Re: [AMBER] Need help for retrained MD

From: Daniel Roe <>
Date: Tue, 7 Oct 2014 08:36:41 -0600


You can use the 'rst' command in cpptraj to generate restraints using
atom mask syntax if you're more familiar with that. For example, if
your target Mg+ is atom 1124 and you want to create a distance
restraint between it and the center of mass of atoms :3.N1 and :11.N3,
you could use the input:

rst .1124 :3.N1|:11.N3 r1 100.0 r2 105.0 r3 105.0 r4 110.0 rk2 2.0 rk3
2.0 out myrestraint.rst

Substitute appropriate values for r1, r2, r3, r4, rk2, and rk3.

Hope this helps,


PS - The 'rst' command can be used to make angle and torsion restraints as well.

On Tue, Oct 7, 2014 at 5:55 AM, Jason Swails <> wrote:
> On Tue, 2014-10-07 at 16:07 +0530, Sudhanshu Shanker wrote:
>> Dear AMBER users,
>> I am trying to put a distance restrain on Mg+ ions from a xyz coordinate
>> (which is a middle point of two atoms like :3.N1 and :11.N3 ). I do not
>> have any idea to use such type of restrain. Kindly suggest me a way to do
>> this.
> You can specify groups of atoms when you define a distance restraint.
> When you specify a group of atoms, it uses the center of mass, I believe
> (it might use the center of geometry, I'm not sure... but when both
> atoms have the same mass those two are the same).
> There are more details in the NMR chapter of the Amber manual, and you
> can find an example in $AMBERHOME/test/nmropt/pme/distance_COM. The
> second restraint in that example defines a distance between atom 1237
> and the center of mass of atoms 1171, 1169, and 1175.
> Hope this helps,
> Jason
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
> _______________________________________________
> AMBER mailing list

Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 307
Salt Lake City, UT 84112-5820
(801) 587-9652
(801) 585-6208 (Fax)
AMBER mailing list
Received on Tue Oct 07 2014 - 08:00:02 PDT
Custom Search