#!/bin/bash

PRMTOP="../1SX4_sol.prmtop"
PREFIX="180_1SX4_prod"
SUFFIX_ORIG=".mdcrd"
SUFFIX_REIMG="_reimg.nc"
#WHOLE="heile_driten.nc"

C=1
END=108
#OFFSET=' 1 5000 1 '
#type=get_chainA_traj
#type=project
type="rmsd"
#type="short"
#type="cluster"
#type="mmtsb_clustering"
#type=qha
#type=correl
#type=proj
ptraj_file=${type}.ptraj

if [ -f $ptraj_file ]; then
	rm $ptraj_file
fi

if [ ! $WHOLE == "" ]; then
	echo 'trajin '${WHOLE} $OFFSET >> $ptraj_file
else 
	let END=${END}+1
	while [ $C -lt $END ]; do
		traj_orig=${PREFIX}${C}${SUFFIX_ORIG}
		traj_reimg=${PREFIX}${C}${SUFFIX_REIMG}

		if [ -f $traj ]; then
			echo 'trajin '${traj_orig} $OFFSET >> $ptraj_file 
		fi	
	
		let C=${C}+1
	done
fi

echo `cat $type >> $ptraj_file`

ptraj $PRMTOP $ptraj_file