[gmx-users] (no subject)

pirate man mansour.bouneb.med at gmail.com
Thu Mar 26 15:45:59 CET 2015


* TOP FILE (CYCLODEXTRINE) (topol.top) generated by PRODRG
; Include forcefield parameters
#include "ffG43a1.itp"

[ moleculetype ]
; Name                         nrexcl
UNK                              3

[ atoms ]
;   nr      type  resnr resid  atom  cgnr   charge     mass
     1        OA     1  UNK      O2     1   -0.227  15.9994
     2         H     1  UNK     H22     1    0.027   1.0080
     3       CH1     1  UNK      C2     1    0.107  13.0190
     4       CH1     1  UNK      C3     1    0.107  13.0190
     5        OA     1  UNK      O3     1   -0.227  15.9994
     6         H     1  UNK     H32     1    0.027   1.0080
     7       CH1     1  UNK      C4     1    0.186  13.0190
     8        OA     1  UNK      O4     2   -0.164  15.9994
     9       CH1     1  UNK      C5     2    0.261  13.0190
    10       CH2     1  UNK      C6     2    0.104  14.0270
    11        OA     1  UNK      O6     2   -0.171  15.9994
    12         H     1  UNK     H69     2    0.036   1.0080
    13        OA     1  UNK      O5     2   -0.163  15.9994
    14       CH1     1  UNK      C1     2    0.261  13.0190
    15        OA     1  UNK      O1     2   -0.164  15.9994
    16       CH1     1  UNK     CAJ     3    0.199  13.0190
    17       CH1     1  UNK     CAK     3    0.199  13.0190
    18        OA     1  UNK     OBY     3   -0.206  15.9994
    19       CH2     1  UNK     CAL     3    0.065  14.0270
    20        OA     1  UNK     OBZ     3   -0.215  15.9994
..
..

; Include Position restraint file

#ifdef POSRES
#include "posre.itp"
#endif


; Include ligand topology
#include "drg.itp"

; Include water topology
#include "spc.itp"

[ molecules ]
; Compound        #mols
UNK                  1
LIG                  1
SOL              1682

* ITP FILE ( SULFAMIDE ) (drg.itp) generated by PRODRG


[ moleculetype ]
; Name nrexcl
LIG      3

[ atoms ]
;   nr      type  resnr resid  atom  cgnr   charge     mass
     1         O     1  LIG      O1     1   -0.695  15.9994
     2         C     1  LIG      C8     1    0.361  12.0110
     3        OA     1  LIG       O     1   -0.199  15.9994
     4       CH1     1  LIG      C7     1    0.207  14.0270
     5       CH2     1  LIG      C6     1    0.044  14.0270
     6        NR     1  LIG      N1     1    0.011  14.0067
     7     SDMSO     1  LIG       S     1    2.271  32.0600
     8        OM     1  LIG      O2     2   -1.000  15.9994
     9        OM     1  LIG      O3     2   -1.000  15.9994
    10         N     1  LIG       N     3    0.108  14.0067
    11         H     1  LIG      H2     3   -0.026   1.0080
    12         C     1  LIG      C2     3    0.109  12.0110
    13       CR1     1  LIG      C1     3   -0.034  12.0110
    14        HC     1  LIG      H1     3   -0.004   1.0080
    15       CR1     1  LIG       C     3   -0.034  12.0110
    16        HC     1  LIG       H     3   -0.004   1.0080
    17       CR1     1  LIG      C5     3   -0.034  12.0110
    18        HC     1  LIG      H5     3   -0.004   1.0080
    19       CR1     1  LIG      C4     3   -0.035  12.0110
    20        HC     1  LIG      H4     3   -0.004   1.0080
    21       CR1     1  LIG      C3     3   -0.034  12.0110
    22        HC     1  LIG      H3     3   -0.004   1.0080

so when i run minimization

( grompp -f em.mdp -p topol.top -c solvated.gro -o em.tpr )

Fatal error:
Syntax error - File topol.top, line 682
Last line read:
'[ molecules ]'
Invalid order for directive molecules

please help me to solved this error


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