Re: [AMBER] constraint of bond

From: case <case.biomaps.rutgers.edu>
Date: Mon, 20 Sep 2010 21:09:12 -0400

On Mon, Sep 20, 2010, Jorgen Simonsen wrote:

>
> I would like to introduce a distance constraint between two atom - a ligand
> and protein where the ligand is allowed to move 3 tp 6 angstrom away from a
> certain atom - how to do this. The bond option is a harmonic potential
> around some equilibrium value - is there an easier away?

This is exactly what "NMR" distance restraints are designed to do..they
have a "flat bottom" with separate upper and lower bounds. See section 6.1
in the Users' Manual.

...dac


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Received on Mon Sep 20 2010 - 18:30:03 PDT
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