AMBER Archive (2008)

Subject: AMBER: Problem with setting the NMR restraints

From: Alex Spasic (als254_at_cornell.edu)
Date: Mon Aug 04 2008 - 09:15:25 CDT

Hello everyone,

I am trying to run a simulation of a small single chain DNA fragment
using Amber 10 while holding fixed the torsion angle formed by the:

(phosphate)i-(center of mass of sugar)i-(phosphate)i+1-(center of mass
of sugar)i+1

The restraint is defined by the following lines:

# psps restraint
 &rst restraint = "torsion[:2_at_P,
com(:2_at_C1',:2_at_C2',:2_at_C3',:2_at_C4',:2_at_O4'),:3_at_P,com(:3_at_C1',:3_at_C2',:3_at_C3',:3_at_C4',:3_at_O4')]",
          r1 = -180, r2 = -150.0, r3 = -150.0, r4 = -120.0,
          rk2 = 30.0, rk3 = 30.0
          /

However this restraint doesn't produce the angles centered around -150.
If I use just one of the of the atoms from the sugar (instead of their
center of mass) the results are fine. My question is whether I have made
a mistake in setting up these restrains or if this is a bug in the code?
Has anyone else had similar problems?

Thanks in advance,
Alex
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