[AMBER] Use of semiempirical QM/MM method in Amber to obtain free energy profile of a reaction

From: Dmitry Nilov <nilovdm.gmail.com>
Date: Tue, 22 Feb 2011 19:11:29 +0300

Dear Amber community!
Recently I have calculated free energy barrier of an enzymatic
reaction using multiple steered RM1/MM MD method in Amber 10 (with
subsequent Jarzynski exponential averaging) and the results are in
very good agreement with experimental rate constant. However I cannot
be quite satisfied since "ab initio" people around do not trust in
suitability of semiempirical methods for calculation of reaction free
energy profile.
Could you be so kind to give me an advice or a link on appropriate
paper to clear up my confusion!

Dmitry Nilov,
Faculty of Bioengineering and Bioinformatics,
Lomonosov Moscow State University
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Received on Tue Feb 22 2011 - 08:30:04 PST
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