AMBER Archive (2009)

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

From: Thomas Cheatham (
Date: Wed May 27 2009 - 19:35:30 CDT

> 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

Usually in my experience this means a mismatch between the prmtop and
coordinates; when the coordinates were stripped, was "nobox" specified?
Are you sure that the prmtop and coords match? You can look in vmd or
chimera movies; if there is a mismatch the first frame will look OK and
then jump to the long bonded wierdness.

> 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

Probably need the "nobox" option on the trajout of ptraj.


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