AMBER Archive (2007)

Subject: Re: AMBER: How to change the force field equation in amber by programming...

From: David A. Case (case_at_scripps.edu)
Date: Fri Jan 05 2007 - 15:34:41 CST

On Sat, Jan 06, 2007, Gobind Singh Bisht wrote:

> I am interested in changing
> the functional form of the force field equation in amber, as in add or
> remove some terms from the eqn. I know that i have to do some programming
> and i'm willing to do that, but i would be very grateful if someone could
> guide me abt how shld i got abt it. Which source file contains the code for
> the eqn? And at what all levels i'll have to make the changes?

This depends on what sorts of terms you want to change. The
bond,angle,dihedral terms are in ene.f. Electrostatics and Lennard-Jones
terms are scattered in many places (LJ are collected in short_ene.f).
Generalized Born terms are in egb.f. But be prepared for work: you might
want to consider something like Tinker, which was explicitly designed to
provide a platform for the sort of changes you seem to have in mind.

...regards...dac

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