AMBER Archive (2003)

Subject: Re: AMBER: NAD+ and NADH amber parameters

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Mon Dec 08 2003 - 00:22:56 CST

Dear Jiten,

If you look at this paper (1) I derive a set of RESP charges for NADH for
use with the Amber force field and then go on to show that simulations using
these charges along with the parameters of Pavelites et al (2) successfully
reproduce the equilibrium fluctuations of NADH within the LADH protein
matrix.

(1) Walker, R.C., de Souza, M.M., Mercer, I.P., Gould, I.R., Klug, D.R. J.
Phys. Chem. B., 2002, 106(44) pp11658-11665

(2) Pavelites, J.J., Gao, Bash, P.A., Mackerell Jr, A.D., J., J. Comp.
Chem., 1997, 18, p221-239

I hope this helps
All the best
Ross

/\
\/
|\oss Walker

| Department of Molecular Biology TPC15 |
| The Scripps Research Institute |
| Tel:- +1 858 784 8889 |
| EMail:- ross_at_rosswalker.co.uk |
| http://www.rosswalker.co.uk/ | PGP Key available on request |

> -----Original Message-----
> From: owner-amber_at_scripps.edu
> [mailto:owner-amber_at_scripps.edu] On Behalf Of Jiten
> Sent: 07 December 2003 20:18
> To: amber_at_scripps.edu
> Subject: Re: AMBER: NAD+ and NADH amber parameters
>
> I am wondering if anybody has developed newer parameters of NAD+/NADH
> specially the partail charges of the atoms. The NAD+/NADH
> parameters in
> http://pharmacy.man.ac.uk/amber/ seems to be old, because
> when I compare the
> adenine partail charges of the NAD+ with that of DA/DA3/DA5 in the new
> parameter in all_nucleic02.lib of amber7 - they are quite different.
>
> I wish to develop new partial charges of NAD+/NADH taking the partial
> charges from DA/DA3/DA3(or doing a fresh RESP calculations
> for the adenine
> ribose group ) and drriving the partial charges for
> pyrophosphate-nicotinamide ( and reduced form) using RESP.
>
> I am not sure what level of calculations has been used for
> deriving the
> DA/DA3/DA5 - so I am bit confused what level of ab-initio
> calculation should
> be used for the pyrophosphate-nicotinamide RESP calculations.
>
> Could anyone suggest me the appropriate level of ab-initio
> calculations to
> be conducted for this system.
>
> Or is it still okay - if I continue to use the comibination of new
> parameters for protiens and old parameters for NAD+/NADH.
>
> Thanking you in advance.
>
> Regards,
>
> Jiten
>
> ----- Original Message -----
> From: "David A. Case" <case_at_scripps.edu>
> To: <amber_at_scripps.edu>
> Sent: Tuesday, December 02, 2003 1:35 AM
> Subject: Re: AMBER: NAD+ and NADH amber parameters
>
>
> > On Mon, Dec 01, 2003, Jiten wrote:
> > >
> > > Does anybody tell me where could I get the NAD+ and NADH
> parameters.
> > >
> >
> > Check the "contributed parameters" page (accessible from
> > http://amber.scripps.edu):
> >
> > http://pharmacy.man.ac.uk/amber/
> >
> > These are kind of old, but might help you get started.
> >
> > ..hope this helps...dac
> >
> > --
> >
> > ==================================================================
> > David A. Case | e-mail: case_at_scripps.edu
> > Dept. of Molecular Biology, TPC15 | fax: +1-858-784-8896
> > The Scripps Research Institute | phone: +1-858-784-9768
> > 10550 N. Torrey Pines Rd. | home page:
> > La Jolla CA 92037 USA | http://www.scripps.edu/case
> > ==================================================================
> >
> --------------------------------------------------------------
> ---------
> > The AMBER Mail Reflector
> > To post, send mail to amber_at_scripps.edu
> > To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu
> >
> >
>
>
> --------------------------------------------------------------
> ---------
> The AMBER Mail Reflector
> To post, send mail to amber_at_scripps.edu
> To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu
>

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu