Hi, I have a homology based protein. I want to
minimize it first. However the common minimization
(even freeze part of or the whole protein) fails each
time because of the bad energetics. I wonder if there
is a way to minimize more effectively. Thanks.
Eric
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From cuigl_at_morita.chem.sunysb.edu 11 Dec 2002 00:07:20 -0500
Message-id: <1039583240.1701.8.camel.dhcp-27-30>
Date: 11 Dec 2002 00:07:20 -0500
From: Guanglei Cui <cuigl_at_morita.chem.sunysb.edu>
To: AMBER list <amber.heimdal.compchem.ucsf.edu>
Subject: Re: bad protein structure
In-Reply-to: <20021211013052.65352.qmail.web13403.mail.yahoo.com>
Hi,
You might want to visually check your structure and see if there's
any clash between atoms. If there's serious overlap, removing it by hand
might be easier. Usually, the minimization output can tell you the
offending part of the molecule.
On Tue, 2002-12-10 at 20:30, eric hu wrote:
> Hi, I have a homology based protein. I want to
> minimize it first. However the common minimization
> (even freeze part of or the whole protein) fails each
> time because of the bad energetics. I wonder if there
> is a way to minimize more effectively. Thanks.
>
> Eric
>
> __________________________________________________
> Do you Yahoo!?
> Yahoo! Mail Plus - Powerful. Affordable. Sign up now.
> http://mailplus.yahoo.com
--
Guanglei Cui <cuigl_at_morita.chem.sunysb.edu>
SUNY at Stony Brook
Received on Tue Dec 10 2002 - 17:30:52 PST
