[gmx-users] pdb2gmx error

delara aghaie d_aghaie at yahoo.com
Tue Jun 12 13:59:31 CEST 2012

Dear Gromacs users
Using bdp2gmx command to obtain topology and .gro file for 1AU1.pdb I get the following error:
I should mention that I have selected OPLS force field.

1) how can I reach to the conclusion that special forcefield is better fo my system?

2) This is the error:

Program pdb2gmx, VERSION 4.5.5
Source code file: pdb2gmx.c, line: 655

Fatal error:
Atom HB3 in residue ARG 71 was not found in rtp entry ARG with 24 atoms
while sorting atoms.

For a hydrogen, this can be a different protonation state, or it
might have had a different number in the PDB file and was rebuilt
(it might for instance have been H3, and we only expected H1 & H2).
Note that hydrogens might have been added to the entry for the N-terminus.
Remove this hydrogen or choose a different protonation state to solve it.
Option -ignh will ignore all hydrogens in the input.
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
Any help would be greatly appreciated..
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