("PRTA", "ASP" , 2),
("PRTA", "GLU", 14),
("PRTA", "ARG", 15), )
mcModelGMCT = MCModelGMCT (pathGMCT="/home/mikolaj/local/bin/")
mcModelDefault = MCModelDefault ()
for mcModel, folded, direc, message, sedFile, substateFile in (
(None , True , "curves_analytic" , "analytically" , "prob_ph7_analytic.sed" , "substate_ph7_analytic.tex" ),
(mcModelGMCT , True , "curves_gmct" , "using GMCT" , "prob_ph7_gmct.sed" , "substate_ph7_gmct.tex" ),
(mcModelDefault , True , "curves_custom" , "using custom MC sampling" , "prob_ph7_custom.sed" , "substate_ph7_custom.tex" ),
):
electrostaticModel.DefineMCModel (mcModel)
logFile.Text ("\n***Calculating titration curves %s***\n" % message)
curves = TitrationCurves (electrostaticModel, curveSampling=.5)
curves.CalculateCurves ()
curves.WriteCurves (directory=direc)
logFile.Text ("\n***Calculating protonation states at pH=7 %s***\n" % message)
electrostaticModel.CalculateProbabilities (pH=7.)
electrostaticModel.SummaryProbabilities ()
electrostaticModel.SedScript_FromProbabilities (filename=sedFile, overwrite=True)
logFile.Text ("\n***Calculating substate energies at pH=7 %s***\n" % message)
substate = MEADSubstate (electrostaticModel, sites)
substate.CalculateSubstateEnergies ()
substate.Summary ()
substate.Summary_ToLatex (filename=substateFile, includeSegment=True)
mol = CHARMMPSFFile_ToSystem(
"setup/ifp20_xplor_separated.psf",
isXPLOR=True,
parameters=CHARMMParameterFiles_ToParameters(parameters))
mol.coordinates3 = CHARMMCRDFile_ToCoordinates3("setup/ifp20.crd")
mol.Summary()
mead = MEADModel(system=mol,
pathMEAD="/home/mikolaj/local/bin/",
pathScratch="mead",
nthreads=1)
mead.Initialize(excludeResidues=(("PRTA", "CYS", 24), ))
mead.Summary()
mead.WriteJobFiles()
mead.CalculateElectrostaticEnergies(calculateETA=False)
sampling = MCModelDefault()
mead.DefineMCModel(sampling)
tc = TitrationCurves(mead)
tc.CalculateCurves()
tc.WriteCurves(directory="curves")
selection = (("PRTA", "HIS", 260), ("CHRO", "BLF", 1), ("CHRO", "ACB", 2),
("CHRO", "ACC", 3))
substate = MEADSubstate(mead, selection, pH=7.0)
substate.CalculateSubstateEnergies()
substate.Summary()
increment = statevector.Increment()
logFile.Text(
"\n*** Calculating protonation probabilities at pH=7 analytically ***\n")
cem.CalculateProbabilities(pH=7.0)
cem.SummaryProbabilities()
logFile.Text(
"\n*** Calculating protonation probabilities at pH=7 using in-house MC sampling ***\n"
)
mc = MCModelDefault(nprod=30000)
cem.DefineMCModel(mc)
cem.CalculateProbabilities()
cem.SummaryProbabilities()
# ===========================================
logFile.Text("\n*** Calculating titration curves analytically ***\n")
cmc = TitrationCurves(cem, curveSampling=0.5)
cmc.CalculateCurves()
cmc.WriteCurves(directory="curves_analytic")
logFile.Text(
"\n*** Calculating titration curves using in-house MC sampling ***\n")
cem.DefineMCModel(None)
ca = TitrationCurves(cem, curveSampling=0.5)
ca.CalculateCurves()
ca.WriteCurves(directory="curves_mc")
# ===========================================
logFile.Footer()
model = MEADModel(
system=protein,
pathMEAD="/home/mikolaj/local/bin/",
pathScratch=meadDir,
nthreads=1,
)
model.Initialize(excludeResidues=exclusions, includeTermini=True)
model.Summary()
model.SummarySites()
model.WriteJobFiles()
model.CalculateElectrostaticEnergies()
mcModel = MCModelDefault()
model.DefineMCModel(mcModel)
curves = TitrationCurves(model, curveSampling=0.5)
curves.CalculateCurves()
curves.WriteCurves(directory=curveDir)
curves.CalculateHalfpKs()
models[label] = [model, curves]
logFile.Text("\n*** pK1/2 values for the old model ***\n")
model, curves = models["old"]
curves.PrintHalfpKs()
logFile.Text("\n*** pK1/2 values for the new model ***\n")
model, curves = models["new"]
curves.PrintHalfpKs()
# End of script
logFile.Footer()
("PRTA", "CYS", 80),
("PRTA", "CYS", 76),
("PRTA", "CYS", 94),
("PRTA", "ARG", 0),
)
cem.Initialize(excludeResidues=exclusions, includeTermini=True)
cem.Summary()
cem.SummarySites()
cem.WriteJobFiles()
cem.CalculateElectrostaticEnergies(calculateETA=False)
cem.CalculateProbabilities(pH=7.0)
cem.SummaryProbabilities()
curves = TitrationCurves(cem)
curves.CalculateCurves()
curves.WriteCurves(directory="curves_analytic")
curves.PrintHalfpKs(decimalPlaces=1)
sampling = MCModelDefault()
cem.DefineMCModel(sampling)
cem.CalculateProbabilities(pH=7.0)
cem.SummaryProbabilities()
mcc = TitrationCurves(cem)
mcc.CalculateCurves()
mcc.WriteCurves(directory="curves_mc")
mcc.PrintHalfpKs(decimalPlaces=1)