[AMBER] Chirality Restraint

From: Ilyas Yildirim <yildirim.pas.rochester.edu>
Date: Wed, 7 Apr 2010 13:46:25 -0400 (EDT)

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) - =
   = http://www.pas.rochester.edu/~yildirim/ =

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Received on Wed Apr 07 2010 - 11:00:04 PDT
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