AMBER Archive (2008)

Subject: Re: AMBER: regarding :scee

From: David A. Case (
Date: Wed Jan 23 2008 - 10:45:07 CST

On Wed, Jan 23, 2008, jani sahil wrote:

> I am simulating a aspartic protease a protein.
> When one uses the scee i have no idea in this regard
> can any guide me about using of scee.

Same answer I would give to most such questions: the defaults in Amber are
fairly carefully chosen. If you are uncertain about the meaning of something,
leave it as the default.

In the case of scee, it would be changed from its default only if you are
using *very* old force fields (from the 1980's, which I do not recommend), or
if you are running some verison of the recent GLYCAM force fields. In the
latter case, there will be specific instructions about what to do in the force
field descriptions themselves.


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