AMBER: Question about free energy with mm_pbsa

From: William Wei <>
Date: Thu, 31 Aug 2006 14:50:11 -0400

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

Thanks in advance,

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Received on Sun Sep 03 2006 - 06:07:15 PDT
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