parm ../ZAP70_WTact.no_wat.prmtop
trajin /raid4/lia/HARC/ZAP70/Short/WT_act/Production/Stripped/ZAP70_WTact.8x10ns-2.nowat.mdcrd.bz2 parm ZAP70_WTact.no_wat.prmtop
trajin /raid4/lia/HARC/ZAP70/Short/WT_act/Production/Stripped/ZAP70_WTact.8x10ns-2a.nowat.mdcrd.bz2 parm ZAP70_WTact.no_wat.prmtop
trajin /raid4/lia/HARC/ZAP70/Short/WT_act/Production/Stripped/ZAP70_WTact.8x10ns-2b.nowat.mdcrd.bz2 parm ZAP70_WTact.no_wat.prmtop
trajin /raid4/lia/HARC/ZAP70/Short/WT_act/Production/Stripped/ZAP70_WTact.8x10ns-2c.nowat.mdcrd.bz2 parm ZAP70_WTact.no_wat.prmtop

#C-helix position
distance :22@CA :52@CB out distF349_D379.out

#C-helix secondary structure
secstruct :53-66 out C-helix_struc.out

#Opening of binding groove
distance :21@CA :174@CA out distN348_W501.out

#align kinase domain
rmsd rms5 :1-287@N,CA,C,O bymask

#solvent exposure
surf surfkin :1-287 out surf_kinase.out