Exemple #1
0
dyn = IVM()

# Minimize in Cartesian space with only the covalent constraints.
# Note that bonds, angles and many impropers can't change with the
# 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)
Exemple #2
0
dyn = IVM()

# Minimize in Cartesian space with only the covalent constraints.
# Note that bonds, angles and many impropers can't change with the
# 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)