Mercurial > repos > chemteam > ambertools_parmchk2
changeset 1:a0099ea2ef8b draft
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit f1620d2eb7fd3ea43bb4dfe6cee5b45015fd13a3
| author | chemteam |
|---|---|
| date | Thu, 13 Jun 2019 06:15:51 -0400 |
| parents | a1a204464657 |
| children | 00ff41b1d49a |
| files | test-data/JZ4.mol2 test-data/base_GMX.gro test-data/base_GMX.itp |
| diffstat | 3 files changed, 295 insertions(+), 0 deletions(-) [+] |
line wrap: on
line diff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/JZ4.mol2 Thu Jun 13 06:15:51 2019 -0400 @@ -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
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/base_GMX.gro Thu Jun 13 06:15:51 2019 -0400 @@ -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
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/base_GMX.itp Thu Jun 13 06:15:51 2019 -0400 @@ -0,0 +1,218 @@ +; base_GMX.itp created by acpype (v: 2019-03-22T14:36:00UTC) on Fri May 31 15:21:44 2019 + +[ atomtypes ] +;name bond_type mass charge ptype sigma epsilon Amb + c3 c3 0.00000 0.00000 A 3.39967e-01 4.57730e-01 ; 1.91 0.1094 + ca ca 0.00000 0.00000 A 3.39967e-01 3.59824e-01 ; 1.91 0.0860 + oh oh 0.00000 0.00000 A 3.06647e-01 8.80314e-01 ; 1.72 0.2104 + hc hc 0.00000 0.00000 A 2.64953e-01 6.56888e-02 ; 1.49 0.0157 + ha ha 0.00000 0.00000 A 2.59964e-01 6.27600e-02 ; 1.46 0.0150 + ho ho 0.00000 0.00000 A 0.00000e+00 0.00000e+00 ; 0.00 0.0000 + +[ moleculetype ] +;name nrexcl + base 3 + +[ atoms ] +; nr type resi res atom cgnr charge mass ; qtot bond_type + 1 c3 1 JZ4 C4 1 -0.093100 12.01000 ; qtot -0.093 + 2 ca 1 JZ4 C7 2 -0.162000 12.01000 ; qtot -0.255 + 3 ca 1 JZ4 C8 3 -0.095000 12.01000 ; qtot -0.350 + 4 ca 1 JZ4 C9 4 -0.211000 12.01000 ; qtot -0.561 + 5 ca 1 JZ4 C10 5 0.124100 12.01000 ; qtot -0.437 + 6 ca 1 JZ4 C11 6 -0.099000 12.01000 ; qtot -0.536 + 7 ca 1 JZ4 C12 7 -0.098300 12.01000 ; qtot -0.634 + 8 c3 1 JZ4 C13 8 -0.032100 12.01000 ; qtot -0.666 + 9 c3 1 JZ4 C14 9 -0.075400 12.01000 ; qtot -0.742 + 10 oh 1 JZ4 OAB 10 -0.500101 16.00000 ; qtot -1.242 + 11 hc 1 JZ4 H 11 0.032700 1.00800 ; qtot -1.209 + 12 hc 1 JZ4 H1 12 0.032700 1.00800 ; qtot -1.177 + 13 hc 1 JZ4 H2 13 0.032700 1.00800 ; qtot -1.144 + 14 ha 1 JZ4 H3 14 0.133000 1.00800 ; qtot -1.011 + 15 ha 1 JZ4 H4 15 0.132000 1.00800 ; qtot -0.879 + 16 ha 1 JZ4 H5 16 