AMBER Archive (2002)

Subject: Re: bad protein structure

From: Guanglei Cui (cuigl_at_morita.chem.sunysb.edu)
Date: Tue Dec 10 2002 - 23:07:20 CST

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