The files in this directory contain contributed parameters for NADH
and NAD+ prepared for use in AMBER by Ross Walker
(http://www.rosswalker.co.uk).

The charges were derived from RESP fits to NADH and NAD+ and are suitable
for use with the FF94 and FF99 force fields. The parameters were adapted
for use in AMBER from the CHARMM parameters of Pavelites et al. These
parameters have been tested using a linear response approach to relaxation
dynamics for calculating optical spectra of proteins and have been found
to reproduce the reorganization energy of LADH+NADH to within 13 % of
experiment.

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

1) Walker, R.C, de Souza, M.M., Mercer, I.P., Gould, I.R., Klug, D.R.,
J. Phys. Chem. B., 2002, 106(44), 11658-11665

2) Pavelites, J.J., Gao, J.L., Bash, P.A., Mackerell, A.D.,
J. Comput. Chem. 1997, 18, 221

The files in this directory are as follows:

NADH.lib   leap library file of NADH with RESP calculated charges
           (e.g. load in xleap with: loadoff NADH.lib)
           Unit name is NAD (e.g edit NAD)

NAD+.lib   leap library file of NAD+ with RESP calculated charges.
           Unit name is NDP (e.g edit NDP)

frcmod.NADH Force field parameters for NADH.
            Adapted from the Pavelites et al. paper for Charmm NICH
            parameters converted to AMBER using the NICH parameters
            of Pavelites et al. and the default AMBER parameters for
            the sugar and ribose sections of NADH.

frcmod.NAD+ Force field parameters for NAD+.
            Adapted in same method as above. 

NADH_vac.prmtop
NADH_vac.prmcrd
NAD+_vac.prmtop
NAD+_vac.prmcrd  (Amber FF99 topology and coordinate files
                  for NADH and NAD+ in vacuum)

NADH_2xNa+_8A_Oct_TIP3P.prmtop
NADH_2xNa+_8A_Oct_TIP3P.prmcrd (Amber FF99 topology and coordinate
                                files for NADH, solvated in a truncated
                                octahedral box of TIP3P water with an 8
                                angstrom buffer space and then charge
                                neutralized with the addition of 2 sodium
                                ions)

NAD+_2xNa+_8A_Oct_TIP3P.prmtop
NAD+_2xNa+_8A_Oct_TIP3P.prmcrd (Amber FF99 topology and coordinate
                                files for NAD+, solvated in a truncated
                                octahedral box of TIP3P water with an 8
                                angstrom buffer space and then charge
                                neutralized with the addition of 1 sodium
                                ion)

leap_NADH_prmtop.log
leap_NAD+_prmtop.log          (xleap log files for the creation of the
                               prmtop and prmcrd files described above)

More details on the use and testing of these parameters are available
in the PhD thesis of Ross Walker - see 
http://www.rosswalker.co.uk/files/Ross_Walker_Thesis_Final.pdf

Any problems / comments please contact Ross Walker
(amber_params@rosswalker.co.uk)


