camkii-test2_v1.bngl

begin model
begin parameters
	#  initial amounts
	CaMCa4_init	25
	CaMKII_init	2

	#  Rate constants
	kf1		1/10000
	kr1		1
	kf2		1
	kf3		1
	kf4		1
	kr4		0.08
	kf5		10	
	
end parameters

begin molecule types
	CaMCa4(cmk)
	CaMKII(T286~0~p,CaM~0~b,x~1~2~3~4~5~6,y~0~1,L,R)
end molecule types

begin seed species
	CaMCa4(cmk)  CaMCa4_init
	CaMKII(T286~0,CaM~0,x~1,y~0,L!6,R!1).CaMKII(T286~0,CaM~0,x~2,y~0,L!1,R!2).CaMKII(T286~0,CaM~0,x~3,y~0,L!2,R!3).CaMKII(T286~0,CaM~0,x~4,y~0,L!3,R!4).CaMKII(T286~0,CaM~0,x~5,y~0,L!4,R!5).CaMKII(T286~0,CaM~0,x~6,y~0,L!5,R!6) 	CaMKII_init
end seed species

begin observables
	01: Molecules CaMKII_inhibit		CaMKII(T286~0,CaM~0)
	02: Molecules CaMKII_bound		CaMKII(CaM~b)
	03: Molecules CaMKII_phosph		CaMKII(T286~p)
	Q4: Molecules CaMCa4_unbound		CaMCa4(cmk)
end observables

begin reaction rules
	# CaMCa4 binding
	R1: CaMKII(T286~0,CaM~0) + CaMCa4(cmk) -> CaMKII(T286~0,CaM~b)  kf1

	# autophosphorylation	

#	R2: CaMKII(T286~0,CaM~b,x~1,y~0).CaMKII(T286~0,CaM~b,x~2,y~0)-> CaMKII(T286~p,CaM~b,x~1,y~0).CaMKII(T286~p,CaM~b,x~2,y~0) kf2
#	R2: CaMKII(T286~0,CaM~b,x~2,y~0).CaMKII(T286~0,CaM~b,x~3,y~0)-> CaMKII(T286~p,CaM~b,x~2,y~0).CaMKII(T286~p,CaM~b,x~3,y~0) kf2
#	R2: CaMKII(T286~0,CaM~b,x~3,y~0).CaMKII(T286~0,CaM~b,x~4,y~0)-> CaMKII(T286~p,CaM~b,x~3,y~0).CaMKII(T286~p,CaM~b,x~4,y~0) kf2
#	R2: CaMKII(T286~0,CaM~b,x~4,y~0).CaMKII(T286~0,CaM~b,x~5,y~0)-> CaMKII(T286~p,CaM~b,x~4,y~0).CaMKII(T286~p,CaM~b,x~5,y~0) kf2
#	R2: CaMKII(T286~0,CaM~b,x~5,y~0).CaMKII(T286~0,CaM~b,x~6,y~0)-> CaMKII(T286~p,CaM~b,x~5,y~0).CaMKII(T286~p,CaM~b,x~6,y~0) kf2
#	R2: CaMKII(T286~0,CaM~b,x~6,y~0).CaMKII(T286~0,CaM~b,x~1,y~0)-> CaMKII(T286~p,CaM~b,x~6,y~0).CaMKII(T286~p,CaM~b,x~1,y~0) kf2

#	R4: CaMKII(T286~p)-> CaMKII(T286~0)  kf4
#	R5: CaMKII(CaM~0)-> CaMKII(CaM~0)    kf5

end reaction rules
end model
generate_network({overwrite=>1,max_iter=>1})