#!/bin/bash

ptraj_file="tmp.ptraj"
OUT="50ns_noWAT_1000frames_noADP_noH"

REF="1XCK_chainA_sol.inpcrd"

PRMTOP="../../1SX4_noWAT.prmtop"

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


MASK[1]=":1-524,3669-4192,6813-7336"
MASK[2]=":525-1048,3669-4192,4193-4716"
MASK[3]=":1049-1572,4193-4716,4717-5240"
MASK[4]=":1573-2096,4717-5240,5241-5764"
MASK[5]=":2097-2620,5241-5764,5765-6288"
MASK[6]=":2621-3144,5765-6288,6289-6812"
MASK[7]=":3145-3668,6289-6812,6813-7336"




#MASK[1]=":1-524,3669-4192,6813-7336,8016,8023"
#MASK[2]=":525-1048,3669-4192,4193-4716,8017,8024"
#MASK[3]=":1049-1572,4193-4716,4717-5240,8018,8025"
#MASK[4]=":1573-2096,4717-5240,5241-5764,8019,8026"
#MASK[5]=":2097-2620,5241-5764,5765-6288,8021,8027"
#MASK[6]=":2621-3144,5765-6288,6289-6812,8020,8028"
#MASK[7]=":3145-3668,6289-6812,6813-7336,8022,8029"

rm ${ptraj_file}


for index in 1 2 3 4 5 6 7;
do
        echo 'trajin '${DIR[index]}${TRAJIN[1]} 1 2500 5 >> ${ptraj_file}
        echo 'trajin '${DIR[index]}${TRAJIN[2]} 1 2500 5 >> ${ptraj_file}


        echo "strip '* & !"${MASK[index]}"'" >> ${ptraj_file}
        echo "strip @H*" >> ${ptraj_file}

	#echo 'rms first mass :8-27,52-58-133,416-456,496-514@N,CA,C' >> $ptraj_file
	echo 'rms first mass @N,CA,C' >> $ptraj_file
        echo 'trajout '${OUT}"_chain_"${index}".nc nobox netcdf" >> ${ptraj_file}

        ptraj ${PRMTOP} ${ptraj_file}

        rm ${ptraj_file}
done