Contributors

Comments

Force-field parameters for NADH, NAD+, NADP+ and NADPH are
taken from the amber adenine and ribose input (residue RA5 in
all_nuc94.in) with the nicotinamide and pyrophosphate moieties added using
quantum chemically calculated charges with the RESP method and RHF/6-31G*
calculations. They are fully compatible to Amber 4.1 and the Cornell et
al. 1995 force field, but they can also be used with later verions of
Amber. For NADPX, the charge of the 2'-phosphate group is not clear
(pKa=6-7) so two different molecules were developed, one with a total
charge of -2 and the other with a total charge of -3.

It should be noted that Charmm22 force field parameters for NAD+ and
NADH were recently published: Paverlites et al, J. Comput. Chem. 18(97)
221-239. Their force constants and equilibrium values are probably more
accurate, whereas our charges are better and more compatible with Amber.

Please, do not hesitate to contact me if you have any questions:
Ulf.Ryde@teokem.lu.se

If you use these parameters please cite the following two papers:

NADH:  U. Ryde, Proteins, Struct. Funct. Genet. 21(1995)40-50
       "Molecular dynamic simulations of alcohol dehydrogenase
        with varying coordination number of the catalytic zinc ion"
NAD+:  U. Ryde, Prot. Sci. 4(1995)1124-1132
       "On the role of Glu-68 in alcohol dehydrogenase"
NADP+: N. Holmberg, U. Ryde, and L. Bulow, Prot. Engin., 12 (1999)
851-856.
       "Redesign of the coenzyme specificity in L-lactate dehydrogenase
        from Bacillus stearothermophilus using site-directed mutagenesis
        and media engineering."
Update:U. Ryde, "Force field parameters for NAD and NADP", manuscript
        in preparation.