#!/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"

MASK=":1-134,525-658,1049-1182,1573-1706,2097-2230,2621-2754,3145-3278,409-524,933-1048,1457-1572,1981-2096,2505-2620,3029-3144,3553-3668@CA :3669-3802,4193-4326,4717-4850,5241-5374,5765-5898,6289-6422,6813-6946,4077-4192,4601-4716,5125-5240,5649-5764,6173-6288,6697-6812,7221-7336@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"
DIR_PREFIX[7]="/net/lutefisk/slars/groel_md/mutants/152_E461K_apo_temp350s"


PRMTOP[1]="E461K_apo_noWAT.prmtop"
PRMTOP[2]="E461K_MGATP_noWAT.prmtop"
PRMTOP[3]="E434K_apo_noWAT.prmtop"
PRMTOP[4]="3FBH_MGATP_noWAT.prmtop"
PRMTOP[5]="1XCK_apo_noWAT.prmtop"
PRMTOP[6]="1XCK_MGATP_noWAT.prmtop"
PRMTOP[7]="E461K_apo_noWAT.prmtop"


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

TRAJIN[1]="50ns_5000frames_noWAT.nc"

# for 350K simulations
TRAJIN[5]="40ns_4000frames_temp350.nc"


for index in 7; 
do
	rm ${ptraj_file}

	TRJDIR=${DIR_PREFIX[index]}"/results/traj/"
	
	echo 'trajin '${TRJDIR}${TRAJIN[1]} 1 5000 10 >> ${ptraj_file}

        if [ -f ${TRJDIR}${TRAJIN[5]} ]; then
		 echo 'trajin '${TRJDIR}${TRAJIN[5]} 1 5000 10 >> ${ptraj_file}
	fi

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

done



#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
#