10-15 ns seems like a very short time to use for MMPBSA, IMHO.
If it is as flexible as you're saying, you'll probably want more sampling
to account for different conformations it can occupy across time to get a
good average.
Best,
Kenneth
On Wednesday, May 11, 2016, Mary Varughese <maryvj1985.gmail.com> wrote:
> 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
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Ask yourselves, all of you, what power would hell have if those imprisoned
here could not dream of heaven?
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed May 11 2016 - 05:00:03 PDT
