trajin ../1/prods.nc  [traj1] 

# Generate RMSDs for THR backbone and for Sugar heavy atoms

reference ../input/1.rst7 [ref1]
rms Back_1 :4-7&@CA,C,O,N,H out Back_prod_rmsd_t1_r-all.dat ref [ref1] parm ../input/1.parm7
rms Sugr_1 :12-15&!@H= out Sugr_prod_rmsd_t1_r-all.dat ref [ref1] parm ../input/1.parm7

go
