Version=3.20301
EndTime=3.750000e+003
Points=300
RealTime=0
SleepTime=1
TimeUnit=s
ConcentrationUnit=uM
VolumeUnit=ml
TimeElasticities=0
Dynamics=1
SteadyState=0
Report=1
DynTitles=0
SSTitles=0
DynQuotes=0
SSQuotes=0
DynColWidth=12
SSColWidth=12
DynSeparator=32
SSSeparator=32
SSMCAUnscaled=0
SSStrategy=0
SSBackIntegration=1
RepStructuralAnalysis=0
RepStabilityAnalysis=0
RepMCA=1
NewtonLimit=50
SSResoltion=1.000000e-009
RelativeTolerance=1.000000e-006
AbsoluteTolerance=1.000000e-012
AdamsMaxOrder=12
BDFMaxOrder=5
DerivationFactor=1.000000e-003
ReportFile=hivfit.txt
DynamicsFile=hivfit.dyn
SSFile=simresults.ss
Title=Irreversible inhibition of HIV proteinase
TotalMetabolites=10
TotalSteps=6
TotalMoieties=3
TotalCompartments=1
Stoichiometry
-2.000000 0.000000 0.000000 0.000000 0.000000 0.000000 
1.000000 -1.000000 1.000000 -1.000000 -1.000000 0.000000 
0.000000 -1.000000 0.000000 0.000000 0.000000 0.000000 
0.000000 1.000000 -1.000000 0.000000 0.000000 0.000000 
0.000000 0.000000 1.000000 -1.000000 0.000000 0.000000 
0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 
0.000000 0.000000 0.000000 0.000000 -1.000000 0.000000 
0.000000 0.000000 0.000000 0.000000 1.000000 -1.000000 
0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 
0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 
TotalUDKinetics=0
Metabolite=M
Concentration=0
Compartment=0
Type=1
Metabolite=E
Concentration=0.004
Compartment=0
Type=1
Metabolite=S
Concentration=25
Compartment=0
Type=1
Metabolite=ES
Concentration=0
Compartment=0
Type=1
Metabolite=P
Concentration=0
Compartment=0
Type=1
Metabolite=EP
Concentration=0
Compartment=0
Type=2
Metabolite=I
Concentration=0.004
Compartment=0
Type=2
Metabolite=EI
Concentration=0
Compartment=0
Type=1
Metabolite=EJ
Concentration=0
Compartment=0
Type=2
Metabolite=offset
Concentration=0.1
Compartment=0
Type=0
Metabolite=  M - E + S + P + I 
Concentration=25
Compartment=0
Type=7
Metabolite=  S + ES + P + EP 
Concentration=25
Compartment=0
Type=7
Metabolite=  M + E - S - P + EI + EJ 
Concentration=-24.996
Compartment=0
Type=7
Step=R1
Equation=M + M = E
KineticType=Mass action (reversible)
Flux=0
Reversible=1
Substrates=2
Products=1
Modifiers=0
Constants=2
Subs0=0
Subs1=0
Prod0=1
Param0=0.1
Param1=0.0001
Step=R2
Equation=E + S = ES
KineticType=Mass action (reversible)
Flux=0
Reversible=1
Substrates=2
Products=1
Modifiers=0
Constants=2
Subs0=1
Subs1=2
Prod0=3
Param0=100
Param1=300
Step=R3
Equation=ES -> E + P
KineticType=Mass action (irreversible)
Flux=0
Reversible=0
Substrates=1
Products=2
Modifiers=0
Constants=1
Subs0=3
Prod0=1
Prod1=4
Param0=10
Step=R4
Equation=E + P = EP
KineticType=Mass action (reversible)
Flux=0
Reversible=1
Substrates=2
Products=1
Modifiers=0
Constants=2
Subs0=1
Subs1=4
Prod0=5
Param0=100
Param1=500
Step=R5
Equation=E + I = EI
KineticType=Mass action (reversible)
Flux=0
Reversible=1
Substrates=2
Products=1
Modifiers=0
Constants=2
Subs0=1
Subs1=6
Prod0=7
Param0=100
Param1=0.1
Step=R6
Equation=EI -> EJ
KineticType=Mass action (irreversible)
Flux=0
Reversible=0
Substrates=1
Products=1
Modifiers=0
Constants=1
Subs0=7
Prod0=8
Param0=0.1
Compartment=compartment
Volume=1.000000e+000
Comments
Example 1 of Kuzmic (1996) Anal. Biochem. 237, 260-273

Fitting 5 kinetic constants considering that the initial concentrations 
of enzyme and substrate and the offset of the fluorimeter have some 
uncertainty.
