AMBER Archive (2008)

Subject: Re: AMBER: regarding :scee

From: jani sahil (genomejani_at_gmail.com)
Date: Wed Jan 23 2008 - 22:37:48 CST

Thank you for reply.

On Jan 23, 2008 10:15 PM, David A. Case <case_at_scripps.edu> wrote:

> 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.
>
> ...dac
>
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