AMBER Archive (2008)

Subject: Re: AMBER: Protein rotating out of box

From: David A. Case (case_at_scripps.edu)
Date: Tue Apr 08 2008 - 20:54:29 CDT

On Wed, Apr 02, 2008, Lars Skjærven wrote:
>
> By the way, sleap does not like the closeness parameter:

Just a note that we haven't forgotten about this, and will get it resolved
soon (promises, promises....)

Thanks for the report.

The original problem (that the solute stays outside the box) was looked at a
bit by Tom Cheatham, but he may not have used a big enough solute.(?)

> > When I reduce the size of the same protein by 50%, it solvates as expected.

Understood. As soon as some people recover from getting Amber10 out the door,
we will try to track this down.

...regards...dave

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