Hi, The answer is (or should be) in:
@article{Oostenbrink2004, 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 53A6}, Journal = {J. Comput. Chem.}, Volume = {25}, Pages = {1656-1676}, Year = {2004} } Good luck, Ran. 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. > > _______________________________________________ gmx-users mailing list gmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php