| Previous changeset 0:c01897428864 (2019-06-13) Next changeset 2:59a0424937cc (2019-10-07) |
|
Commit message:
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit f1620d2eb7fd3ea43bb4dfe6cee5b45015fd13a3 |
|
added:
test-data/JZ4.mol2 test-data/base_GMX.gro test-data/base_GMX.itp |
| b |
| diff -r c01897428864 -r 511c4bd8aa6d test-data/JZ4.mol2 --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/JZ4.mol2 Thu Jun 13 06:16:14 2019 -0400 |
| b |
| @@ -0,0 +1,52 @@ +@<TRIPOS>MOLECULE +/data/dnb02/galaxy_db/files/009/501/dataset_9501918.dat + 22 22 0 0 0 +SMALL +GASTEIGER + +@<TRIPOS>ATOM + 1 C4 0.7939 1.3702 2.1983 C.3 167 JZ4167 -0.0650 + 2 C7 6.5984 0.4172 2.4451 C.ar 167 JZ4167 -0.0613 + 3 C8 7.3182 0.9119 1.3612 C.ar 167 JZ4167 -0.0583 + 4 C9 6.6461 1.3322 0.2147 C.ar 167 JZ4167 -0.0199 + 5 C10 5.2522 1.2617 0.1608 C.ar 167 JZ4167 0.1200 + 6 C11 5.2053 0.3427 2.3837 C.ar 167 JZ4167 -0.0551 + 7 C12 4.5084 0.7745 1.2426 C.ar 167 JZ4167 -0.0060 + 8 C13 3.0004 0.6682 1.1973 C.3 167 JZ4167 -0.0245 + 9 C14 2.3079 1.4796 2.2975 C.3 167 JZ4167 -0.0518 + 10 OAB 4.5987 1.6713 -0.9677 O.3 167 JZ4167 -0.5065 + 11 H 0.3197 1.9287 3.0114 H 167 JZ4167 0.0230 + 12 H 0.4705 0.3267 2.2700 H 167 JZ4167 0.0230 + 13 H 0.4322 1.7786 1.2494 H 167 JZ4167 0.0230 + 14 H 7.1195 0.0849 3.3395 H 167 JZ4167 0.0618 + 15 H 8.4028 0.9664 1.4088 H 167 JZ4167 0.0619 + 16 H 7.2222 1.7087 -0.6246 H 167 JZ4167 0.0654 + 17 H 4.6638 -0.0590 3.2368 H 167 JZ4167 0.0621 + 18 H 2.7296 -0.3918 1.2845 H 167 JZ4167 0.0314 + 19 H 2.6172 0.9976 0.2247 H 167 JZ4167 0.0314 + 20 H 2.6004 2.5342 2.2276 H 167 JZ4167 0.0266 + 21 H 2.6177 1.1288 3.2886 H 167 JZ4167 0.0266 + 22 H 5.2561 1.9626 -1.6199 H 167 JZ4167 0.2921 +@<TRIPOS>BOND + 1 4 3 ar + 2 4 5 ar + 3 3 2 ar + 4 10 5 1 + 5 5 7 ar + 6 2 6 ar + 7 7 6 ar + 8 7 8 1 + 9 8 9 1 + 10 9 1 1 + 11 1 11 1 + 12 1 12 1 + 13 1 13 1 + 14 2 14 1 + 15 3 15 1 + 16 4 16 1 + 17 6 17 1 + 18 8 18 1 + 19 8 19 1 + 20 9 20 1 + 21 9 21 1 + 22 10 22 1 |
| b |
| diff -r c01897428864 -r 511c4bd8aa6d test-data/base_GMX.gro --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/base_GMX.gro Thu Jun 13 06:16:14 2019 -0400 |
| b |
| @@ -0,0 +1,25 @@ +base6_GMX.gro created by acpype (v: 2018-04-24T22:34:57UTC) on Tue Jun 11 14:15:01 2019 + 22 + 1 JZ4 C4 1 0.079 0.137 0.220 + 1 JZ4 C7 2 0.660 0.042 0.244 + 1 JZ4 C8 3 0.732 0.091 0.136 + 1 JZ4 C9 4 0.665 0.133 0.022 + 1 JZ4 C10 5 0.525 0.126 0.016 + 1 JZ4 C11 6 0.521 0.034 0.238 + 1 JZ4 C12 7 0.451 0.077 0.124 + 1 JZ4 C13 8 0.300 0.067 0.120 + 1 JZ4 C14 9 0.231 0.148 0.230 + 1 JZ4 OAB 10 0.460 0.167 -0.097 + 1 JZ4 H 11 0.032 0.193 0.301 + 1 JZ4 H1 12 0.047 0.033 0.227 + 1 JZ4 H2 13 0.043 0.178 0.125 + 1 JZ4 H3 14 0.712 0.009 0.334 + 1 JZ4 H4 15 0.840 0.097 0.141 + 1 JZ4 H5 16 0.722 0.171 -0.062 + 1 JZ4 H6 17 0.466 -0.006 0.324 + 1 JZ4 H7 18 0.273 -0.039 0.128 + 1 JZ4 H8 19 0.262 0.100 0.023 + 1 JZ4 H9 20 0.260 0.253 0.223 + 1 JZ4 H10 21 0.262 0.113 0.329 + 1 JZ4 H11 22 0.526 0.196 -0.162 + 16.16600 5.85200 9.92000 |
