[AMBER] salt concentration in the production run and MMPBSA

From: Prasanth G, Research Scholar <prasanthghanta.sssihl.edu.in>
Date: Wed, 10 Jul 2019 22:20:55 +0530

Dear all,
Q1: I would like to know, if it is essential to carry out the production
run with a salt concentration (eg: 0.15M or 0.1M) if we want to carry out
MMPBSA analysis (post production)?
Q2: another question is to do with choice of frames and the number needed
for analysis. As i understand, we should pick the frames from the region of
the simulation post convergence (as observed from rmsd of protein).
Regarding number of frames, since post convergence, the protein is more or
less in a similar configuration, the number of frames should not be an
But then, since this analysis is to do with both protein and ligand, may be
we should consider the region of simulation where the ligand seems to have
a stable rmsd?

Thank you in advance.

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Received on Wed Jul 10 2019 - 10:00:04 PDT
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