Re: calculate interaction energies for a system with amber forcefield

From: Peter Freddolino (
Date: Sun Sep 02 2007 - 17:18:22 CDT

Hi Rima,
namdenergy should work with amber files as of vmd 1.8.6. Please let me
know if you have problems with it.

Rima Chaudhuri wrote:
> Hi,
> I ran a MD of a protein ligand complex, using amber force-field. I
> want to calculate interaction energies between the protein and the
> ligand (vdw, electrostatic) etc. Unfortunately, the 'NAMD Energy'
> module in VMD1.8.5 does not let me do it, it complains that I am
> lacking a psf file (since I have a prmtop file from Amber). Is there a
> way/ modified script that will allow me to calculate the interaction
> energy for my case?
> Thanks,
> Rima
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