The sum of EEL and EGB is about 10K kcal/mol. The STD is ~30 kcal/mol. The
mmpba.mpi is not installed on the cluster I'm on and running a serial
version of PB is just too expensive and might not be that necessary. I
understand that it's not ideal to toss residues out. However for things like
ribosomes, i might have to be practical and make some compromises. Thanks
again.
Victor
On Mon, Oct 3, 2011 at 2:50 PM, Jason Swails <jason.swails.gmail.com> wrote:
> On Mon, Oct 3, 2011 at 3:30 PM, Victor Ma <victordsmagift.gmail.com>
> wrote:
>
> > Thanks Jason. I am working on a highly charged system. When doing MMPBSA,
> I
> > typically get a EEL, EGB of ~ 30-50K kcal/mol for the complex and
> receptor
> > system and a difference of ~1-3K kcal/mol. That gives me a too large
> margin
> > of uncertainty in the free energy calculation. So besides extracting some
> > residues out of the trajectory, do you have any other suggestions? Thanks
> a
> > lot.
> >
>
> What do the standard deviations of the differences come out to be? The
> real
> term I would suggest looking at is the sum of EEL and EGB (since they're
> really just 2 parts of the same calculation). I would also suggest trying
> the PB solvation method (perhaps even using the non-linear equation) as an
> improved level of theory. However, I think that just tossing residues out
> on a whim isn't the best way of going about things.
>
> Others may have other advice.
>
> HTH,
> Jason
>
>
> >
> > Victor
> >
> >
> > On Fri, Sep 30, 2011 at 6:40 PM, Jason Swails <jason.swails.gmail.com
> > >wrote:
> >
> > > On Fri, Sep 30, 2011 at 5:02 PM, Victor Ma <victordsmagift.gmail.com>
> > > wrote:
> > >
> > > > hi all
> > > >
> > > > I have a completed MD trajectory. I'd like to perform binding free
> > energy
> > > > calculation with MMPBSA (python version, ambertool1.5). However, I'd
> > like
> > > > to
> > > > include only residues within a certain range of the ligand. How can I
> > do
> > > > that? Thanks a lot.
> > > >
> > >
> > > You can't automatically with either version of MMPBSA.py. The only way
> > you
> > > can do this is if you strip out every atom/residue that you *don't*
> want
> > > and
> > > create a new topology from that (I wouldn't suggest this method, since
> > > there
> > > will probably be issues arising from converting free-floating residues
> > into
> > > termini, etc.).
> > >
> > > The closest you can really come is one of the decomposition schemes
> (and
> > be
> > > clever about how you add the terms up), but you won't actually save any
> > > time
> > > doing it this way (in fact it will take a lot longer). For entropy,
> > > there's
> > > no way to do this automatically (we may think about implementing Ryde's
> > > approach or something similar later, but that's not on the radar for
> > right
> > > now).
> > >
> > > HTH,
> > > Jason
> > >
> > >
> > > > Victor
> > > > _______________________________________________
> > > > AMBER mailing list
> > > > AMBER.ambermd.org
> > > > http://lists.ambermd.org/mailman/listinfo/amber
> > > >
> > >
> > >
> > >
> > > --
> > > Jason M. Swails
> > > Quantum Theory Project,
> > > University of Florida
> > > Ph.D. Candidate
> > > 352-392-4032
> > > _______________________________________________
> > > 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
> >
>
>
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Candidate
> 352-392-4032
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Mon Oct 03 2011 - 13:30:03 PDT
