[gmx-users] pdb2gmx error

Justin A. Lemkul jalemkul at vt.edu
Tue Jun 12 14:07:20 CEST 2012

On 6/12/12 7:59 AM, delara aghaie wrote:
> 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?

The choice of the force field is motivated by weighing pros and cons of the 
parameter set, its inherent assumptions, and what has been demonstrated to be 
effective for similar systems.

> 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..

Read the error message.  It contains the exact instructions you need.



Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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