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

From: Gobind Singh Bisht <>
Date: Sun, 7 Jan 2007 19:36:06 +0530

Hi david,
             thanx for your reply.. *I would like to know what suite of
programs sander uses to run MD. That would include programs for energy
calculations and trajectory calculations*. Isn't thr any manual which would
give an outline of what each program in the src code does, something like a
programmer's manual. That would be really helpful.
thanx a lot
with regards

On 1/6/07, David A. Case <> wrote:
> 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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Received on Wed Jan 10 2007 - 06:07:05 PST
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