Re: [AMBER] puting restrains

From: Brian Radak <>
Date: Thu, 15 Mar 2012 09:59:11 -0400

Hi Urszula,

You would really have to check the literature for such things (I'm not
really an expert on proteins, perhaps someone else can suggest specific
references). A rather ambiguous question: Do you want strong or gentle
restraints? In my experience/opinion, a "strong" restraint would be around
100-500 kcal/mol-A^2, but that doesn't really mean anything in general.

A technical note, I believe the nmropt and ntr flags uses the restraint
form U(x) = k(x - x_ref)**2, whereas the NCSU modules use the form U(x) =
0.5k(x - x_ref)**2.


On Thu, Mar 15, 2012 at 9:24 AM, Urszula Uciechowska <> wrote:

> Dear Amber users,
> I would like to put some restraints on residues in my protein between the
> Val270-Ala357 and Asn78-Phe180. Could someone suggest me what force value
> should I use to keep those chains in kind of stable position? Attached is
> the protein that I am going to use in MD.
> /Urszula
> _______________________________________________
> AMBER mailing list

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 Brian Radak                                             :     BioMaPS
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Received on Thu Mar 15 2012 - 07:00:02 PDT
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