[gmx-users] Problem importing PDB to Gromacs

Justin Lemkul jalemkul at vt.edu
Fri May 10 12:05:55 CEST 2013

On 5/10/13 5:16 AM, Jernej Zidar wrote:
> Hi,
>    In CHARMM I generated a short peptide. The N-terminal is a regular
> -NH2 (patch NNEU) while  the C-terminal is amidated (patch CT2).
>    I would like to import the PDB to GROMACS using pdb2gmx by using the
> CHARMM27 forcefield later. I issue the following command:
>   pdb2gmx -v -f irik-l.pdb -inter
> and choose the appropriate protonation states of the aminoacids, the
> N-/C- terminal patches, solvent but the import fails:
> Program pdb2gmx, VERSION 4.6
> Source code file: /home/zidar/utils/gromacs-4.6/src/kernel/pdb2gmx.c, line: 727
> Fatal error:
> Atom H1 in residue ILE 1 was not found in rtp entry ILE with 20 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
> - - - -
>    Atom H1 (and H2) is the atom from the both the N-/C- terminals that
> in CHARMM is part of the residue ILE but Gromacs (4.6.1) does not
> recognize it properly as they are renamed:
> Renaming atom 'HT1' in residue 1 ILE to 'H1'
> Renaming atom 'HT2' in residue 1 ILE to 'H2'
>    How can one solve this problem?

Have you tried -ignh like the error output suggests?



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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