[gmx-users] fatal error [using pdb2gmx]

[Sven Huttenhouse]

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?
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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