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

Moore, Jonathan (J) JMoore2 at dow.com
Tue Oct 10 20:17:11 CEST 2006

As I mentioned recently:

I get that kind of error ("number of coordinates in the coordinate file (XXXX atoms) does not match topology (0 atoms)") when I've modified the .mdp file under Windows.  Try opening the .mdp file under unix and removing the Windows end-of-line characters (others have suggested using the unix2dos program to do this automatically).


Jonathan Moore, Ph.D.
Research and Engineering Sciences - New Products
Core R&D
The Dow Chemical Company
1702 Building, Office 300E
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Phone:  (989) 636-9765 
Fax: (989) 636-4019
E Mail: jmoore2 at dow.com

-----Original Message-----
From: gmx-users-bounces at gromacs.org [mailto:gmx-users-bounces at gromacs.org] On Behalf Of David van der Spoel
Sent: Tuesday, October 10, 2006 10:59 AM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] RE: no coordinates in .top file

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. ________________________________________________________________________
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
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