AMBER Archive (2009)

Subject: Re: [AMBER] ff03 parameter for GDP and GTP

From: FyD (fyd_at_q4md-forcefieldtools.org)
Date: Sat Oct 10 2009 - 00:52:27 CDT

Dr Case,

> Carlos: not sure if this is what you are looking for, or if you already know
> of it:
> Meagher KL, Redman LT, Carlson HA
> Journal of Computational Chemistry 2003,24,1016

I do not think this is the only paper available for such a molecule in
this field... & for each structure one can find various charge sets.

For instance, the comparison of
http://personalpages.manchester.ac.uk/staff/Richard.Bryce/amber/cof/NAD+.lib
  &
http://personalpages.manchester.ac.uk/staff/Richard.Bryce/amber/cof/nad+.prep
is quite informative - if one is interested in charge values. I do not
think such differences has something to do with ... numerical errors.

This is why we have decided to adopt a global strategy highly similar
to that found in "Cieplak et al. J.Comput.Chem. 1995, 16, 1357" for a
large list of co-factors. The data will be available in R.E.DD.B. with
not only the FF libraries but with all the computational conditions so
that every user will be able to reproduce & even
critize/modify/compare what we have done.

regards, Francois

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