[AMBER] Unexpected prochirality change from si to re during MD simulation

From: Michael Shokhen <michael.shokhen.biu.ac.il>
Date: Thu, 9 Jul 2015 11:28:59 +0300

Dear Amber List members,

I am doing MD simulation at 310K by amber 14 of Michaelis complex (MC) of
with peptide substrate applying the ff14sb force field and tip3p water in
periodic box.

Enzyme nucleophile like Ser or Cys can attack carbonyl carbon atom of
amide group from si- or re-site.

The initial prochirality of the carbonyl carbon atom in the amide group
of peptide substrate was of si-type. During 10 ns simulation the
remains as si-type.
Examining again the MC structure after 17 ns I have observed unexpected
change of substrate prochirality from si to re.

What is the reason of such abnormal structural isomerization of peptide
amide group during amber MD simulation, and what commands should I
add to the md.in script file in order to avoid irrelevant amide group

Thank you,


Michael Shokhen, PhD
Associate Professor
Department of Chemistry
Bar Ilan University,
Ramat Gan, 52900
email: michael.shokhen.gmail.com
email: shokhen.mail.biu.ac.il
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Received on Thu Jul 09 2015 - 01:30:03 PDT
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