Dear all
I’m using a modified “tor_cross_two_all.py" script to calculate an ensemble of
structures of a peptide containing proline rings.
Everything works fine, except that ca. 90% of the total energy of the
calculated structures comes from the ANGL term. (I set all the force constants
of the experimental restraints to 0)
When I set the violation threshold to 1°, I see violations of the proline
angles. So I assume there is something wrong with the set up of the proline
rings.
Here is the part of the script where the dynamics manipulators are set up:
############
dyn = ivm.IVM(esim) #manipulator for T-A dynamics
dynx = ivm.IVM(esim) #manipulator for Cartesian dynamics
for manip in (dyn,dynx):
manip.setPotList( potList )
configIVM(oTensor,manip)
configIVM_varyDa(oTensor,manip)
configIVM_varyRh(oTensor,manip)
selectTools.IVM_breakProlines(manip)
selectTools.IVM_groupRigidSidechain(dyn)
dyn.autoTorsion()
dynx.breakAllBondsIn( AtomSel("not resname ANI"))
dynx.setBaseAtoms( AtomSel("not resname ANI”))
############
I hope someone can help me with that!
Carla
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