EndComments
PlotType=2
PlotDyn=1
Plot3d=0
PlotGrid=0
PlotKey=0
PlotTitles=1
PlotMultiplot=0
PlotContour=0
PlotHidden3d=0
PlotLogX=0
PlotLogY=0
PlotLogZ=0
PlotXEntry=0
PlotYTotal=1
PlotZTotal=1
PlotY0=2
PlotZ0=-1
User-defined functions
Items=2
Name=dP/dt
Description=t-q
Nodes=4
Node=37,64
Node=73,116
Title=J(R3)
Type=4
I=R3
Node=79,45
Node=73,113
Title=J(R4)
Type=4
I=R4
Name=signal
Description=p*0.024+o
Nodes=6
Node=37,64
Node=73,112
Title=[P]
Type=2
I=P
Node=79,42
Node=78,64
Value=2.400000e-002
Node=79,43
Node=73,111
Title=[offset]i
Type=1
I=offset
Interactive time course
Items=0
Time-course output
Items=12
Title=time
Type=14
Title=[I]i
Type=1
I=I
Title=signal
Type=24
Title=[M]t
Type=3
I=M
Title=[E]t
Type=3
I=E
Title=[S]t
Type=3
I=S
Title=[ES]t
Type=3
I=ES
Title=[P]t
Type=3
I=P
Title=[EP]t
Type=3
I=EP
Title=[I]t
Type=3
I=I
Title=[EI]t
Type=3
I=EI
Title=[EJ]t
Type=3
I=EJ
Steady-state output
Items=0
Scan
Enabled=0
Dimension=1
Title=[I]i
Type=1
I=I
Min=0.0000000000000000
Max=0.0040000000000000
Density=4
Log=0
Independent=1
Grid=0
Parameter Links
Items=0
Optimisation
Enabled=0
SetModel=0
Sign=1.0
OptimiseDyn=1
Constrained=0
Method=Evolutionary programming
P0=100
P1=1e-005
P2=0.2
P3=1e-005
P4=1
Title=
Type=0
Parameters=0
Fitting
Enabled=1
SetModel=0
FitDyn=1
Constrained=0
FitDataFile=irrevers.txt
FitSeparator=32
FitLines=1500
Method=Levenberg-Marquardt
P0=100
P1=1e-005
P2=0.2
P3=1e-005
P4=1
Parameters=5
MinType=1
MaxType=1
MinIneq=1
MaxIneq=1
MinD=0
MaxD=100000
IsParameter=1
Title=R2(k2)
Type=6
I=R2
J=k2
Min=1.0000000000000000
Max=2.0000000000000000
Density=2
Log=0
Independent=1
Grid=-1
Title=
Type=0
Title=
Type=0
MinType=1
MaxType=1
MinIneq=1
MaxIneq=1
MinD=0
MaxD=100000
IsParameter=1
Title=R3(k)
Type=6
I=R3
J=k
Min=1.0000000000000000
Max=2.0000000000000000
Density=2
Log=0
Independent=1
Grid=-1
Title=
Type=0
Title=
Type=0
MinType=1
MaxType=1
MinIneq=1
MaxIneq=1
MinD=0
MaxD=100000
IsParameter=1
Title=R4(k2)
Type=6
I=R4
J=k2
Min=1.0000000000000000
Max=2.0000000000000000
Density=2
Log=0
Independent=1
Grid=-1
Title=
Type=0
Title=
Type=0
MinType=1
MaxType=1
MinIneq=1
MaxIneq=1
MinD=0
MaxD=100000
IsParameter=1
Title=R5(k2)
Type=6
I=R5
J=k2
Min=1.0000000000000000
Max=2.0000000000000000
Density=2
Log=0
Independent=1
Grid=-1
Title=
Type=0
Title=
Type=0
MinType=1
MaxType=1
MinIneq=1
MaxIneq=1
MinD=0
MaxD=100000
IsParameter=1
Title=R6(k)
Type=6
I=R6
J=k
Min=1.0000000000000000
Max=2.0000000000000000
Density=2
Log=0
Independent=1
Grid=-1
Title=
Type=0
Title=
Type=0
AdjConcentrations=3
MinType=4
MaxType=4
MinIneq=1
MaxIneq=1
MinD=0
MaxD=0.5
IsParameter=1
Title=[S]i
Type=1
I=S
Min=1.0000000000000000
Max=2.0000000000000000
Density=2
Log=0
Independent=1
Grid=-1
Title=
Type=0
Title=
Type=0
MinType=4
MaxType=4
MinIneq=1
MaxIneq=1
MinD=0
MaxD=0.5
IsParameter=1
Title=[E]i
Type=1
I=E
Min=1.0000000000000000
Max=2.0000000000000000
Density=2
Log=0
Independent=1
Grid=-1
Title=
Type=0
Title=
Type=0
MinType=4
MaxType=4
MinIneq=1
MaxIneq=1
MinD=0
MaxD=3
IsParameter=1
Title=[offset]i
Type=1
I=offset
Min=1.0000000000000000
Max=2.0000000000000000
Density=2
Log=0
Independent=1
Grid=-1
Title=
Type=0
Title=
Type=0
FitXItems=2
Title=[I]i
Type=1
I=I
Title=time
Type=14
FitYItems=1
Title=signal
Type=24