[gmx-users] fatal error during running grompp

Berk Hess gmx3 at hotmail.com
Wed Dec 10 09:14:40 CET 2008


This looks like a bug reported before in version 4.0.
It has been fixed in 4.0.2, download that version.


> Date: Wed, 10 Dec 2008 09:27:27 +1100
> From: Mark.Abraham at anu.edu.au
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] fatal error during running grompp
> arie wibowo wrote:
> > Dear all, 
> > 
> > I am a beginner using gromacs. when I start to run gromacs, the calculation always stop in grompp due to fatal error was appeared. the information below the fatal error is "number of coordinates in coordinate file (minimized_water.gro, 26791) does not match topology file (aki.top, 1555)". but when I try to look aki.top file, there are already 1 molecules of protein, 78 molecules of SOL and 8412 molecules of SOL in the end of this file, so I think topology file must contain more than 1555 atom. I have already change .mdp file manually using gedit because I see in internet this error can also occur because .mdp file has been edited under Windows, but the problem still occur. is there any help or suggestion?
> You've probably got something wrong with your .top file format, but we 
> can't guess what. Have a read of the relevant bits of chapter 5, 
> including the examples there.
> Mark
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