rampedParams = []
highTempParams = []
# compare atomic Cartesian rmsd with a reference structure
# backbone and heavy atom RMSDs will be printed in the output
# structure files
#
from posDiffPotTools import create_PosDiffPot
refRMSD = create_PosDiffPot("refRMSD", "name CA C N O", selection2="initial")
from noePotTools import create_NOEPot, readNEF
noe = create_NOEPot("noe", nef=nefData)
noe.setAllowOverlap(False)
noe.setShowAllRestraints(True)
potList.append(noe)
rampedParams.append(MultRamp(2, 30, "noe.setScale( VALUE )"))
import nefTools
from potList import PotList
rdcs = PotList('rdcs')
try:
rdcNames = nefTools.getBlockNames(nefData, 'rdc')
except:
rdcNames = []
pass
tensors = []
for name in rdcNames:
print(f"reading RDC block {name}")
block = nefTools.getBlock(nefData, 'rdc', name)
from rdcPotTools import readNEF
def structLoopAction(loopInfo):
#
# this function calculates a single structure.
#
#
# set some high-temp force constants
#
noe.setScale(20) #use large scale factor initially
command("parameters nbonds repel %f end end" % ini_rad)
command("parameters nbonds rcon %f end end" % ini_con)
setConstraints(ini_ang, ini_imp)
# Initial weight--modified later
command("restraints dihedral scale=5. end")
#
# high temp dynamics
# note no Van der Waals term
#
init_t = 3500
ini_timestep = 0.010
bath = init_t
timestep = ini_timestep
protocol.initDynamics(
dyn,
potList=hitemp_potList, # potential terms to use
bathTemp=bath,
initVelocities=1,
finalTime=20,
printInterval=100)
dyn.setETolerance(bath / 100) #used to det. stepsize. default: bath/1000
dyn.run()
# increase dihedral term
command("restraints dihedral scale=200. end")
#
# cooling and ramping parameters
#
global k_ang, k_imp
# MultRamp ramps the scale factors over the specified range for the
# simulated annealing.
from simulationTools import MultRamp
k_noe = MultRamp(ini_noe, 30., "noe.setScale( VALUE )")
radius = MultRamp(ini_rad, 0.8,
"command('param nbonds repel VALUE end end')")
k_vdw = MultRamp(ini_con, 4, "command('param nbonds rcon VALUE end end')")
k_ang = MultRamp(ini_ang, 1.0)
k_imp = MultRamp(ini_imp, 1.0)
protocol.initDynamics(dyn,
potList=potList,
bathTemp=bath,
initVelocities=1,
finalTime=2,
printInterval=100,
stepsize=timestep)
from simulationTools import AnnealIVM
AnnealIVM(initTemp =init_t,
finalTemp=100,
tempStep =25,
ivm=dyn,
rampedParams = [k_noe,radius,k_vdw,k_ang,k_imp],
extraCommands= lambda notUsed: \
setConstraints(k_ang.value(),
k_imp.value())).run()
#
# final torsion angle minimization
#
protocol.initMinimize(dyn, printInterval=50)
dyn.run()
#
# final all atom minimization
#
protocol.initMinimize(minc, potList=potList, printInterval=100)
minc.run()
#
# analyze and write out structure
#
print "Starting writeStructure"
loopInfo.writeStructure(potList)
potList = PotList()
rampedParams=[]
# set up NOE potential
noe=PotList('noe')
potList.append(noe)
from noePotTools import create_NOEPot
for (name,scale,file) in [('all',1,"constraints/yourfolder/yourfoldernoe.tbl"),
#add entries for additional tables
]:
pot = create_NOEPot(name,file)
# pot.setPotType("soft") - if you think there may be bad NOEs
pot.setScale(scale)
noe.append(pot)
rampedParams.append( MultRamp(2,30, "noe.setScale( VALUE )") )
# Set up dihedral angles
from xplorPot import XplorPot
protocol.initDihedrals("constraints/yourfolder/yourfolder_dihed_g_all.tbl",
useDefaults=False)
potList.append( XplorPot('CDIH') )
rampedParams.append( StaticRamp("potList['CDIH'].setScale(200)") )
from simulationTools import StructureLoop
def calcOneStructure( structData ):
from waterRefineTools import refine
refine(outFilename=structData.filename(),
potList=potList,
def structLoopAction(loopInfo):
#
# this function calculates a single structure.
#
#
# set some high-temp force constants
#
noe.setScale( 20 ) #use large scale factor initially
command("parameters nbonds repel %f end end" % ini_rad)
command("parameters nbonds rcon %f end end" % ini_con)
setConstraints(ini_ang, ini_imp)
# Initial weight--modified later
command("restraints dihedral scale=5. end")
#
# high temp dynamics
# note no Van der Waals term
#
init_t = 3500
ini_timestep = 0.010
bath = init_t
timestep = ini_timestep
protocol.initDynamics(dyn,
potList=hitemp_potList, # potential terms to use
bathTemp=bath,
initVelocities=1,
finalTime=20,
printInterval=100)
dyn.setETolerance( bath/100 ) #used to det. stepsize. default: bath/1000
dyn.run()
# increase dihedral term
command("restraints dihedral scale=200. end")
#
# cooling and ramping parameters
#
global k_ang, k_imp
# MultRamp ramps the scale factors over the specified range for the
# simulated annealing.
from simulationTools import MultRamp
k_noe = MultRamp(ini_noe,30.,"noe.setScale( VALUE )")
radius = MultRamp(ini_rad,0.8,
"command('param nbonds repel VALUE end end')")
k_vdw = MultRamp(ini_con,4, "command('param nbonds rcon VALUE end end')")
k_ang = MultRamp(ini_ang,1.0)
k_imp = MultRamp(ini_imp,1.0)
protocol.initDynamics(dyn,
potList=potList,
bathTemp=bath,
initVelocities=1,
finalTime=2,
printInterval=100,
stepsize=timestep)
from simulationTools import AnnealIVM
AnnealIVM(initTemp =init_t,
finalTemp=100,
tempStep =25,
ivm=dyn,
rampedParams = [k_noe,radius,k_vdw,k_ang,k_imp],
extraCommands= lambda notUsed: \
setConstraints(k_ang.value(),
k_imp.value())).run()
#
# final torsion angle minimization
#
protocol.initMinimize(dyn, printInterval=50)
dyn.run()
#
# final all atom minimization
#
protocol.initMinimize(minc, potList=potList, printInterval=100)
minc.run()
#
# analyze and write out structure
#
print "Starting writeStructure"
loopInfo.writeStructure(potList)