rampedParams.append(MultRamp(0.1, 1, "potList['IMPR'].setScale(VALUE)")) # Give atoms uniform weights, except for the anisotropy axis # protocol.massSetup() # IVM setup # the IVM is used for performing dynamics and minimization in torsion-angle # space, and in Cartesian space. # from ivm import IVM dyn = IVM() # reset ivm topology for torsion-angle dynamics # dyn.reset() protocol.torsionTopology(dyn) # minc used for final cartesian minimization # minc = IVM() protocol.initMinimize(minc) protocol.cartesianTopology(minc) # object which performs simulated annealing # from simulationTools import AnnealIVM init_t = 3000. # Need high temp and slow annealing to converge cool = AnnealIVM(initTemp=init_t,
# internal torsion-angle dynamics # breaks bonds topologically - doesn't change force field dyn.potList().add( XplorPot("BOND") ) dyn.potList().add( XplorPot("ANGL") ) dyn.potList().add( XplorPot("IMPR") ) dyn.breakAllBondsIn("all") protocol.initMinimize(dyn,numSteps=1000) dyn.run() # # reset ivm topology for torsion-angle dynamics # dyn.reset() dyn.potList().removeAll() protocol.torsionTopology(dyn) # # minc used for final cartesian minimization # minc = IVM() protocol.initMinimize(minc) IVM_groupRigidSidechain(minc) minc.breakAllBondsIn("all") def setConstraints(k_ang,k_imp): command(""" constraints