From: Axel Kohlmeyer (
Date: Fri Jun 12 2015 - 05:57:23 CDT

On Fri, Jun 12, 2015 at 5:54 AM, Daniel Moore <> wrote:
> Hello,
> I would really appreciate if anyone can provide some input to the following
> question:
> I have several MD simulations created with Desmond source v3.6.1.1.
> Is there anyway I can calculate the non bonded interaction energy between
> two residues?
> The simulations were setup using the OPLS_2005 forcefield and I only have
> the .cms files and .dtr files associated with each simulation. Initially the
> files were prepared in maestro although I have just been informed that there
> are compatability issues between desmond source and desmond/maestro paired
> version. Simply put this means I cannot analyise my trajectorys with
> maestro.
> I have looked at NAMDenergy althogh I need to have a psf file. I have tried
> creating this although I have been faced with a plethora of problems.

you need more than just a .psf file. you also need a complete set of
topology and parameter files that represent the same OPLS_2005 force
field. otherwise you'd bee computing the energies based on CHARMM.

> Perhaps there is a simpler method.

doubt it. what you want to compute requires to re-do the force/energy
computations with selected interactions turned off. that requires
using some MD code that can read a trajectory file instead of doing
time integration and then uses a regular force field parameter set.


> Again, I would really appreciate any input on this.
> Best,
> Daniel Moore

Dr. Axel Kohlmeyer
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.