Dear Amber experts,
I’m 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 I’d 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 that’s 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 empirical… But I’m not so sure about it in Amber as it’s for entropy calculation at the all-atom level.
2 My system is a bit too large and it probably won’t be affordable to compute the normal mode entropy for the entire system… 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.
Bests,
Amy
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Received on Fri Sep 16 2022 - 06:30:03 PDT
