[gmx-users] Missing H's in NADH topology?

Tsjerk Wassenaar tsjerkw at gmail.com
Tue Jul 1 06:51:01 CEST 2008

Hi Rui,

In the previous version of the gromos force field, the hydrogens on
these groups would be collapsed to the carbons. In the newer force
fields (53*) they are treated explicitly, but I think NADH has not yet
been reparameterized.



On Mon, Jun 30, 2008 at 9:14 PM, Joaquim Rui Rodrigues
<joaquim.rodrigues at estg.ipleiria.pt> wrote:
> Dear all,
> In the .rtp files for the gromos96 forcefield (G43a1, G43a2, G43b1, G45a3, G53a5 and
> G53a6), the aromatic hydrogens that should be bonded to the adenine and nicotinamide
> moieties are missing in NADH. Why is that so? Shouldn't these hydrogens be explicit?
> On the other hand, if I generate a topology with prodrg beta, the aromatic hydrogens are
> added as I would expect...
> Many thanks,
> Rui Rodrigues
> --
> Webmail ESTG de Leiria (http://webmail.estg.ipleiria.pt)
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Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623

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