On Thu, Mar 28, 2013 at 2:36 AM, dbaogen <dbaogen.gmail.com> wrote:
> Dear all,
>
> In the AmberTools manual, it provides some options to carry
> out QM/MM-GBSA method using MMPBSA.py script. But the corresponding parts
> in the PBSA method is not included. Dose it mean that QM/MM-PBSA method can
> not carry out in Amber software?
Correct.
If not, how could I implement this method. Thank you in advance!
>
If it was this simple, someone would have probably already done it ;). If
you look at several of the introductory computational chemistry books
(e.g., Cramer or Leach), they provide the basic ideas for how you could
modify the QM hamiltonian to include the polarizing effects from a PB
model. If I recall correctly, several of the existing QM solvation methods
(e.g., PCM and COSMO), originate from these ideas, but it is still an area
of active research.
Short answer: I don't know, and I doubt anybody could explain it
satisfactorily in an email. If it's very important to your project, I
suggest familiarizing yourself with QM solvation methods in the literature
and preparing yourself for a time-consuming endeavor (or perhaps looking
for another piece of software that does it, though I don't know of any).
HTH,
Jason
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Thu Mar 28 2013 - 06:00:02 PDT
