Re: [AMBER] Constraints

From: Roitberg,Adrian E <>
Date: Tue, 15 Nov 2016 14:21:01 +0000

Not easy, but could set nmropt=1 and create a boatload of restraints with large force constants, for every bond, angle and torsion in your molecule.

You can also restrain all pair distances.

If you a willing to live with small internal movements of your molecule, you can restrain the distances between 6 atoms far apart, creating something like axes of inertia.

Trial and error will be needed for this.

Sent from my Verizon, Samsung Galaxy smartphone

-------- Original message --------
From: David A Case <>
Date: 11/15/16 6:19 AM (GMT-07:00)
To: AMBER Mailing List <>
Subject: Re: [AMBER] Constraints

On Fri, Nov 11, 2016, Ol Sta wrote:
> I have a question regarding molecular constraints.
> What is the easiest way of constraining a molecule
> in a box of water solvent ?
> I would like to constrain all bonds, bends, and torsions,
> keeping the geometry fixed but let the molecule float
> around in the box.

Amber does not offer any easy way to do this sort of calculation. Generally,
Amber users would be likely to use restraints (setting ntr=1), and let the
water equilibrate around the solute. But we don't have any good way that I
know of to do rigid body dynamics. (I hope someone will chime in if I am
missing something here....)


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Received on Tue Nov 15 2016 - 06:30:03 PST
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