if [ $# -eq 0 ] then root="scr" else root="$1" fi # create root.m file cat <${root}.m #rate constant reactants -> products #values for lysozyme, from banerjee et al, jbc 250, 4355 (1975) #pH = 6.3, 25 deg #species: 1=E,2=S,3=EU1,4=EU2,5=ESB1.6=ESB2,7=ESG,8=P1,9=P2 1.e8 E + S -> EU1 6.25e3 EU1 -> E + S 200 EU1 -> EU2 20 EU2 -> EU1 1.e8 E + S -> ESB1 5e3 ESB1 -> E + S 14 ESB1 -> ESB2 5 ESB2 -> ESB1 .46 ESB2 -> ESG .13 ESG -> ESB2 .038 ESG -> E + P1 + P2 EOF # create root.p file cat <${root}.p #iopt 1 #itol istate jt itask 4 1 2 1 #ml mu ixpr mxstep mxhnil mxordn mxords #iwork1 iwork2 iwork5 iwork6 iwork7 iwork8 iwork9 0 0 0 500 0 0 0 #tcrit h0 hmax hmin #rwork1 rwork5 rwork6 rwork7 0. 0. 0. 0. #start_time end_time {time_step|0} deflt_tolerance [first_time time_factor] #0.0 0.0001 .000003 1.0e-10 #0 1.0e6 0 1.0e-10 1.e-9 1.2589253 0 1.0e6 0 1.0e-10 1.e-9 1.2589254117 #species initial concn absol. tolerance relat. tolerance E 1.e-5 1.e-15 1.e-10 S 1.e-5 1.e-15 1.e-10 EU2 0 1.e-15 1.e-10 EU1 0 1.e-15 1.e-10 ESB1 0 1.e-15 1.e-10 ESB2 0 1.e-15 1.e-10 ESG 0 1.e-15 1.e-10 P1 0 1.e-15 1.e-10 P2 0 1.e-15 1.e-10 EOF #run it and graph it react ${root} | tee ${root}.r | prep | ttygraph