Re: [AMBER] Putting a harmonic constraint between atoms

From: Jason Swails <>
Date: Thu, 19 Nov 2015 09:26:28 -0500

On Thu, Nov 19, 2015 at 8:52 AM, Debodyuti Dutta <>

> Dear amber users, Is there any way to put a harmonic constraint between
> two atoms, so that they always tend to move together (subject to the force
> applied)? The atoms are not covalently bonded.
> It is easy in Amber to apply constraints in atom or residue position (with
> ntr=1, restraint_wt and restraintmask). But that is is not applicable for
> my problem. Any help will be very useful. Thanks in advance.

​You need to use the "nmropt=1" keyword and add some &rst and &wt namelists.

See the chapter on NMR restraints in the Amber manual for more details.
There is also an example in $AMBERHOME/test/nmropt/gb/distance where the
Run.dist_gb script has an example input file.


Jason M. Swails
Rutgers University
Postdoctoral Researcher
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Received on Thu Nov 19 2015 - 06:30:03 PST
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