AMBER Archive (2008)

Subject: Re: AMBER: who can give a sample input file regarding the energy decomposition with sander?

From: David A. Case (case_at_biomaps.rutgers.edu)
Date: Mon Sep 08 2008 - 16:31:50 CDT

On Mon, Sep 08, 2008, Yongmei Pan wrote:
>
> I'm trying to calculate the binding energy between ligand and protein with
> polarizable potentials leaprc.ff02(EP). I know the sander output file can
> print out the interaction between individual residues with idecomp=1, but
> just don't know the format on how to define the residues. Can anyone give me
> a sample file? Thanks!

I don't think any of the standard decomposition routines will work with
polarizable potentials: these are "non-additive", and you can't just
break the energies down into pieces.

I think you will need to carry out three calculations: complex,
ligand, and protein, then manually do the total energy subtraction.
There is no unambigous way to break this down into residue
contributions.

Also note: ff02 and especially ff02EP are not well tested. If you do use
ff02, I recommend you load in the leaprc.ff02pol.r1 modifications (and read
the associated publications). Work on polarizable force fields has come
a long way in the last six years, so don't expect too much from this
model.

...dac
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