run.avg_struc

#!/bin/bash
#
# This script file generates an average structure of loaded 
# trajs and outputs:
# 1. RMSD file aligned along CA values
# 2. average structure of only CA atoms
# 3. frame with closest RMSD @ CA to avg. structure 
#
# TO RUN FILE: 
# 1. In terminal: chmod u+x run.avg_struc
# 2. In terminal: ./run.avg_struc > run.avg_struc.log
#########################################

# load variables
#REC=STXBP4
#t=1us
ff=n

# stuff within EOF loads into cpptraj
cpptraj << EOF

# load prmtop 
parm norre.stripped_1.rre.rev_${ff}.com.wat.leap.prmtop

# load traj files
trajin stripped.06-07_prod_revonly_${ff}_1.wat.nc 
trajin stripped.06-07_prod_revonly_${ff}_2.wat.nc
trajin stripped.06-07_prod_revonly_${ff}_3.wat.nc
trajin stripped.06-07_prod_revonly_${ff}_4.wat.nc
trajin stripped.06-07_prod_revonly_${ff}_5.wat.nc

# align all CA atoms to first frame
rms first @CA

# output average pdb
average average.pdb PDB @CA 

# average coordinates only CA
average crdset average_structure @CA
run 

# output RMSD ref to avg_structure
rms ref average_structure @CA out test_avg.dat

run
quit


EOF

####################

# print out the frame that is the smallest RMSD 
tail -n+3 test_avg.dat | awk 'NR == 1 || $2 < min {line = $0; min = $2}END{print line}' 

# make that into a variable
number=`tail -n+3 test_avg.dat | awk 'NR == 1 || $2 < min {line = $0; min = $2}END{print line}' | awk '{print $1}'`

echo $number

####################

cpptraj << EOF

parm norre.stripped_1.rre.rev_${ff}.com.wat.leap.prmtop
trajin stripped.06-07_prod_revonly_${ff}_1.wat.nc 
trajin stripped.06-07_prod_revonly_${ff}_2.wat.nc
trajin stripped.06-07_prod_revonly_${ff}_3.wat.nc
trajin stripped.06-07_prod_revonly_${ff}_4.wat.nc
trajin stripped.06-07_prod_revonly_${ff}_5.wat.nc

# ouput the frame with lowest RMSD to avg structure
outtraj frame_closest_avg_${number}_${REC}.pdb onlyframes ${number}
run 
quit
EOF