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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Received on Tue May 03 2005 - 21:53:00 PDT
