parm ../../build/full.topo.hmr [traj]
parm ../../../../../B-form.pdb [striped]
reference ../../../../../B-form.pdb parm [striped] [a-form]

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trajin ../../traj.1.01 remdtraj remdtrajtemp 298.41 trajnames ../../traj.1.02,../../traj.1.03,../../traj.1.04,../../traj.1.05,../../traj.1.06,../../traj.1.07,../../traj.1.08,../../traj.1.09,../../traj.1.10,../../traj.1.11,../../traj.1.12,../../traj.1.13,../../traj.1.14,../../traj.1.15,../../traj.1.16,../../traj.1.17,../../traj.1.18 start 1 stop 1000

autoimage origin

rmsd rms_2_aform :1,2&!@H= ref [a-form]
distance dist_O2'-O4' :1@O2' :2@O4'
distance COM :1@N1,C6,H6,C5,H5,C4,O4,N3,H3,C2,O2 :2@N1,C6,H6,C5,H5,C4,O4,N3,H3,C2,O2

dihedral g1 :1@O5' :1@C5' :1@C4' :1@C3'  type gamma
dihedral d1 :1@C5' :1@C4' :1@C3' :1@O3'  type delta
dihedral e1 :1@C4' :1@C3' :1@O3' :2@P    type epsilon
dihedral z1 :1@C3' :1@O3' :2@P   :2@O5'  type zeta
dihedral c1 :1@O4' :1@C1' :1@N1  :1@C2   type chi
dihedral a2 :1@O3' :2@P   :2@O5' :2@C5'  type alpha
dihedral b2 :2@P   :2@O5' :2@C5' :2@C4'  type beta
dihedral g2 :2@O5' :2@C5' :2@C4' :2@C3'  type gamma
dihedral d2 :2@C5' :2@C4' :2@C3' :2@O3'  type delta
dihedral c2 :2@O4' :2@C1' :2@N1  :2@C2   type chi
run

hist rms_2_aform,0,6,0.1 out rmsd-hist_Run1.agr name rmsd_298.41K norm
hist dist_O2'-O4',0,10,0.1 out distO2O4-hist_Run1.agr name Oxygen_distance_298.41K norm
hist COM,0,10,0.1 out COM-hist_Run1.agr name COM_distance_298.41K norm

hist g1,-180,180,1 out dihed_g1-hist_Run1.dat norm
hist d1,-180,180,1 out dihed_d1-hist_Run1.dat norm
hist e1,-180,180,1 out dihed_e1-hist_Run1.dat norm
hist z1,-180,180,1 out dihed_z1-hist_Run1.dat norm
hist c1,-180,180,1 out dihed_c1-hist_Run1.dat norm
hist a2,-180,180,1 out dihed_a2-hist_Run1.dat norm
hist b2,-180,180,1 out dihed_b2-hist_Run1.dat norm
hist g2,-180,180,1 out dihed_g2-hist_Run1.dat norm
hist d2,-180,180,1 out dihed_d2-hist_Run1.dat norm
hist c2,-180,180,1 out dihed_c2-hist_Run1.dat norm

