AMBER Archive (2006)

Subject: AMBER: MM_PBSA : Question about Stability?

From: Guillaume Bollot (Guillaume.Bollot_at_chiorg.unige.ch)
Date: Wed Aug 16 2006 - 02:00:15 CDT

Dear Amber Community,
I have a macromolecule which contain 32 lysines. I changed manually the
protonation state of the lysines (ex: 50% protonated lysine and 50% neutral
lysines). I already performed molecular dynamic in vacuo for each
arrangement (100%LYN; 25%LYN-75%LYS; etc...). After that, I would like to
know the relative stability for each arrangement with MM_PBSA.PL. My
questions are :

1- Could I use GBTOT in mm_pbsa log file to know the stability?
2- GBTOT represent the Absolute Free Energy?
3- Is my methodology correct?

Thank you very much in advance.

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

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