[gmx-users] pdb2gmx and hydrogen nomenclature

Bert de Groot bgroot at gwdg.de
Fri Oct 15 17:36:13 CEST 2004

David van der Spoel wrote:

> 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? 

The translation translates it to the gromacs nomenclature, so yes, it gets the "wrong"
(ie non-IUPAC conform) nomenclature ;-)

But I guess that's not what you mean. I guess what you mean is : does it  translate into the wrong
"stereochemistry"? (which would lead to a swapping of all HB1 <> HB2 during an EM or MD started
from a topology generated this way). This depends on the definition of the impropers.
I had a quick look at the OPLS ff (the only one so far in gmx that treats the involved atoms explicitly) and
couldn't find impropers for these hydrogens, so I assumed that gromacs is happy either way.

If not, then I don't think it can be resolved simply by renaming atoms in xlateat.dat anymore,
since then you'd easily end up with duplicate atom names....

So I guess the xlateat.dat could provide a reasonable workaround, but for the long term it
would of course be better to have native pdb2gmx support for IUPAC nomenclature input
(or even output?)



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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