[gmx-users] fatal error during running grompp
wibowo_arie at yahoo.com
Thu Dec 11 14:01:24 CET 2008
Dear Berk and Mark,
thank you for your suggestion. I will try to download that version.
--- On Wed, 12/10/08, Berk Hess <gmx3 at hotmail.com> wrote:
> From: Berk Hess <gmx3 at hotmail.com>
> Subject: RE: [gmx-users] fatal error during running grompp
> To: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
> Date: Wednesday, December 10, 2008, 12:14 AM
> 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
> > 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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