AMBER Archive (2005)

Subject: Re: AMBER: NOE constraints

From: David A. Case (case_at_scripps.edu)
Date: Tue May 03 2005 - 15:25:44 CDT


On Tue, May 03, 2005, Hui-Hsu Tsai wrote:
>
> Does NOE constraint in Amber count for the periodic boundary condition?
> For example, if NOE constraints are applied for inter-strand distances
> between two short peptides, once one of the peptide leaves the box and
> enter the box from other side, will this condition cause the problem in
> NOE calculations?

This should not cause any problems, as long as the starting reasonably
satisfies the constraints. Just be sure to set iwrap=0 when running sander
(to prevent any molecule from being translated across the unit cell).

...good luck...dac

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