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