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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Received on Tue Aug 23 2011 - 06:30:03 PDT
