 78 80 3 \n+ 77 75 78 81 3 \n+ 75 78 81 82 3 \n+ 75 78 81 83 3 \n+ 79 78 81 82 3 \n+ 79 78 81 83 3 \n+ 80 78 81 82 3 \n+ 80 78 81 83 3 \n+ 78 81 83 84 3 \n+ 78 81 83 87 3 \n+ 82 81 83 84 3 \n+ 82 81 83 87 3 \n+ 81 83 84 85 3 \n+ 81 83 84 86 3 \n+ 87 83 84 85 3 \n+ 87 83 84 86 3 \n+ 81 83 87 88 3 \n+ 81 83 87 89 3 \n+ 84 83 87 88 3 \n+ 84 83 87 89 3 \n+\n+[ dihedrals ]\n+; ai aj ak al funct c0 c1 c2 c3\n+ 5 25 23 24 1 improper_O_C_X_Y\n+ 23 27 25 26 1 improper_Z_N_X_Y\n+ 27 41 39 40 1 improper_O_C_X_Y\n+ 39 43 41 42 1 improper_Z_N_X_Y\n+ 43 61 59 60 1 improper_O_C_X_Y\n+ 45 48 51 49 1 improper_Z_CA_X_Y\n+ 48 53 49 50 1 improper_Z_CA_X_Y\n+ 48 55 51 52 1 improper_Z_CA_X_Y\n+ 49 57 53 54 1 improper_Z_CA_X_Y\n+ 51 57 55 56 1 improper_Z_CA_X_Y\n+ 53 55 57 58 1 improper_Z_CA_X_Y\n+ 59 63 61 62 1 improper_Z_N_X_Y\n+ 63 68 66 67 1 improper_O_C_X_Y\n+ 66 70 68 69 1 improper_Z_N_X_Y\n+ 70 91 90 92 1 improper_O_C_X_Y\n+ 78 83 81 82 1 improper_Z_N_X_Y\n+ 81 84 83 87 1 improper_O_C_X_Y\n+ 83 85 84 86 1 improper_Z_N_X_Y\n+ 83 88 87 89 1 improper_Z_N_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+TEST in water\n+\n+[ molecules ]\n+; Compound #mols\n+Protein 1\n+CL 2\n' |
| b |
| diff -r 2c349b027a01 -r 1d4dd4f908d4 test-data/topol_solv.top --- a/test-data/topol_solv.top Mon Nov 23 10:46:34 2020 +0000 +++ b/test-data/topol_solv.top Wed Sep 29 07:42:14 2021 +0000 |
| [ |
| @@ -907,4 +907,6 @@ [ molecules ] ; Compound #mols Protein 1 -CL 2 +SOL 2130 +NA 41 +CL 43 |