Dear Dr. Jason,
Thank you for the clarification and additional inputs.
On Tue, Aug 23, 2011 at 6:58 PM, Jason Swails <jason.swails.gmail.com>wrote:
> On Tue, Aug 23, 2011 at 9:06 AM, vaibhav dixit <vaibhavadixit.gmail.com
> >wrote:
>
> > Dear Dr. Jason and amber users,
> > Thank you very much for this help.
> > I had one more doubt.
> > Are the two versions of MMPBSA (ambertools 1.2 and ambertools 1.5)
> similar
> > and comparable?
> > That is: Can I compare the free energy values that I have calculated
> using
> > a
> > combination of amber10 and MMPBSA.py script installed in ambertools 1.2
> > with
> > the ones that I will get using amber11 and ambertools 1.5?
> > Or is it better to repeat the MMPBSA calculation using latest version to
> > make realistic and meaningful comaprisons of binding free energies for
> > different ligands?
> >
>
> They are comparable, but there have also been a couple changes. The new
> version is a little bit better about centering and imaging the original
> trajectory (if it's from a solvated topology), but due to the limitation in
> ASCII mdcrd precision, you're likely to see some small differences in
> energies just due to this. There have also been significant updates to
> pbsa
> since then, so if you're using the PBE to calculate solvation effects, it's
> likely that you'll have slightly different numbers just due to this. It
> would probably be safer to re-run your simulations using the newer version
> if possible.
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Candidate
> 352-392-4032
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>
--
With regards
Vaibhav A. Dixit
Ph.D. Scholar
Department of Medicinal Chemistry
Natl. Inst. Pharm. Edu. & Res. (NIPER)
Sector 67, Phase X, S.A.S. Nagar (Mohali)
Punjab -160 062 INDIA
Phone (Mobile): +919915214408
E-mail: vaibhavadixit.gmail.com
www.niper.nic.in
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Received on Tue Aug 23 2011 - 07:00:03 PDT
