sites = (
("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)
isXPLOR=True,
parameters=CHARMMParameterFiles_ToParameters(parameters),
)
mol.coordinates3 = CHARMMCRDFile_ToCoordinates3("charmm/testpeptide.crd")
cem = MEADModel(system=mol,
pathMEAD="/home/mikolaj/local/bin/",
pathScratch="mead",
nthreads=1)
cem.Initialize()
cem.Summary()
cem.SummarySites()
cem.WriteJobFiles()
cem.CalculateElectrostaticEnergies()
logFile.Text(
"\n*** Calculating microstate energies of all states at pH=7 ***\n")
statevector = StateVector(cem)
increment = True
while increment:
Gmicro = cem.CalculateMicrostateEnergy(statevector, pH=7.0)
statevector.Print(title="Gmicro = %f" % Gmicro)
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"
"setup/7LYZ/lysozyme1977.crd",
"mead/7LYZ",
"curves/7LYZ",
"Old lysozyme",
),
(
"new",
"setup/2LZT/lysozyme1990_xplor.psf",
"setup/2LZT/lysozyme1990.crd",
"mead/2LZT",
"curves/2LZT",
"New lysozyme",
),
):
logFile.Text("\n*** Now calculating: %s ***\n" % message)
protein = CHARMMPSFFile_ToSystem(
proteinPsf,
isXPLOR=True,
parameters=CHARMMParameterFiles_ToParameters(parameters),
)
protein.coordinates3 = CHARMMCRDFile_ToCoordinates3(proteinCrd)
model = MEADModel(
system=protein,
pathMEAD="/home/mikolaj/local/bin/",
pathScratch=meadDir,
nthreads=1,
)
model.Initialize(excludeResidues=exclusions, includeTermini=True)
"par_all27_prot_na.inp",
"par.inp",
)
mol = CHARMMPSFFile_ToSystem(
"parent_waterbox.psf",
isXPLOR=True,
parameters=CHARMMParameterFiles_ToParameters(parameters))
mol.coordinates3 = XYZFile_ToCoordinates3("geometry.xyz")
mol.Summary()
trajectory = XTCTrajectoryFileReader("heat.xtc", mol)
trajectory.Summary()
while trajectory.RestoreOwnerData():
logFile.Text("Frame count: %d\n" % trajectory.currentFrame)
XYZFile_FromSystem("sav%03d.xyz" % trajectory.currentFrame, mol)
trajectory.Summary()
#===========================================================
# This part takes a bit more time to execute, uncomment if you like
# direc = "traj"
#
# if not os.path.exists (direc):
# os.makedirs (direc)
#
# XTCTrajectory_ToSystemGeometryTrajectory ("heat.xtc", direc, mol)
#===========================================================
logFile.Footer()