[AMBER] Normal mode analysis for entropy calculation in MM/GBSA

From: He, Amy via AMBER <amber.ambermd.org>
Date: Fri, 16 Sep 2022 13:04:36 +0000

Dear Amber experts,

Iím learning the normal mode analysis technique in Amber for entropy calculation in MM/GBSA. I have just a few very general questions as a beginner, and Iíd really appreciate your help:

1 Could you direct me to a documentation or literature that talks about the formulation of the normal mode analysis in Amber? Specifically, what is the force constant matrix or the harmonic potential thatís being used in the normal mode analysis?
I have a little bit experience with normal mode analysis on extremely big and coarse-grained systems, where the force constants are just empiricalÖ But Iím not so sure about it in Amber as itís for entropy calculation at the all-atom level.

2 My system is a bit too large and it probably wonít be affordable to compute the normal mode entropy for the entire systemÖ I have read about using normal mode analysis on a truncated protein-ligand system to calculate the relative binding entropy. I was wondering, if we need to break the protein into pieces, how would that impact the calculation of the modes?

3 Do we need to use a trajectory (multiple snapshots), or can it be just one snapshot?

Many thanks to you for your time and kind advice.


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Received on Fri Sep 16 2022 - 06:30:03 PDT
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