[gmx-users] fatal error [using pdb2gmx]

[David van der Spoel]

On Sun, 2005-10-16 at 16:31 -0500, Sven Huttenhouse wrote:
> Dear Tsjerk
> thak you for replying. If I want to write my own .pdb file how can I get the 
> configuration for it?
> I have a paper talking about the bond length and angles in the Glycine. how 
> can I use this information to write my own .pdb file?
use e.g. pymol instead.
> kind regards
> Sven Huttenhouse
> 
> 
> 
> >From: Tsjerk Wassenaar <tsjerkw at gmail.com>
> >Reply-To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> >To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> >Subject: Re: [gmx-users] fatal error [using pdb2gmx]
> >Date: Sun, 16 Oct 2005 20:09:49 +0100
> >
> >Hi Sven,
> >
> >The pdb file contains all hydrogens, while you chose a united-atom force
> >field probably. Use the option -ignh.
> >
> >Cheers,
> >
> >Tsjerk
> >
> >On 10/16/05, Sven Huttenhouse <mdsimulation at hotmail.com> wrote:
> > >
> > > dear GROMACS users.
> > >
> > > I'm a new gromacs user from Illinois Institute of Technology (IIT).
> > >
> > > I'm trying to get the pdb file of Glycine to study glycine
> > > crystallization.
> > > I found an online pdb file for it. but when I used pdb2gmx to convert it
> > > to
> > > a .gro file I got the following error message:
> > >
> > > fatal error: atom H9 in risidue GLY 1 not found in rtp enrty with 7 
> >atoms
> > > while sorting atoms. maybe different protonation state. remove this
> > > hydrogen
> > > or chose a different protonation state.
> > > option -ignh will ignore all hydrogen in the input.
> > >
> > > I got the glycine pdb file from the following link
> > >
> > > http://wbiomed.curtin.edu.au/teach/biochem/tutorials/pdb/
> > >
> > > can any one help me please. and is there any other way to construct my
> > > .pdb
> > > file for any molecule.
> > > kind regards
> > > Sven Huttenhouse.
> > >
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> >
> >--
> >
> >Tsjerk A. Wassenaar, M.Sc.
> >Groningen Biomolecular Sciences and Biotechnology Institute (GBB)
> >Dept. of Biophysical Chemistry
> >University of Groningen
> >Nijenborgh 4
> >9747AG Groningen, The Netherlands
> >+31 50 363 4336
> 
> 
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