[gmx-users] topology file with grompp program

วันเวลา อมรนพ avrilevil at gmail.com
Fri May 15 16:59:44 CEST 2009


Dear gmx users

I want to simulate propane molecule and I use PRODGE website to generate
both .gro and .top file.
Then I run the grompp program and there is an error said that

Fatal error:
Invalid order for directive moleculetype, file ""topol.top"", line 17
and below is my topology file of a propane molecule

;
;
;       This file was generated by PRODRG version 071121.0636
;       PRODRG written/copyrighted by Daan van Aalten
;       and Alexander Schuettelkopf
;
;       Questions/comments to dava at davapc1.bioch.dundee.ac.uk
;
;       When using this software in a publication, cite:
;       A. W. Schuettelkopf and D. M. F. van Aalten (2004).
;       PRODRG - a tool for high-throughput crystallography
;       of protein-ligand complexes.
;       Acta Crystallogr. D60, 1355--1363.
;
;
[ moleculetype ]
; name nrexcl
DRG      3
[ atoms ]
;   nr      type  resnr resid  atom  cgnr   charge     mass
     1       CH3     1  DRG     CAA     1   -0.007  15.0350
     2       CH2     1  DRG     CAB     1    0.015  14.0270
     3       CH3     1  DRG     CAC     1   -0.008  15.0350
[ bonds ]
; ai  aj  fu    c0, c1, ...
   1   2   1    0.153    334720.0    0.153    334720.0 ;   CAA  CAB
   2   3   1    0.153    334720.0    0.153    334720.0 ;   CAB  CAC
[ pairs ]
; ai  aj  fu    c0, c1, ...
[ angles ]
; ai  aj  ak  fu    c0, c1, ...
   1   2   3   1    111.0       460.2    111.0       460.2 ;   CAA  CAB
CAC
[ dihedrals ]
; ai  aj  ak  al  fu    c0, c1, m, ...

Please help me figure out what is the error

Thanks for advance

Suwit
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