[gmx-users] running grompp

Erik Lindahl lindahl at stanford.edu
Thu May 23 02:41:57 CEST 2002

Valentin Gogonea wrote:

> Dear Gromacs users,
> I am trying to get grompp running for the following files. I 
> constructed the topology by hand. I get  an error message. It says:
>  Fatal error: number of coordinates in coordinate file 
> (MeCO_Met_NHMe.pdb, 16)
>              does not match topology (MeCO_Met_NHMe.top, 0)
> I attached the pdb, top and output files, I hope that somebody can 
> tell me what is wrong with my topology file.

1. You have defined the molecule, but you forget the system description 
that tells how many such molecules are in your system.
2. There is no atom type "s3" in the gmx forcefield.
3. Your pdb file isn't correctly formatted; note that the alignment and 
whitespace is extremely significant in the PDB format!
4. A couple of the improper dihedrals had the last two atoms switched; 
this isn't wrong, but the gmx forcefield just happens to
use a different definition.

The attached versions will probably be accepted by grompp, but you will 
have to check if the atom type change is ok.



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