You could combine all the coordinate frames for each cluster into their own
"trajectory" using ptraj and run each of those trajectories through
MMPBSA.py.
I hope that helps.
-Bill
On Fri, Jul 29, 2011 at 9:21 AM, George Tzotzos <gtzotzos.me.com> wrote:
> I've conducted a 16ns MD production simulation of a protein-ligand complex.
> I've obtained the delta G energy of the complex using MMPBSA.py. I've also
> obtained clusters of coordinate frames from the trajectory.
>
> My question is whether there's a way of obtaining the delta Gs of these
> clusters.
>
> Thanks in advance for any advice
>
> George
>
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--
Bill Miller III
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-6715
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Received on Fri Jul 29 2011 - 07:00:03 PDT
