[gmx-users] pdb2gmx and hydrogen nomenclature

[Bert de Groot]

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?)

cheers,

Bert

____________________________________________________________________________
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
http://www.mpibpc.gwdg.de/abteilungen/073
____________________________________________________________________________