Re: [AMBER] Understanding Distance Restraint

From: Charles Lin <Charles.lin.silicontx.com>
Date: Wed, 2 Jan 2019 16:43:04 +0000

I think the error that is getting thrown to you has to do with the atom limit for each of the group lists (not sure because you didn't post your error).

You're only allowed like 512 or 1024 atoms in each of those atom lists. In general you are usually okay with just getting the atoms near the center of mass, and if that isn't accurate enough you can probably strip the hydrogens off of the atom mask list. Also do note that using distance restraints for pulling might not give very reasonable results as you're essentially forcing the system into your new state and if the potential you're defining for your restraint is too steep the system may just explode.

-Charlie

´╗┐On 1/2/19, 9:19 AM, "Ara R" <aradrive1.gmail.com> wrote:

    Dear Amber Users,
     I am trying to understand distance restraint syntax to perform SMD.
     I went through Amber18 manual (24.1. Distance, angle and torsional
    restraints), the NMR distance restraints tutorial in amber website along
    with some discussions in amber mailing list.
     Though I understand how to move two atoms away from from each other, I am
    not able to create a distance restraint file for the system of my interest.
    The system which I am working on consist of large domain movement(basically
    open and close form of a protein). Domain A(1-74 residues OR 1-1232 atoms)
    moves 40A away from Domain B(74- 225 residues OR atoms 1233-3603).
    So I want to move the COM of Domain A from that of Domain B.
     How can I define the centre of mass for Domain A as one end of the
    distance restraint.
    I tried the following, which throws error:
     &rst
             iat=-1,-1,
             r1=0.0, r2=10.0, r3=10.0, r4=40.0, rk2 =1.0, rk3 = 1.,
             igr1=1,2,3..1231,1232, #(all the atoms of domain A)
             igr2=1233..3603 #(all the atoms of domain B)
      &end
    Can somebody help me in understanding distance restraint format?
    Best regards and many thanks in advance,
    Aravind R
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Received on Wed Jan 02 2019 - 09:00:03 PST
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