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# This script is to check the stability of an experimental run using RMSD to determine the length of equilibration dynamics
# prmtop file
parm /mindstore/home33ext/kscopino/5JUP_PROTOCOL/PIGGYBACKING/COD1_C2_1S_50PS/5JUP_GC_179C_nowat.prmtop [modi3]

# reference for RMSD (should be the average structure for the entire trajectory)
trajin /mindstore/home33ext/kscopino/5JUP_PROTOCOL/PIGGYBACKING/COD1_C2_1S_50PS/COD1_C2_19/DATA/avg_struct.rst

# experimental neutral dynamics trajectory
trajin /mindstore/home33ext/kscopino/5JUP_PROTOCOL/PIGGYBACKING/COD1_C2_1S_50PS/COD1_C2_19/mdcrd_nd_19_strip parm [modi3]

# RMSD of unrestrained backbone atoms
rms unrestr_resid first :6-10,18-21,34,36-38,42-72,96-97,102-107,113-115,127-129,133-138,147-152,163-164,166-170,172-183,188-203,216-226,243-251,266-268,313-329,344-349,361-371,378,445-450,480-493@N,CA,C,O,P,O5',O3',C5' out rmsd_19_NOTrestr_bkbone.dat
# RMSD of restrained backbone atoms
rms restr_resid first :1-5,11-17,22-33,35,39-41,73-95,98-101,108-112,116-126,130-132,139-146,153-162,165,171,184-187,204-215,227-242,252-265,269-312,330-343,350-360,372-377,379-444,451-479,494-495@N,CA,C,O,P,O5',O3',C5' out rmsd_19_restr_bkbone.dat
# RMSD of mRNA (A-site codon, +1 codon), tRNA anticodon, and CAR
rms unrestr_resid_local first :105,114,167-169,175-180,368@N,CA,C,O,P,O5',O3',C5' out rmsd_19_local_bkbone.dat
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