[gmx-users] genbox give coord file more waters than top file

Berk Hess gmx3 at hotmail.com
Thu Mar 8 10:22:04 CET 2007

>From: WILLIAM R WELCH <wwelch at wisc.edu>
>Reply-To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>To: gmx-users at gromacs.org
>Subject: [gmx-users] genbox give coord file more waters than top file
>Date: Wed, 07 Mar 2007 16:53:11 -0600
>Dear gromacs guys
>Why would genbox put more water molecules in my .gro file than in my .top 
>file? I'm sure all I have to do is edit the number in my top file, but I 
>have not had this happen before, does anyone know of  a reason that this 
>happens so I can fix my file?

I have seen this problem for the first time on our Gromacs workshop last 
I think the problem is that genbox does not recognize some crystal waters in
your input coordinate file. genbox currently checks for SOL, WAT and HOH.
What is the residue name of your crystal waters?

The solution for the moment is to manually count the water molecules in
the gro file and then correct the top file.


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