AMBER Archive (2009)

Subject: [AMBER] problem with MM-PBSA

From: Maryam Hamzehee (
Date: Sat May 23 2009 - 23:48:05 CDT

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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