AMBER Archive (2009)

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

From: David A. Case (
Date: Tue May 26 2009 - 06:37:31 CDT

On Mon, May 25, 2009, Maryam Hamzehee wrote:

> 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.

You should try to see what is different between the simulations you are doing
now and those you did earlier. Also, please give details of how you decided
that you had bad bond lengths and angles, and exactly which trajectories in
the tutorial appear to have this problem. I don't recognize the symptoms you
are reporting.


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