[gmx-users] pdb2gmx and hydrogen nomenclature

David van der Spoel spoel at xray.bmc.uu.se
Fri Oct 15 16:18:19 CEST 2004

On Fri, 2004-10-15 at 15:34, Bert de Groot wrote:
> 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).
Doesn't this mean that what we call HB1 should be HB2 and what is now
HB2 should be HB3, meaning that your translation still gets the wrong

David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel

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