AMBER Archive (2006)

Subject: AMBER: Question about free energy with mm_pbsa

From: William Wei (william.wei_at_utoronto.ca)
Date: Thu Aug 31 2006 - 13:50:11 CDT

Hi All,

Question 1: While we use mm-pbsa for calculating the delta G, both GB and
PB do not minimize the complex, receptor and ligand. The complex snapshots
are at a relatively low energy conformations, but those snapshots of
receptor and ligand are at a relatively high energy conformation because the
induced fit. The delta E (orH) from this calculation may be lower than what
they should be! Could anybody point me out if I am wrong.

Question 2: In mm-pbsa NM section, if we use the same number of snapshots
as we used for delta E calculation, it will take too long time to finish the
Nmode calculation. For the continuous snapshots, after minimization, I can
imagine that many snapshots would share the same conformation. So is that
okay if we use fewer snapshots for Nmode calculation, let's say 1 in about
10 snapshots?

Question 3: After the simulation system reached equilibrium, how many
snapshots we should use for delta G calculation? What is the reasonable
period?

Thanks in advance,
William

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