Dear Amber List members,
I used amber 14 MD simulation of Michaelis complex (MC) in periodic box with
ff14sb and tip3p.The interatomic distance between reaction centers -
enzyme nucleophile
and substrate electrophile should be around 3A in a non-covalent MC.
The substrate drifts out from the enzyme active site and the mentioned
distance dramatically
increases during MD simulation despite the initial complex was minimized in
reasonable position.
I have observed this phenomenon using other MD software and force fields
when ligand is
a small molecule non-covalent inhibitor. A practical solution is a
restraint of interatomic distance
between reaction centers in MC. Unfortunately I failed to find in Amber
manual and archive
a clear example of the command lines how to set the interatomic distance
restraint
and to add it to the md.inp script file for productive MD simulation.
I would appreciate if somebody gives me a clear file example.
Many thanks,
Michael
*****************************
Michael Shokhen, PhD
Associate Professor
Department of Chemistry
Bar Ilan University,
Ramat Gan, 52900
Israel
email: michael.shokhen.gmail.com
email: shokhen.mail.biu.ac.il
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Received on Fri Jul 03 2015 - 00:30:03 PDT
