[gmx-users] Grompp problem?

David spoel at xray.bmc.uu.se
Mon Jul 12 21:21:50 CEST 2004

On Mon, 2004-07-12 at 19:33, Amy Petrik wrote:
> Hi!
> I am running gromacs on an i686 with redhat 7.3.  I have just set it up and so i am trying to work through the tutorials.  When trying to run grompp I get an error stating that the number of coordinates in my coordinate file does not match then number of coordinates in my topology file.  It says that the coordinate files has "X" atoms and the topology file has zero.  By looking at the two files it appears to me that the topology file has no coordinates listed for any atoms.  This leads me to think that the problem is with my pdb2gmx program which generates the coordinate and topology files.  Any suggestions about what is going wrong?  Thanks!!
check grompp error messages. there is something wrong in the topology.
> Amy
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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://xray.bmc.uu.se/~spoel

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