#!/bin/bash
ptraj_file="tmp2.ptraj"


PRMTOP[1]="../1XCK_chainA_noWAT.prmtop"

PREFIX[1]="/net/gulrotkake/slars/groel_md/1XCK/116_1XCK_apo/results/traj_monomer/"
PREFIX[2]="/net/gulrotkake/slars/groel_md/1XCK/129_1XCK_MGATP/results/traj_monomer/"


FILE="500ns_noWAT_5000frames_chain"

rm ${ptraj_file}

for index in 1 2;
do
	
	for j in 1 2 3 4 5 6 7;
	do 
		echo 'trajin '${PREFIX[index]}${FILE}_${j}.nc 3001 5000 10 >> ${ptraj_file}
	done

done

	
echo 'rms first mass :9-515@CA' >> ${ptraj_file}
echo 'cluster out cluster_AL representative pdb average pdb averagelinkage clusters 5 rms mass :9-515@CA' >> ${ptraj_file}

ptraj ${PRMTOP[1]} ${ptraj_file}