Hi,
This looks like a bug reported before in version 4.0.
It has been fixed in 4.0.2, download that version.
Berk
> Date: Wed, 10 Dec 2008 09:27:27 +1100
> From: [EMAIL PROTECTED]
> To: [email protected]
> 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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