0.132000 1.00800 ; qtot -0.747 + 17 ha 1 JZ4 H6 17 0.134000 1.00800 ; qtot -0.613 + 18 hc 1 JZ4 H7 18 0.055700 1.00800 ; qtot -0.557 + 19 hc 1 JZ4 H8 19 0.055700 1.00800 ; qtot -0.501 + 20 hc 1 JZ4 H9 20 0.041700 1.00800 ; qtot -0.460 + 21 hc 1 JZ4 H10 21 0.041700 1.00800 ; qtot -0.418 + 22 ho 1 JZ4 H11 22 0.418000 1.00800 ; qtot -0.000 + +[ bonds ] +; ai aj funct r k + 1 9 1 1.5375e-01 2.5179e+05 ; C4 - C14 + 1 11 1 1.0969e-01 2.7665e+05 ; C4 - H + 1 12 1 1.0969e-01 2.7665e+05 ; C4 - H1 + 1 13 1 1.0969e-01 2.7665e+05 ; C4 - H2 + 2 3 1 1.3984e-01 3.8585e+05 ; C7 - C8 + 2 6 1 1.3984e-01 3.8585e+05 ; C7 - C11 + 2 14 1 1.0860e-01 2.8937e+05 ; C7 - H3 + 3 4 1 1.3984e-01 3.8585e+05 ; C8 - C9 + 3 15 1 1.0860e-01 2.8937e+05 ; C8 - H4 + 4 5 1 1.3984e-01 3.8585e+05 ; C9 - C10 + 4 16 1 1.0860e-01 2.8937e+05 ; C9 - H5 + 5 7 1 1.3984e-01 3.8585e+05 ; C10 - C12 + 5 10 1 1.3637e-01 3.2133e+05 ; C10 - OAB + 6 7 1 1.3984e-01 3.8585e+05 ; C11 - C12 + 6 17 1 1.0860e-01 2.8937e+05 ; C11 - H6 + 7 8 1 1.5156e-01 2.6861e+05 ; C12 - C13 + 8 9 1 1.5375e-01 2.5179e+05 ; C13 - C14 + 8 18 1 1.0969e-01 2.7665e+05 ; C13 - H7 + 8 19 1 1.0969e-01 2.7665e+05 ; C13 - H8 + 9 20 1 1.0969e-01 2.7665e+05 ; C14 - H9 + 9 21 1 1.0969e-01 2.7665e+05 ; C14 - H10 + 10 22 1 9.7300e-02 3.1079e+05 ; OAB - H11 + +[ pairs ] +; ai aj funct + 1 7 1 ; C4 - C12 + 1 18 1 ; C4 - H7 + 1 19 1 ; C4 - H8 + 2 5 1 ; C7 - C10 + 2 8 1 ; C7 - C13 + 2 16 1 ; C7 - H5 + 3 7 1 ; C8 - C12 + 3 10 1 ; C8 - OAB + 3 17 1 ; C8 - H6 + 4 6 1 ; C9 - C11 + 4 8 1 ; C9 - C13 + 4 14 1 ; C9 - H3 + 4 22 1 ; C9 - H11 + 5 9 1 ; C10 - C14 + 5 15 1 ; C10 - H4 + 5 17 1 ; C10 - H6 + 5 18 1 ; C10 - H7 + 5 19 1 ; C10 - H8 + 6 9 1 ; C11 - C14 + 6 10 1 ; C11 - OAB + 6 15 1 ; C11 - H4 + 6 18 1 ; C11 - H7 + 6 19 1 ; C11 - H8 + 7 14 1 ; C12 - H3 + 7 16 1 ; C12 - H5 + 7 20 1 ; C12 - H9 + 7 21 1 ; C12 - H10 + 7 22 1 ; C12 - H11 + 8 10 1 ; C13 - OAB + 8 17 1 ; C13 - H6 + 10 16 1 ; OAB - H5 + 11 8 1 ; H - C13 + 11 20 1 ; H - H9 + 11 21 1 ; H - H10 + 12 8 1 ; H1 - C13 + 12 20 1 ; H1 - H9 + 12 21 1 ; H1 - H10 + 13 8 1 ; H2 - C13 + 13 20 1 ; H2 - H9 + 13 21 1 ; H2 - H10 + 14 15 1 ; H3 - H4 + 14 17 1 ; H3 - H6 + 15 16 1 ; H4 - H5 + 18 20 1 ; H7 - H9 + 18 21 1 ; H7 - H10 + 19 20 1 ; H8 - H9 + 19 21 1 ; H8 - H10 + +[ angles ] +; ai aj ak funct theta cth + 1 9 8 1 1.1151e+02 5.2635e+02 ; C4 - C14 - C13 + 1 9 20 1 1.0980e+02 