AMBER Archive (2009)

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

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Sat Oct 10 2009 - 06:36:35 CDT

Hi Francois,
that's good news, and I strongly urge you to also publish the parameters in
the peer-reviewed literature so that less experienced users can be confident
about adopting them even if they aren't able to evaluate the conditions
themselves. In my opinion it's very important for the validation aspect of
the any group's parameters to be reviewed independently.It's not so much
about comparing raw numerical values for the parameters like you mention
below, but seeing how well they perform in use.
thanks for this service to the community
carlos

On Sat, Oct 10, 2009 at 1:52 AM, FyD <fyd_at_q4md-forcefieldtools.org> wrote:

> 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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