[gmx-users] Topologies and charges for large organic ligands

Ran Friedman r.friedman at bioc.uzh.ch
Wed Apr 15 17:26:50 CEST 2009


The answer is (or should be) in:

   Author = {Oostenbrink, C. and Villa, A. and Mark, A. E. and Van
Gunsteren, W. F.},
   Title = {A biomolecular force field based on the free enthalpy of
hydration and solvation: The GROMOS force-field parameter sets 53A5 and
   Journal = {J. Comput. Chem.},
   Volume = {25},
   Pages = {1656-1676},
   Year = {2004} }

Good luck,

Dean Cuebas wrote:
> Dear colleagues,
> In 53a6, the topology and charges for (NAD+) nicotinamide adenine
> dinucleotide are present (listed as NADH, 52 atoms) in polar hydrogen form
> (without aromatic hydrogens).
> Is there anyone who can tell me how such a molecule was charge group
> parameterized? (with sufficient certainty to be included in the ff).
> Please understand that I am not asking how to use the NAD topology that's
> provided.
> I've read that prodrg is a "good starting point" for parametrizing a ligand,
> but what is the path to "improving" such a ligand from that starting point?
> (the provided topology for NAD+ in the ff shows 17 charge groups with
> an average of 3-4 atoms per charge group, whereas prodrg gives only 11
> charge groups.)
> I'm not concerned about angles and dihedrals, since that is pretty
> painless... it's the charge groups that I'm concerned about.
> In a nutshell, who and how was the final NAD+ parameters decided upon??
> Does anyone know this??  Is it simply chemical intuition of estimated
> charges that reproduce the dipole of the moiety (like an adenine ring), and
> the charge groups contain the minimum number of atoms that reflect this?
> Is there an algorithm to generating "improved" charge groups?
> I ask these questions because my ligands are large organics... MW 800 and
> greater.
> Thanks for any and all help in this regard.

More information about the gromacs.org_gmx-users mailing list