[AMBER] Missing amino acids preparation for long-term simulation

From: jacky zhao <jackyzhao010.gmail.com>
Date: Fri, 01 Sep 2017 16:31:43 +0000

Hi everyone
  Recently, I have performed protein-protein complex MD simulation with
more than 1µs. Although the missing amino acids were not located at the
binding interface, is it nessesary to rebuild missing amino acids for
long-term MD simulation?
  Have some suggestions for missing amino acids rebuild? I used Prime
module in the Schrodinger suite to rebuild missing amino acids, then save
the file as PDB and performed MD by amber.

Thank you for taking your time.


Jacky

-- 
Lei Zhao, Ph.D.
International Joint Cancer Institute of the Second Military Medical
University
National Engineering Research Center for Antibody Medicine
New Library Building 11th floor,800 Xiang Yin Road
Shanghai 200433
P.R.China
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Received on Fri Sep 01 2017 - 10:00:03 PDT