#!/bin/bash

MAL="MAL.ptraj"
ptraj_file="tmp.ptraj"
OUT="rmsd"
MASK=":1-7336@N,CA,C"

DIR_PREFIX[1]="/net/lutefisk/slars/groel_md/mutants/150_E461K_apo"
DIR_PREFIX[2]="/net/lutefisk/slars/groel_md/mutants/151_E461K_ATP"
DIR_PREFIX[3]="/net/lutefisk/slars/groel_md/mutants/161_E434K_apo"
DIR_PREFIX[4]="/net/lutefisk/slars/groel_md/mutants/162_E434K_MGATP"
DIR_PREFIX[5]="/net/gulrotkake/slars/groel_md/1XCK/116_1XCK_apo"
DIR_PREFIX[6]="/net/gulrotkake/slars/groel_md/1XCK/129_1XCK_MGATP"

PRMTOP[1]="E461K_apo_sol.prmtop"
PRMTOP[2]="E461K_MGATP_sol.prmtop"
PRMTOP[3]="E434K_apo_sol.prmtop"
PRMTOP[4]="3FBH_MGATP_sol.prmtop"
PRMTOP[5]="1XCK_sol.prmtop"
PRMTOP[6]="1XCK_MGATP_sol.prmtop"

TRAJIN[1]="1-25ns_imposedOnStart.nc"
TRAJIN[2]="26-50ns_imposedOnStart.nc"
TRAJIN[3]="1-50ns_imposedOnStart.nc"


for index in 1 2 3 4 5 6; 
do
	rm ${ptraj_file}

	TRJDIR=${DIR_PREFIX[index]}"/results/traj/"
	
	if [ -f ${TRJDIR}${TRAJIN[3]} ]; then
		echo 'trajin '${TRJDIR}${TRAJIN[3]} 1 5000 10 >> ${ptraj_file}
	else
		 echo 'trajin '${TRJDIR}${TRAJIN[1]} 1 2500 10 >> ${ptraj_file}
		 echo 'trajin '${TRJDIR}${TRAJIN[2]} 1 2500 10 >> ${ptraj_file}
	fi

	echo 'rms first mass '${MASK}' out '${OUT}_${index}'.dat' >> ${ptraj_file}
	ptraj ${DIR_PREFIX[index]}"/"${PRMTOP[index]} ${ptraj_file}

done