[gmx-users] fatal error [using pdb2gmx]
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.
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