Re: [AMBER] Amber 11 Installment problem

From: Bill Ross <ross.cgl.ucsf.edu>
Date: Wed, 20 Feb 2013 19:36:17 -0800

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
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Feb 20 2013 - 20:00:02 PST
Custom Search