AMBER Archive (2003)

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

From: Jiten (jiten_at_postech.ac.kr)
Date: Sun Dec 07 2003 - 22:17:53 CST

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
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