[gmx-users] pdb2gmx and hydrogen nomenclature

[David van der Spoel]

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
nomenclature? 
 

-- 
David.
________________________________________________________________________
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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