AMBER Archive (2009)

Subject: RE: [AMBER] problem with MM-PBSA

From: Ray Luo (
Date: Tue May 26 2009 - 11:44:14 CDT


Let's make it more informative for people on this list to help you. Do you
have the same problem when running an explicit solvent MD for one of the
molecules in the complex?

All the best,

Ray Luo, Ph.D.
Associate Professor
Dept Molecular Biology & Biochemistry
University of California, Irvine, CA 92697
USPS: PO Box 3900 Email:
Phones: (949) 824-9528, 9562

-----Original Message-----
From: [] On Behalf
Of Maryam Hamzehee
Sent: Monday, May 25, 2009 9:52 PM
To: amber list
Subject: [AMBER] problem with MM-PBSA

Dear List,
I am doing a simulation to calculate binding energy for a complex almost in
a similar way to that mentioned for “Tutorial A3: MM-PBSA”. When I
visualized the trajectories, I realized that atoms are moving too far making
bad bond lengths and angles. Gradually, some of the residues (atom by atom)
move to new locations still keeping their links (very long bonds). I noticed
that the same thing happens with the results of calculations for the
tutorial A3. I was wondering why the bond lengths and angles, as well as the
positions of the residues are so unrealistic during the MD. I have
previously used Amber to do MD simulation of small peptides in vacuum with
no problem. In those simulations, the trajectories were okay and the
peptides smoothly explore different, but feasible conformations.

I will appreciate it if any one can let me know why I get such a strange
behavior in my MD simulation for binding energy calculations.
All the best,

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