I am running simulated annealing with NMR derived torsion restraints using sander in Amber 14. When a torsion restraint is violated sander reports the violation using the two central atoms of the four that are used to define the torsion. I have several cases where there are two different torsion restraints that use the same two central atoms but different first and last atoms, and I can't tell which one the violation corresponds to. Here is an example of two different restraints that are labelled the same in the violation report.
# 1 PAL C19 1 PAL C14 1 PAL C15 1 PAL H153 -150 -120 0 30
&rst
iat = 1, 7, 6, 57,
r1 = -150.0, r2 = -120.0, r3 = 0.0, r4 = 30.0,
rk2 = 2.0, rk3 = 2.0,
&end
# 1 PAL C19 1 PAL C14 1 PAL C15 1 PAL H152 -30 0 120 150
&rst
iat = 1, 7, 6, 56,
r1 = -30.0, r2 = 0.0, r3 = 120.0, r4 = 150.0,
rk2 = 2.0, rk3 = 2.0,
&end
Would it be possible to report torsion violations using the names of the first and last atoms?
Brendan M. Duggan, PhD
NMR Facility Director and Associate Project Scientist
Skaggs School of Pharmacy and Pharmaceutical Sciences
University of California at San Diego
9500 Gilman Drive, MC 0684
La Jolla CA 92093
office phone: (858) 534-8763
lab phone: (858) 822-7826
cell phone: (858) 692-2298
email: bmduggan.ucsd.edu
http://sopnmr.ucsd.edu
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Received on Wed Jun 18 2014 - 12:00:03 PDT
