[gmx-users] fatal error [using pdb2gmx]

[Sven Huttenhouse]

I have the glycine pdb file but I don't know which hydrogen atom to ignore.

I tried to use a program called Ghemical to get the .pdb file of the 
glycine. it gave me the pdb file of glycine with all the atoms included. I 
used this pdb file and riplicated the number of glycine molecules to 250 
using genbox and it worked fine. but when I tried to convert this pdb file 
to .gro file using pdb2gmx I got a fatal error message that I have some 
missed atoms??!!!

I searched the internet and got a (glycine.pdb) file from the site :

http://wbiomed.curtin.edu.au/teach/biochem/tutorials/pdb/

but I had the same problem (I could riplicate it but not generate a .gro 
file using pdb2gmx).
Can any one please help me and explain why is this?
Alternatively If I want to write the .gro file following its format and 
using information from the pdb file how should I name my atoms and which 
atoms should I include??

kind regards
Sven Huttenhouse



>From: David van der Spoel <spoel at xray.bmc.uu.se>
>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: Mon, 17 Oct 2005 09:12:49 +0200
>
>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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