Re: [AMBER] Understanding Distance Restraint

From: Stephan Schott <>
Date: Thu, 3 Jan 2019 11:21:54 +0100

Hi Aravind,
To understand the restraint format take look at the manual and at this site
for FAQ:
Now, to actually make the restraint file, I find it is just easier to
script it through cpptraj, and then modify the output of the restraint file
from there. For this check the rst command.
Hope it helps,

El mié., 2 ene. 2019 a las 15:19, Ara R (<>) escribió:

> 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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> AMBER mailing list

Stephan Schott Verdugo
Heinrich-Heine-Universitaet Duesseldorf
Institut fuer Pharm. und Med. Chemie
Universitaetsstr. 1
40225 Duesseldorf
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Received on Thu Jan 03 2019 - 02:30:01 PST
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