Can anyone verify if the following is possible with nmropt or any other
AMBER module?
I'd like to apply a half harmonic restraint to a dihedral angle, but I'm not
exactly sure how to do this since the angle is obviously periodic. That is,
I'd like there to be a harmonic wall if the well minimum (say 25 for sake of
argument) is approached from one end (e.g. when it was previously 30), but
there to be no restraint far from this value (e.g. at +170 or -160 say,
there would be no restraint).
nmropt lets you set the boundaries of the harmonic well, but it does not let
you (that I know of) set the boundaries of the linear region (how does this
work with periodicity?). It also does not let you set values for the
boundaries that are not numerically ascending (so if r1 = 20 r4 = -20 is not
allowed).
Did that make sense? Here's the restraint file I have tried thus far, it
appeared to apply a restraint when I did not want it to (i.e. very far from
the reference):
&rst iat=14,12,17,18, r1=-50.0, r2=25.0, r3=25.0, r4=360.0, rk2 = 40.0, rk3
= 0.0 /
Thanks,
Brian
--
================================ Current Address =======================
Brian Radak : BioMaPS
Institute for Quantitative Biology
PhD candidate - York Research Group : Rutgers, The State
University of New Jersey
University of Minnesota - Twin Cities : Wright-Rieman Hall 101
Graduate Program in Chemical Physics : 610 Taylor Road,
Department of Chemistry : Piscataway, NJ
08854-8066
radak004.umn.edu :
radakb.biomaps.rutgers.edu
====================================================================
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address.
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Received on Wed Jul 27 2011 - 12:00:03 PDT
