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.P,
com(:2.C1',:2.C2',:2.C3',:2.C4',:2.O4'),:3.P,com(:3.C1',:3.C2',:3.C3',:3.C4',:3.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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Received on Wed Aug 06 2008 - 06:07:21 PDT
