#!/bin/bash

ptraj_file="tmp.ptraj"
OUT="50ns_noWAT_500frames_noATP"

PRMTOP="../../1XCK_MGATP_noWAT.prmtop"
TRAJIN[1]="../traj/50ns_5000frames_ATP_noWAT.nc"

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


# first make it to trimer
rm ${ptraj_file}

for index in 1 2 3 4 5 7;
do
        echo 'trajin '${DIR[index]}${TRAJIN[1]} 1 5000 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 netcdf" >> ${ptraj_file}

        ptraj ${PRMTOP} ${ptraj_file}

        rm ${ptraj_file}
done


# then superimpose and remove H

OUT="MMTK_50ns_noWAT_500frames_noATP_fitted"
REF="1XCK_chainA_sol.inpcrd"

PRMTOP="../../in/trimer/1XCK_chainALM_noWAT.prmtop"
REF="../../in/trimer/1XCK_chainALM_noWAT.inpcrd"

rm ${ptraj_file}

for index in 1 2 3 4 5 7;
do
	TRAJIN="50ns_noWAT_500frames_noATP_chain_${index}.nc"
        echo 'trajin '${DIR[index]}${TRAJIN} >> ${ptraj_file}

	echo 'reference '${REF} >> $ptraj_file
        echo 'rms reference mass :9-21,93-108,433-443@N,CA,C' >> $ptraj_file
        echo "strip @H*" >> ${ptraj_file}

	echo 'trajout '${OUT}"_chain_"${index}".dcd charmm" >> ${ptraj_file}

        ptraj ${PRMTOP} ${ptraj_file}

        rm ${ptraj_file}
done