Subject: Re: CCL:Macromodel_Amber charges

From: "Peter Shenkin" <[email-masked]>
Date: Thu, 10 Nov 1994 18:06:51 -0500

On Nov 8,  9:58pm, <[email-masked]> wrote:
...
> AMBER force field in Macromodel 4.5 gives guanine (also C, T and U) a
> net charge of -0.236.  Does anyone have the same experience with other
> molecules ?
....

Mr. Wang,

The charges you obtained were put into the forcefield directly from
Kollman's 1984 paper.  They are designed for use in the context of
ribo- or deoxyribonucleic acids.  When they are used in this context,
the sugar has a net charge of +0.236, which balances the net charge
of -0.236 on the base.  Thus, these substructures must be used in the
proper context in order for the charges to make sense.

I have to say that I am not completely happy with this situation.  I
think that we should not really have charge substructures in our
force-field file that correspond to neutral species, because this can
lead to  funny side-effects, such as you observe, when not used in the
proper context.

Perhaps we should really have, for example, guanine-ribose and
guanine-deoxyribose in the force-field as substructures.  These
overall substructures would be neutral.  Of course, in this situation,
plain old guanine, with no sugar, would not be matched by a special
substructure, and would not be given high-quality parameters unless
someone went out and derived them from QM calculations.

Certainly, as implied by my discussion above, the parameters given
for guanine are appropriate to guanine only with ribose or deoxyribose
attached, and not to isolated guanine.

We will consider altering the force-field to remove things like guanine,
and put them back in attached to the appropriate sugars.  This will
not give you good parameters if what you really want to model is
isolated guanine, but good parameters for isolated guanine do
not, I beleve, exist in standard AMBER.  If they exist in the
literature, or if someone does a credible job of deriving them,
we'd be happy to add them to MacroModel's AMBER* forcefield.

	-P.

-- 
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*Peter S. Shenkin, Box 768 Havemeyer Hall, Chemistry, Columbia Univ.,*
* New York, NY  10027;     [email-masked];     (212) 854-5143  *
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