[gmx-users] topology file with grompp program

[Justin A. Lemkul]

วันเวลา อมรนพ wrote:
> 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
>  

You must #include the appropriate force field file before you can define your 
molecule type.

A few notes and suggestions:

1. If using the original PRODRG server, consider using the newer PRODRG 2.5 
server.  The original PRODRG gives ffgmx-compatible topologies.  This force 
field is deprecated.  PRODRG 2.5 is compatible with the newer Gromos96 variants.

2. Check the charges and charge groups carefully, and consider changing them. 
Does it make sense to have permanent dipoles in a propane molecule?

-Justin

> ;      
> ;      
> ;       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 
> <mailto: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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-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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