From: Jason Swails <>
Date: Thu, 21 May 2015 08:37:53 -0400

On Thu, May 21, 2015 at 1:46 AM, Ramin Ekhteiari <>

> Hi dears,
> I have generated around 10,000 conformations for a complex
> (bound-receptor) using MC simulation and now I attempt to perform MM-PBSA
> calculation to estimate binding-free energy of these conformations. Each of
> the conformations is in .PDB format, so I would be grateful if you advise
> me on how to carry this process. The big question is that whether I should
> convert them to trajectory format or not. If so, how can I do it.

‚ÄčNo, you do not have to convert them to a trajectory. If you feed them all
to, then they will all be read, regardless of their format (so
long as cpptraj supports that file type): -O -i -y *.pdb ... and so on


Jason M. Swails
Rutgers University
Postdoctoral Researcher
AMBER mailing list
Received on Thu May 21 2015 - 06:00:03 PDT
Custom Search