Thank you Bill,
ptraj cluster generates cluster trajectories. I assume that I should run these trajectories through MMPBSA.py using new prmtop files for protein, ligand and complex
Cheers
George
On Jul 29, 2011, at 3:56 PM, Bill Miller III wrote:
> 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 - 08:00:07 PDT
