[gmx-users] Re: What is wrong with my .top file?

Nuno R. L. Ferreira nunolf at ci.uc.pt
Fri Mar 19 19:46:02 CET 2004

On Friday 19 March 2004 04:45 pm, xiaobing tian wrote:
> Hi, Nuno,
> Thank you for your patience. I followed your instructions, and it works
> well. However, when i run grompp, it results the following error messages
> (see below). I can not figure out why. Any advices would be very
> appreciated.
> calling C:\gromacs\bin\cpp...
> processing topology...
> processing coordinates...
> Fatal error: number of coordinates in coordinate file (speptide_b4em.gro,
> 9035)
>              does not match topology (speptide.top, 0)
> C:\gromacs\share\tutor\speptide>

Are you following the speptide just like the instructions in the Getting 
started "manual"? Or are you trying to solvate the peptide in a different 
solvent than water, say DMSO?

Check the tail of your top file, it must have 1 molecule for the peptide and # 
molecules for the solvent.


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