[gmx-users] pdb2gmx error

tarak karmakar tarak20489 at gmail.com
Tue Jun 12 14:13:59 CEST 2012

check your aminoacid.rtp file present in
check all the atom types of that particular residue in your pdb file and
match them properly with the atoms types present in the aminoacid.rtp file
.....and then proceed ....

On Tue, Jun 12, 2012 at 5:29 PM, delara aghaie <d_aghaie at yahoo.com> 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?
> 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..
> Thanks
> Regards
> D.M
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*Tarak Karmakar
Molecular Simulation Lab.
Chemistry and Physics of Materials Unit
Jawaharlal Nehru Centre for Advanced Scientific Research
Jakkur P. O.
Bangalore - 560 064
Karnataka, INDIA
Ph. (lab) : +91-80-22082809 *
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