AMBER Archive (2006)

Subject: Re: AMBER: energy data for limited part of system

From: David A. Case (case_at_scripps.edu)
Date: Sun Sep 17 2006 - 18:56:23 CDT

On Wed, Sep 13, 2006, Tanya Johannsen wrote:
>
> I would like to record energy data for a limited part
> of the system during minimization and molecular
> dynamics runs (in addition to calculating the energy
> of the entire system). My system has about 2500
> protein residues plus a lot of explicit water; I want
> the energy of a specific chain of about 400 residues
> within that system. Is there any way that it is
> possible to do this in AMBER?
>

The main types of Amber simulations (PME and GB) involve energies that are not
pair-wise decomposable, so the notion of the energy of a particlar part of the
system is not well-defined. You could try mm-pbsa, defining the 400 residue
chain as a "ligand", and the rest as the "receptor". Depending on what you
need, this may help out.

...good luck...dac

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