| b |
| diff -r c01897428864 -r 511c4bd8aa6d test-data/base_GMX.itp --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/base_GMX.itp Thu Jun 13 06:16:14 2019 -0400 |
| [ |
| b'@@ -0,0 +1,218 @@\n+; base_GMX.itp created by acpype (v: 2019-03-22T14:36:00UTC) on Fri May 31 15:21:44 2019\n+\n+[ atomtypes ]\n+;name bond_type mass charge ptype sigma epsilon Amb\n+ c3 c3 0.00000 0.00000 A 3.39967e-01 4.57730e-01 ; 1.91 0.1094\n+ ca ca 0.00000 0.00000 A 3.39967e-01 3.59824e-01 ; 1.91 0.0860\n+ oh oh 0.00000 0.00000 A 3.06647e-01 8.80314e-01 ; 1.72 0.2104\n+ hc hc 0.00000 0.00000 A 2.64953e-01 6.56888e-02 ; 1.49 0.0157\n+ ha ha 0.00000 0.00000 A 2.59964e-01 6.27600e-02 ; 1.46 0.0150\n+ ho ho 0.00000 0.00000 A 0.00000e+00 0.00000e+00 ; 0.00 0.0000\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 c3 1 JZ4 C4 1 -0.093100 12.01000 ; qtot -0.093\n+ 2 ca 1 JZ4 C7 2 -0.162000 12.01000 ; qtot -0.255\n+ 3 ca 1 JZ4 C8 3 -0.095000 12.01000 ; qtot -0.350\n+ 4 ca 1 JZ4 C9 4 -0.211000 12.01000 ; qtot -0.561\n+ 5 ca 1 JZ4 C10 5 0.124100 12.01000 ; qtot -0.437\n+ 6 ca 1 JZ4 C11 6 -0.099000 12.01000 ; qtot -0.536\n+ 7 ca 1 JZ4 C12 7 -0.098300 12.01000 ; qtot -0.634\n+ 8 c3 1 JZ4 C13 8 -0.032100 12.01000 ; qtot -0.666\n+ 9 c3 1 JZ4 C14 9 -0.075400 12.01000 ; qtot -0.742\n+ 10 oh 1 JZ4 OAB 10 -0.500101 16.00000 ; qtot -1.242\n+ 11 hc 1 JZ4 H 11 0.032700 1.00800 ; qtot -1.209\n+ 12 hc 1 JZ4 H1 12 0.032700 1.00800 ; qtot -1.177\n+ 13 hc 1 JZ4 H2 13 0.032700 1.00800 ; qtot -1.144\n+ 14 ha 1 JZ4 H3 14 0.133000 1.00800 ; qtot -1.011\n+ 15 ha 1 JZ4 H4 15 0.132000 1.00800 ; qtot -0.879\n+ 16 ha 1 JZ4 H5 16 0.132000 1.00800 ; qtot -0.747\n+ 17 ha 1 JZ4 H6 17 0.134000 1.00800 ; qtot -0.613\n+ 18 hc 1 JZ4 H7 18 0.055700 1.00800 ; qtot -0.557\n+ 19 hc 1 JZ4 H8 19 0.055700 1.00800 ; qtot -0.501\n+ 20 hc 1 JZ4 H9 20 0.041700 1.00800 ; qtot -0.460\n+ 21 hc 1 JZ4 H10 21 0.041700 1.00800 ; qtot -0.418\n+ 22 ho 1 JZ4 H11 22 0.418000 1.00800 ; qtot -0.000\n+\n+[ bonds ]\n+; ai aj funct r k\n+ 1 9 1 1.5375e-01 2.5179e+05 ; C4 - C14 \n+ 1 11 1 1.0969e-01 2.7665e+05 ; C4 - H \n+ 1 12 1 1.0969e-01 2.7665e+05 ; C4 - H1 \n+ 1 13 1 1.0969e-01 2.7665e+05 ; C4 - H2 \n+ 2 3 1 1.3984e-01 3.8585e+05 ; C7 - C8 \n+ 2 6 1 1.3984e-01 3.8585e+05 ; C7 - C11 \n+ 2 14 1 1.0860e-01 2.8937e+05 ; C7 - H3 \n+ 3 4 1 1.3984e-01 3.8585e+05 ; C8 - C9 \n+ 3 15 1 1.0860e-01 2.8937e+05 ; C8 - H4 \n+ 4 5 1 1.3984e-01 3.8585e+05 ; C9 - C10 \n+ 4 16 1 1.0860e-01 2.8937e+05 ; C9 - H5 \n+ 5 7 1 1.3984e-01 3.8585e+05 ; C10 - C12 \n+ 5 10 1 1.3637e-01 3.2133e+05 ; C10 - OAB \n+ 6 7 1 1.3984e-01 3.8585e+05 ; C11 - C12 \n+ 6 17 1 1.0860e-01 2.8937e+05 ; C11 - H6 \n+ 7 8 1 1.5156e-01 2.6861e+05 ; C12 - C13 \n+ 8 9 1 1.5375e-01 2.5179e+05 ; C13 - C14 \n+ 8 18 1 1.0969e-01 2.7665e+05 ; C13 - H7 \n+ 8 19 1 1.0969e-01 2.7665e+05 ; C13 - H8 \n+ 9 20 1 1.0969e-01 2.7665e+05 ; C14 - H9 \n+ 9 21 1 1.0969e-01 2.7665e+05 ; C14 - H10 \n+ 10 '..b'C7- H3\n+ 4 5 7 6 9 180.00 15.16700 2 ; C9- C10- C12- C11\n+ 4 5 7 8 9 180.00 15.16700 2 ; C9- C10- C12- C13\n+ 4 5 10 22 9 180.00 3.76560 2 ; C9- C10- OAB- H11\n+ 5 4 3 15 9 180.00 15.16700 2 ; C10- C9- C8- H4\n+ 5 7 6 17 9 180.00 15.16700 2 ; C10- C12- C11- H6\n+ 5 7 8 9 9 0.00 0.00000 0 ; C10- C12- C13- C14\n+ 5 7 8 18 9 0.00 0.00000 0 ; C10- C12- C13- H7\n+ 5 7 8 19 9 0.00 0.00000 0 ; C10- C12- C13- H8\n+ 6 2 3 15 9 180.00 15.16700 2 ; C11- C7- C8- H4\n+ 6 7 5 10 9 180.00 15.16700 2 ; C11- C12- C10- OAB\n+ 6 7 8 9 9 0.00 0.00000 0 ; C11- C12- C13- C14\n+ 6 7 8 18 9 0.00 0.00000 0 ; C11- C12- C13- H7\n+ 6 7 8 19 9 0.00 0.00000 0 ; C11- C12- C13- H8\n+ 7 5 4 16 9 180.00 15.16700 2 ; C12- C10- C9- H5\n+ 7 5 10 22 9 180.00 3.76560 2 ; C12- C10- OAB- H11\n+ 7 6 2 14 9 180.00 15.16700 2 ; C12- C11- C7- H3\n+ 7 8 9 20 9 0.00 0.65084 3 ; C12- C13- C14- H9\n+ 7 8 9 21 9 0.00 0.65084 3 ; C12- C13- C14- H10\n+ 8 7 5 10 9 180.00 15.16700 2 ; C13- C12- C10- OAB\n+ 8 7 6 17 9 180.00 15.16700 2 ; C13- C12- C11- H6\n+ 10 5 4 16 9 180.00 15.16700 2 ; OAB- C10- C9- H5\n+ 11 1 9 8 9 0.00 0.66944 3 ; H- C4- C14- C13\n+ 11 1 9 20 9 0.00 0.62760 3 ; H- C4- C14- H9\n+ 11 1 9 21 9 0.00 0.62760 3 ; H- C4- C14- H10\n+ 12 1 9 8 9 0.00 0.66944 3 ; H1- C4- C14- C13\n+ 12 1 9 20 9 0.00 0.62760 3 ; H1- C4- C14- H9\n+ 12 1 9 21 9 0.00 0.62760 3 ; H1- C4- C14- H10\n+ 13 1 9 8 9 0.00 0.66944 3 ; H2- C4- C14- C13\n+ 13 1 9 20 9 0.00 0.62760 3 ; H2- C4- C14- H9\n+ 13 1 9 21 9 0.00 0.62760 3 ; H2- C4- C14- H10\n+ 14 2 3 15 9 180.00 15.16700 2 ; H3- C7- C8- H4\n+ 14 2 6 17 9 180.00 15.16700 2 ; H3- C7- C11- H6\n+ 15 3 4 16 9 180.00 15.16700 2 ; H4- C8- C9- H5\n+ 18 8 9 20 9 0.00 0.62760 3 ; H7- C13- C14- H9\n+ 18 8 9 21 9 0.00 0.62760 3 ; H7- C13- C14- H10\n+ 19 8 9 20 9 0.00 0.62760 3 ; H8- C13- C14- H9\n+ 19 8 9 21 9 0.00 0.62760 3 ; H8- C13- C14- H10\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+ 2 4 3 15 4 180.00 4.60240 2 ; C7- C9- C8- H4\n+ 2 7 6 17 4 180.00 4.60240 2 ; C7- C12- C11- H6\n+ 3 5 4 16 4 180.00 4.60240 2 ; C8- C10- C9- H5\n+ 3 6 2 14 4 180.00 4.60240 2 ; C8- C11- C7- H3\n+ 4 7 5 10 4 180.00 4.60240 2 ; C9- C12- C10- OAB\n+ 5 6 7 8 4 180.00 4.60240 2 ; C10- C11- C12- C13\n' |