3.8744e+02 ; C4 - C14 - H9 + 1 9 21 1 1.0980e+02 3.8744e+02 ; C4 - C14 - H10 + 2 3 4 1 1.2002e+02 5.5731e+02 ; C7 - C8 - C9 + 2 3 15 1 1.1988e+02 4.0334e+02 ; C7 - C8 - H4 + 2 6 7 1 1.2002e+02 5.5731e+02 ; C7 - C11 - C12 + 2 6 17 1 1.1988e+02 4.0334e+02 ; C7 - C11 - H6 + 3 2 6 1 1.2002e+02 5.5731e+02 ; C8 - C7 - C11 + 3 2 14 1 1.1988e+02 4.0334e+02 ; C8 - C7 - H3 + 3 4 5 1 1.2002e+02 5.5731e+02 ; C8 - C9 - C10 + 3 4 16 1 1.1988e+02 4.0334e+02 ; C8 - C9 - H5 + 4 3 15 1 1.1988e+02 4.0334e+02 ; C9 - C8 - H4 + 4 5 7 1 1.2002e+02 5.5731e+02 ; C9 - C10 - C12 + 4 5 10 1 1.1990e+02 5.8158e+02 ; C9 - C10 - OAB + 5 4 16 1 1.1988e+02 4.0334e+02 ; C10 - C9 - H5 + 5 7 6 1 1.2002e+02 5.5731e+02 ; C10 - C12 - C11 + 5 7 8 1 1.2077e+02 5.3137e+02 ; C10 - C12 - C13 + 5 10 22 1 1.0858e+02 4.1003e+02 ; C10 - OAB - H11 + 6 2 14 1 1.1988e+02 4.0334e+02 ; C11 - C7 - H3 + 6 7 8 1 1.2077e+02 5.3137e+02 ; C11 - C12 - C13 + 7 5 10 1 1.1990e+02 5.8158e+02 ; C12 - C10 - OAB + 7 6 17 1 1.1988e+02 4.0334e+02 ; C12 - C11 - H6 + 7 8 9 1 1.1207e+02 5.2802e+02 ; C12 - C13 - C14 + 7 8 18 1 1.1047e+02 3.9162e+02 ; C12 - C13 - H7 + 7 8 19 1 1.1047e+02 3.9162e+02 ; C12 - C13 - H8 + 8 9 20 1 1.0980e+02 3.8744e+02 ; C13 - C14 - H9 + 8 9 21 1 1.0980e+02 3.8744e+02 ; C13 - C14 - H10 + 9 1 11 1 1.0980e+02 3.8744e+02 ; C14 - C4 - H + 9 1 12 1 1.0980e+02 3.8744e+02 ; C14 - C4 - H1 + 9 1 13 1 1.0980e+02 3.8744e+02 ; C14 - C4 - H2 + 9 8 18 1 1.0980e+02 3.8744e+02 ; C14 - C13 - H7 + 9 8 19 1 1.0980e+02 3.8744e+02 ; C14 - C13 - H8 + 11 1 12 1 1.0758e+02 3.2970e+02 ; H - C4 - H1 + 11 1 13 1 1.0758e+02 3.2970e+02 ; H - C4 - H2 + 12 1 13 1 1.0758e+02 3.2970e+02 ; H1 - C4 - H2 + 18 8 19 1 1.0758e+02 3.2970e+02 ; H7 - C13 - H8 + 20 9 21 1 1.0758e+02 3.2970e+02 ; H9 - C14 - H10 + +[ dihedrals ] ; propers +; for gromacs 4.5 or higher, using funct 9 +; i j k l func phase kd pn + 1 9 8 7 9 0.00 0.65084 3 ; C4- C14- C13- C12 + 1 9 8 18 9 0.00 0.66944 3 ; C4- C14- C13- H7 + 1 9 8 19 9 0.00 0.66944 3 ; C4- C14- C13- H8 + 2 3 4 5 9 180.00 15.16700 2 ; C7- C8- C9- C10 + 2 3 4 16 9 180.00 15.16700 2 ; C7- C8- C9- H5 + 2 6 7 5 9 180.00 15.16700 2 ; C7- C11- C12- C10 + 2 6 7 8 9 180.00 15.16700 2 ; C7- C11- C12- C13 + 3 2 6 7 9 180.00 15.16700 2 ; C8- C7- C11- C12 + 3 2 6 17 9 180.00 15.16700 2 ; C8- C7- C11- H6 + 3 4 5 7 9 180.00 15.16700 2 ; C8- C9- C10- C12 + 3 4 5 10 9 180.00 