RE: [AMBER] Chirality Restraint

From: Seetin, Matthew <>
Date: Wed, 7 Apr 2010 13:58:47 -0400

The restraint defines an improper torsion restraint that's a flat bottomed well between 60 and 80 degrees at with parabolic sides from 60 to 10 degrees and from 80 to 130 degrees. The spring constant is 10 kcal/mol/rad^2. Outside of 130 degrees, like your example of 200, the force is constant from what it was at 130. The section of the manual covering NMR refinement and restraints will have more details if you wish to customize the restraint.

--Matt Seetin

-----Original Message-----
From: on behalf of Ilyas Yildirim
Sent: Wed 4/7/2010 1:46 PM
Subject: [AMBER] Chirality Restraint
Dear All,

I would like to know how chirality restraints work in the NMR structure
prediction. I know that when the temperature is increased in the
simulated annealing protocol, the structure can go to some unwanted
geometries. As a result, chirality restraints are used to keep the
structures in their known geometries.

makeCHIR_RST will create the necessary chiral restraints, but I do not
understand what the created restraint output means. For instance, I have
the following lines in the rst.CHIRALITY file:

# chirality for residue 1 atoms: C2' O4' N9 H1'
  &rst iat=28,8,11,10,
    r1=10., r2=60., r3=80., r4=130., rk2 = 10., rk3=10., &end

What exactly do these lines mean? I assume that r_i's are the angles, but
how would someone calculate the restraint energy if the angle is, let's
say 200? I tried to make an analogy with the definition of improper
torsions, but could not figure it out. Any information/link is
appreciated. Thanks in advance.

   Ilyas Yildirim, Ph.D.
   = Hutchison Hall B#10 - Department of Chemistry =
   = - University of Rochester =
   = 585-275-6766 (office) - =
   = =

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Received on Wed Apr 07 2010 - 11:30:04 PDT
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