[AMBER] How to set interatomic distance restraint?

From: Michael Shokhen <michael.shokhen.biu.ac.il>
Date: Fri, 3 Jul 2015 10:19:37 +0300

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
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 Shokhen, PhD
Associate Professor
Department of Chemistry
Bar Ilan University,
Ramat Gan, 52900
email: michael.shokhen.gmail.com
email: shokhen.mail.biu.ac.il
AMBER mailing list
Received on Fri Jul 03 2015 - 00:30:03 PDT
Custom Search