camkii-test2_v3.bngl

begin model
begin parameters
	#  initial amounts
	CaMCa4_init	13
	CaMKII_init	1

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

begin molecule types
	CaMCa4(cmk)
	bCaMKII(T~0~p,C~0~b,T~0~p,C~0~b,L,R)
	gCaMKII(T~0~p,C~0~b,S~0~p,T~0~p,C~0~b,S~0~p,L,R)

end molecule types

begin seed species
	CaMCa4(cmk)  CaMCa4_init
	bCaMKII(T~0,C~0,T~0,C~0,L!1,R!2).bCaMKII(T~0,C~0,T~0,C~0,L!2,R!3).bCaMKII(T~0,C~0,T~0,C~0,L!3,R!1) 	CaMKII_init
	gCaMKII(T~0,C~0,T~0,C~0,S~p,S~p,L!1,R!2).gCaMKII(T~0,C~0,T~0,C~0,S~p,S~p,L!2,R!3).gCaMKII(T~0,C~0,T~0,C~0,S~p,S~p,L!3,R!1) 	CaMKII_init
end seed species

begin reaction rules
	# CaMCa4 binding
	# R1 works good; seems BioNetGen knows which graph patterns are isomorphic; can test it by set max_iter=1, 2
	R1: bCaMKII(T~0,C~0) + CaMCa4(cmk) -> bCaMKII(T~0,C~b)  kf1 

	# autophosphorylation	
	R2: bCaMKII(T~0,C~b,T~0,C~b)-> bCaMKII(T~p,C~b,T~p,C~b) kf2
	R4: bCaMKII(T~p) -> bCaMKII(T~0)  kf4 
	R5: bCaMKII(C~b) -> bCaMKII(C~0)  kf5 

	#========================================================================
	R6: gCaMKII(T~0,C~0) + CaMCa4(cmk) -> gCaMKII(T~0,C~b)  kf1 
	R7: gCaMKII(T~p) -> gCaMKII(T~0)  kf4 
	R8: gCaMKII(C~b) -> gCaMKII(C~0)  kf5 	
	R9:	gCaMKII(S~p) -> gCaMKII(S~0)  kf2

	#==========================================================================
	R27: bCaMKII(T~p)+gCaMKII(T~0,C~b)-> bCaMKII(T~p)+gCaMKII(T~p,C~b) kf2


end reaction rules
end model
#generate_network({overwrite=>1,max_iter=>2})
generate_network({overwrite=>1})