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.
Cheers, Tsjerk On Mon, Jun 30, 2008 at 9:14 PM, Joaquim Rui Rodrigues <[EMAIL PROTECTED]> 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) > > _______________________________________________ > gmx-users mailing list [email protected] > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- 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 _______________________________________________ gmx-users mailing list [email protected] http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
