AMBER Archive (2009)

Subject: [AMBER] ABMD Reaction Coordinates

From: stephane acoca (stephane.acoca_at_gmail.com)
Date: Mon Aug 24 2009 - 00:04:58 CDT

Dear all,

I am trying to set up a biased MD using as my variables the distance
between a ligand molecule and the receptor, along with the angle
defined by the principal axis of inertia of the ligand and the line
connecting the ligand to the centroid of receptor. However, looking at
the definitions provided in the AMBER manual (section 4.6.2 in amber
10), I have an impossible time trying to derive the appropriate format
of the variable definitions. Any guidance towards this end would be
extremely helpful.

Stephane Acoca
McGill University

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