From: Daniel Moore (
Date: Fri Jun 12 2015 - 04:54:02 CDT


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.

Perhaps there is a simpler method.

Again, I would really appreciate any input on this.


Daniel Moore