[gmx-users] fatal error [using pdb2gmx]

Sven Huttenhouse mdsimulation at hotmail.com
Sun Oct 16 20:43:44 CEST 2005

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


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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