#!/bin/bash

ptraj_file="tmp.ptraj"
OUT="10ns_noWAT-noH"

REF="1XCK_chainA_sol.inpcrd"

PRMTOP="../../1XCK_apo_noWAT.prmtop"

TRAJIN[1]="../traj/50ns_5000frames_noWAT.nc"


MASK[1]=":1-524"
MASK[2]=":525-1048"
MASK[3]=":1049-1572"
MASK[4]=":1573-2096"
MASK[5]=":2097-2620"
MASK[6]=":2621-3144"
MASK[7]=":3145-3668"
MASK[8]=":3669-4192"
MASK[9]=":4193-4716"
MASK[10]=":4717-5240"
MASK[11]=":5241-5764"
MASK[12]=":5765-6288"
MASK[13]=":6289-6812"
MASK[14]=":6813-7336"




rm ${ptraj_file}

for index in 1; 
do
        echo 'trajin '${DIR[index]}${TRAJIN[1]} 1 1000 10 >> ${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