[gmx-users] fatal error [using pdb2gmx]

Tsjerk Wassenaar tsjerkw at gmail.com
Sun Oct 16 21:09:49 CEST 2005

Hi Sven,

The pdb file contains all hydrogens, while you chose a united-atom force
field probably. Use the option -ignh.



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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