I have never tried running MMPBSA.py with ptraj-generated cluster
trajectories, but I don't see any reason that won't work.
-Bill
On Fri, Jul 29, 2011 at 10:58 AM, George Tzotzos <gtzotzos.me.com> wrote:
> 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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>
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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 - 08:30:03 PDT
