[gmx-users] Coordinate file does not match topology

Alan Dodd anoddlad at yahoo.com
Fri Jun 8 08:26:01 CEST 2007

Small errors like that are usually down to things like running genion and not changing the .top.  I think I made a problem for myself once with non-consecutive atom numbering, too.

----- Original Message ----
From: Mark Abraham <Mark.Abraham at anu.edu.au>
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Sent: Friday, June 8, 2007 3:48:28 AM
Subject: Re: [gmx-users] Coordinate file does not match topology

Sheyore Omovie wrote:
> Dear gromacs users,
> While trying to preprocess my files with grompp, i got the ff error 
> message:
> "Number of coordinates in coordinate file (b4em.gro, 2312) does not 
> match topology (twopolypeptide.top, 2291)"
> How can I fix this?

Make them match. Assuming you haven't managed a gross mismatch of files, 
your [molecules] section of your .top probably isn't right. Chapter five 
of the manual is your friend here.

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