How did you generate the pdb, and what program did you view it in?
One possibility is that there is a format incompatibility.
Bill
-------- Original message --------
From: Changqing Yan <ycqchemical.gmail.com>
Date:
To: amber.ambermd.org
Subject: [AMBER] Amber 11 Installment problem
Hi everyone,
I have completed installment of Amber 11. However, when I run a
minimization of a protein, the pdb structure from the last trajectory of
minimization seems creepy. Some atoms in the structure are very close to
each other. So when you look at it, it seems there are many small clusters
in one protein structure. Does anyone else encounter this problem? What is
the problem and how to fix that? Thx.
Rgds,
C.Q.yAN
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Received on Wed Feb 20 2013 - 20:00:02 PST
