AMBER Archive (2009)

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

From: Bill Ross (ross_at_cgl.ucsf.edu)
Date: Wed May 27 2009 - 19:52:19 CDT

> 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).

This happens when residues cross the edge of the periodic box and
are translated to the other side. If you are running periodic, search
the archive for 'ptraj image'.

Bill

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