AMBER: Amber 8.0 MM_PBSA Stability : question about methodology

From: Guillaume Bollot <>
Date: Mon, 17 Jul 2006 14:18:41 +0200

Dear Amber community,
I have a macromolecule which containt 32 LYS and 32 HIS residues (total 64
residues). I want to know the free energy (absolute free energy) when I
change manually the protonation state. I already performed molecular
dynamic in gas phase for 5 protonation states (S1 : total charge 0; S2 :
totale charge +16; S3 : totale charge +32; etc... until S5 : totale charge
+64). I would like to know which protonation state (S1 to S5) is the most
stable with the absolute free energy, is it correct?
First of all, I generated the snapshots form my trajectory file on the last
50ps (10 snapshots) with
To know the mean free energy from these snapshots, I used GB and not PB in
my mm_pbsa input. (is it correct?)
I obtained many energy in the output file and I keep GBTOT, is it correct?

I would like to know if my methodology is correct? And is it possible to do
the same thing with molecular dynamic in the continuum (IGB=2)?
Thank you vera much i advance!

BOLLOT Guillaume
Organic Chemistry Department
University of Geneva
30, quai Ernest-Ansermet
CH-1211 Geneva 4
tel. +41-22 379 6155

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Received on Wed Jul 19 2006 - 06:07:06 PDT
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