[gmx-users] Problem importing PDB to Gromacs

Jernej Zidar jernej.zidar at gmail.com
Fri May 10 11:16:40 CEST 2013

  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?

Thanks in advance,

More information about the gromacs.org_gmx-users mailing list