15.16700 2 ; C8- C9- C10- OAB + 4 3 2 6 9 180.00 15.16700 2 ; C9- C8- C7- C11 + 4 3 2 14 9 180.00 15.16700 2 ; C9- C8- C7- H3 + 4 5 7 6 9 180.00 15.16700 2 ; C9- C10- C12- C11 + 4 5 7 8 9 180.00 15.16700 2 ; C9- C10- C12- C13 + 4 5 10 22 9 180.00 3.76560 2 ; C9- C10- OAB- H11 + 5 4 3 15 9 180.00 15.16700 2 ; C10- C9- C8- H4 + 5 7 6 17 9 180.00 15.16700 2 ; C10- C12- C11- H6 + 5 7 8 9 9 0.00 0.00000 0 ; C10- C12- C13- C14 + 5 7 8 18 9 0.00 0.00000 0 ; C10- C12- C13- H7 + 5 7 8 19 9 0.00 0.00000 0 ; C10- C12- C13- H8 + 6 2 3 15 9 180.00 15.16700 2 ; C11- C7- C8- H4 + 6 7 5 10 9 180.00 15.16700 2 ; C11- C12- C10- OAB + 6 7 8 9 9 0.00 0.00000 0 ; C11- C12- C13- C14 + 6 7 8 18 9 0.00 0.00000 0 ; C11- C12- C13- H7 + 6 7 8 19 9 0.00 0.00000 0 ; C11- C12- C13- H8 + 7 5 4 16 9 180.00 15.16700 2 ; C12- C10- C9- H5 + 7 5 10 22 9 180.00 3.76560 2 ; C12- C10- OAB- H11 + 7 6 2 14 9 180.00 15.16700 2 ; C12- C11- C7- H3 + 7 8 9 20 9 0.00 0.65084 3 ; C12- C13- C14- H9 + 7 8 9 21 9 0.00 0.65084 3 ; C12- C13- C14- H10 + 8 7 5 10 9 180.00 15.16700 2 ; C13- C12- C10- OAB + 8 7 6 17 9 180.00 15.16700 2 ; C13- C12- C11- H6 + 10 5 4 16 9 180.00 15.16700 2 ; OAB- C10- C9- H5 + 11 1 9 8 9 0.00 0.66944 3 ; H- C4- C14- C13 + 11 1 9 20 9 0.00 0.62760 3 ; H- C4- C14- H9 + 11 1 9 21 9 0.00 0.62760 3 ; H- C4- C14- H10 + 12 1 9 8 9 0.00 0.66944 3 ; H1- C4- C14- C13 + 12 1 9 20 9 0.00 0.62760 3 ; H1- C4- C14- H9 + 12 1 9 21 9 0.00 0.62760 3 ; H1- C4- C14- H10 + 13 1 9 8 9 0.00 0.66944 3 ; H2- C4- C14- C13 + 13 1 9 20 9 0.00 0.62760 3 ; H2- C4- C14- H9 + 13 1 9 21 9 0.00 0.62760 3 ; H2- C4- C14- H10 + 14 2 3 15 9 180.00 15.16700 2 ; H3- C7- C8- H4 + 14 2 6 17 9 180.00 15.16700 2 ; H3- C7- C11- H6 + 15 3 4 16 9 180.00 15.16700 2 ; H4- C8- C9- H5 + 18 8 9 20 9 0.00 0.62760 3 ; H7- C13- C14- H9 + 18 8 9 21 9 0.00 0.62760 3 ; H7- C13- C14- H10 + 19 8 9 20 9 0.00 0.62760 3 ; H8- C13- C14- H9 + 19 8 9 21 9 0.00 0.62760 3 ; H8- C13- C14- H10 + +[ dihedrals ] ; impropers +; treated as propers in GROMACS to use correct AMBER analytical function +; i j k l func phase kd pn + 2 4 3 15 4 180.00 4.60240 2 ; C7- C9- C8- H4 + 2 7 6 17 4 180.00 4.60240 2 ; C7- C12- C11- H6 + 3 5 4 16 4 180.00 4.60240 2 ; C8- C10- C9- H5 + 3 6 2 14 4 180.00 4.60240 2 ; C8- C11- C7- H3 + 4 7 5 10 4 180.00 4.60240 2 ; C9- C12- C10- OAB + 5 6 7 8 4 180.00 4.60240 2 ; C10- C11- C12- C13