[gmx-users] RE: no coordinates in .top file

David van der Spoel spoel at xray.bmc.uu.se
Tue Oct 10 16:59:26 CEST 2006

Owen, Michael wrote:
> Fellow gmx users,
> thanks for the suggestion, however, applying -v to grompp did not yield 
> any additional information.  Shouldn't grompp read the number of 
> coordinates from the list of atoms in the [ atoms ] section?  Could 
> something be wrong with my .itp file?  Could it be that my .top and .itp 
> files are in my working directory instead of the Gromacs "share" directory?

no, the problem is most likely in your topology.
post the output from grompp -v if you can not find the answer yourself.

David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se

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