[AMBER] Protein-protein interaction energy calculation

From: SATYAJIT KHATUA <satyajitkhatua09.gmail.com>
Date: Sun, 25 Jul 2021 19:03:41 +0530

Dear Users,
                   Recently we are working on some superantigen systems in
collaboration with an experimental group. They asked us to provide the
overall protein-protein interaction energies along with some essential
residue-wise contributions. We know that the MM-PBSA technique deals with
such kinds of problems. However, among the five systems, two have the zinc
metal center through which the crucial segments can interact, and they show
a kind of absurd energy values.
Searching for the suggestions in the AMBER archive, there are instances
where the experts raise concerns over the use of MM-PBSA for the systems
that interact through the metal ions. So, what is the possible way out? Can
you suggest other suitable methods to calculate the interaction energies
(overall as well as residue-wise)? It would be of much help.

With regards,
Satyajit Khatua,
IIT Kharagpur,
Kharagpur - 721302.
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Received on Sun Jul 25 2021 - 07:00:02 PDT
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