[gmx-users] Re:

xiaobing tian xiaobingtian at yahoo.com
Fri Mar 19 23:54:00 CET 2004

Hi Nuno,
Thanks, Nuno.  Because the program produce a temp.top, and the speptide.top was empty. I used temp.top and it works.
Thanks again.

"Nuno R. L. Ferreira" <nunolf at ci.uc.pt> wrote:
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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Xiaobing Tian  Ph.D.
Department of Microbiology and Immunology
Thomas Jefferson University
1025 Walnut St., Suite 420
Philadelphia,  PA19107
Phone: 215-955-1364 (Lab)
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