[gmx-users] pdb2gmx and hydrogen nomenclature

Bert de Groot bgroot at gwdg.de
Fri Oct 15 15:34:27 CEST 2004

Hi all,

from time to time pdb2gmx doesn't recognize protons in (protein) PDB files,
giving errors like:

Fatal error: Atom HB3 in residue ARG 2 not found in rtp entry with 24 atoms

the reason being that in the gromacs naming the two hydrogens on the CB are called
HB1 and HB2 (and not HB2 and HB3, or 2HB and 3HB, as they are often called in PDB files,
and as they should be called according to the IUPAC conventions).

The attached  xlateat.dat should be able to prevent the need of throwing away the
proton positions ("-ignh) in such cases.



Dr. Bert de Groot

Max Planck Institute for Biophysical Chemistry
Computational biomolecular dynamics group
Am Fassberg 11
37077 Goettingen, Germany

tel: +49-551-2012308, fax: +49-551-2012302

email: bgroot at gwdg.de
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