#!/bin/bash

OUT="1-100ns_thermo_holo_rmsAvg"
ptraj_file="_"${OUT}"_tmp.ptraj"
avg_pdb="_"${OUT}"_tmp.pdb"
ptraj_avg_out="_"${OUT}"_avg.out"
ptraj_thermo_out="_"${OUT}"_thermo.out"
results="_"${OUT}"_entropy.out"

offset=5
start_a=1
stop_a=5000
start_b=1
stop_b=5000


DIR_PREFIX="/net/lutefisk/slars/groel_md/1XCK_chainA/"
DIR_PREFIX="/home/slars/lutefisk/groel_md/1XCK_chainA/"


PRMTOP[2]=${DIR_PREFIX}"126_1XCK_chainA_MGATP/1XCK_chainA_MGATP_sol.prmtop"

TRAJIN[1]="1-50ns_imposedOnStart.nc"
TRAJIN[2]="51-100ns_imposedOnStart.nc"
#TRAJIN[9]="1-50ns_imposedOnStart.nc"
#TRAJIN[10]="1-50ns_imposedOnStart.nc"
#TRAJIN[11]="1-40ns_imposedOnStart.nc"
#TRAJIN[12]="1-40ns_imposedOnStart.nc"

DIR[7]=${DIR_PREFIX}126_1XCK_chainA_MGATP/results/traj/
DIR[8]=${DIR_PREFIX}126_1XCK_MGATP_p1/results/traj/
DIR[9]=${DIR_PREFIX}126_1XCK_MGATP_p2/results/traj/
DIR[10]=${DIR_PREFIX}126_1XCK_MGATP_p3/results/traj/
#DIR[11]=${DIR_PREFIX}126_1XCK_MGATP_p4/results/traj/
#DIR[12]=${DIR_PREFIX}126_1XCK_MGATP_p5/results/traj/



rm ${ptraj_file}

for index in 7 8 9 10; 
do


        TRAJIN[0]=${DIR[index]}${TRAJIN[index]}

        ## Performing Averags structure calculation ##
        echo 'trajin '${DIR[index]}${TRAJIN[1]} ${start_a} ${stop_a} ${offset}  >> ${ptraj_file}
        echo 'trajin '${DIR[index]}${TRAJIN[2]} ${start_b} ${stop_b} ${offset} >> ${ptraj_file}
        echo 'rms mass first :8-134,410-517@N,CA,C' >> ${ptraj_file}
        echo 'average '${avg_pdb}' pdb'  >> ${ptraj_file}
        ptraj ${PRMTOP[2]} ${ptraj_file} >> ${ptraj_avg_out}
        rm ${ptraj_file}



        ## Performing Entropy calculation ##
        echo 'trajin '${DIR[index]}${TRAJIN[1]} ${start_a} ${stop_a} ${offset}  >> ${ptraj_file}
        echo 'trajin '${DIR[index]}${TRAJIN[2]} ${start_b} ${stop_b} ${offset} >> ${ptraj_file}
        echo 'reference '${avg_pdb} >> ${ptraj_file}
        echo 'rms mass reference :8-134,410-517@N,CA,C' >> ${ptraj_file}
        echo 'matrix mwcovar name rec-var :8-134,410-517' >> ${ptraj_file}
        echo 'analyze matrix rec-var out '${ptraj_thermo_out}' thermo reduce' >> ${ptraj_file}
        ptraj ${PRMTOP[2]} ${ptraj_file} >> ${results}
        rm ${ptraj_file}




	#echo 'rms mass reference :8-134,410-517@N,CA,C' >> ${ptraj_file}
	#echo 'matrix mwcovar name com-var :1-134,410-526' >> ${ptraj_file}
	#echo 'analyze matrix com-var out _thermo_complex.dat thermo reduce' >> ${ptraj_file}

	#echo 'rms mass reference :525-526' >> ${ptraj_file}
	#echo 'matrix mwcovar name lig-var :525-526' >> ${ptraj_file}
	#echo 'analyze matrix lig-var out _thermo_ligand.dat thermo reduce' >> ${ptraj_file}

done