#!/bin/bash

MAL="MAL.ptraj"
ptraj_file="tmp.ptraj"
OUT="distance"
MASK=":10-134,408-515,534-658,932-1039,1058-1182,1456-1563,1582-1706,1980-2087,2106-2230,2504-2611,2630-2754,3028-3135,3154-3278,3552-3659@CA :3678-3802,4076-4183,4202-4326,4600-4707,4726-4850,5124-5231,5250-5374,5648-5755,5774-5898,6172-6279,6298-6422,6696-6803,6822-6946,7220-7327@CA"

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 'distance dist '${MASK}' out '${OUT}_${index}'.dat' >> ${ptraj_file}
	ptraj ${DIR_PREFIX[index]}"/"${PRMTOP[index]} ${ptraj_file}

done