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

[Moore, Jonathan (J)]

As I mentioned recently:
http://www.gromacs.org/pipermail/gmx-users/2006-October/024137.html

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

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-----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.
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