[AMBER] Understanding Distance Restraint

From: Ara R <aradrive1.gmail.com>
Date: Wed, 2 Jan 2019 19:49:54 +0530

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:
         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)
Can somebody help me in understanding distance restraint format?
Best regards and many thanks in advance,
Aravind R
AMBER mailing list
Received on Wed Jan 02 2019 - 06:30:02 PST
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