Subject: Re: CCL:Force Field question

From: "David A. Case" <[email-masked]>
Date: Wed, 29 Jan 2003 23:01:06 -0800

On Wed, Jan 29, 2003, Javier Cuervo wrote:
> 
> We are thinking in obtain a program for doing energy calculation of
> proteins. We would like to be able of have the energy profile given as a
> "contribution per atom" to the total energy, and this contribution split
> in the differents terms (van Der Walls, electrostatic,H-bond, etc).
> 
> We are considering AMBER as an option but we don't now if this package has
> this feature (or if there is any program that can do what we want).
> 

The concept of a "contribution per atom" is a bit foreign to molecular
mechanics.  It is possible (and sometimes useful) to define such a thing,
but it requires pretty artificial assigning of (say) an angle energy among
the three atoms involved, or a dihedral term among the four atoms involved.
And such a decomposition is even more strained for polarizable force fields,
or for Ewald techniques (where the "reciprocal" energy is not easily expressed
in a pairwise format.)

For classical force fields, Amber allows you to decompose systems into
arbitrary groups, and can perform analyses of interactions among these,
including a "contribution per group" term that sums to the total energy.
In principle, each group could be a single atom, although I suspect it
would be pretty unwieldy to do this for any sizeable molecule.  The program
is really designed more to produce "interaction energies between groups",
rather than "contributions per group".

So, it's probably possible, but not really what the program was designed
for.  Maybe other CCL=ers will have alternate suggestions.

..hope this helps....dac

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David A. Case                     |  e-mail:      [email-masked]
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