VMD-L Mailing List
From: Daniel Moore (dmoore33_at_qub.ac.uk)
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 v184.108.40.206.
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.