[gmx-users] Problems with GROMPP

Justin A. Lemkul jalemkul at vt.edu
Sun Jan 13 23:59:47 CET 2008

Quoting Jens Pohl <Pohl.Jens at web.de>:

> > -----Ursprüngliche Nachricht-----
> > Von: Discussion list for GROMACS users <gmx-users at gromacs.org>
> > Gesendet: 12.01.08 03:29:49
> > An: Discussion list for GROMACS users <gmx-users at gromacs.org>
> > Betreff: Re: [gmx-users] Problems with GROMPP
> >
> >
> > > It seems, that my protein is truncated in the xxx.gro file. The number of
> water molecules is ok, but there are about 150 AS residues missing after I
> run GENBOX ??? The xxx.top has them included, so this explains the different
> numbers.
> >
> > Well, read the warning messages from pdb2gmx, genbox and grompp carefully.
> >
> > Mark
> I didn't receive any warnings going through the single steps. No problem with
> pdb2gmx. When I compare the *.gro to the original file there seems to be
> everything ok. Same with editconf. (I rerun pdb3gmx and used -q to get a
> *.pdb to compare to my original one). When I run genbox I get the *.top with
> all residues, but the *.gro is truncated. Did it several times with the same
> result...but no massage, that anything might be wrong (or I was too tired to
> see it. Will do it again tomorrow)

It might be helpful to post to the list the exact commands you issued so far. 
It might be illustrative of the problem.


> Jens
> __________________________________________________________________________
> Erweitern Sie FreeMail zu einem noch leistungsstärkeren E-Mail-Postfach!
> Mehr Infos unter http://produkte.web.de/club/?mc=021131
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php


Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul at vt.edu | (540) 231-9080


More information about the gromacs.org_gmx-users mailing list