sir
I mean it needs long time to converge and has to run separate trajectories.
is it possible to finalize the calculation with 20 or 30 ns?
i tried a 10 ns separate trajectory method as well as 15ns single
trajectory. it fails.
The ligand do bind throughout the simulation time but delta PB and TdeltaS
as seen in MMPBSA calculation varies significantly especially TdeltaS
varies from negative to positive values. (average of such varying values is
not reliable isnt?)
The ligand is very much flexible with CH3-CH3-CH3 chain. The ligand in
individual structure is different from bound structure.
Could you please suggest a reliable approach in such a case?
Thanking you
On Wed, May 11, 2016 at 3:55 PM, Jason Swails <jason.swails.gmail.com>
wrote:
>
>
> > On May 11, 2016, at 12:01 AM, Mary Varughese <maryvj1985.gmail.com>
> wrote:
> >
> > Sir,
> >
> > In the case of a flexible ligand, MMPBSA single trajectory is not ideal
> and
> > multiple trajectory is difficult. Is there any other method you would
> > suggest in such a case.
>
> What is difficult about multiple trajectories?
>
> >
> > thanking you
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Received on Wed May 11 2016 - 04:30:03 PDT
