AMBER Archive (2002)

Subject: Re: carnal output trajectory

From: Bill Ross (photoriot_at_yahoo.com)
Date: Wed Oct 30 2002 - 10:37:00 CST

> The program gives an error message that tells me
> that the BOX option does not work with fit.

This was because trajectories with solvent boxes
present a problem when fitting: rotating the system
to fit some residues will cause solvent molecules to
rotate out of the box. Also the system is translated
to the origin, which in amber is the fixed corner
of the box.

However since molecules can fall outside of box
anyway, this concern was misplaced.

> Does anyone have any suggestions about this??

Remove the restriction in the code.. I would also
consider translating the system to the center of the
box.

Bill Ross