#!/bin/bash

trajfile="tmp.ptraj"
prefix="181_1SX4_atp_prod"
rm  $trajfile

for i in $(seq 1 199); 
do
	tmp_file=${prefix}${i}".mdcrd"
	echo "trajin ../../mdcrd/"${tmp_file}" 1 100 10" >> $trajfile
done


cat <<eof >tmp
center :1-8043 mass origin
image origin center

rms first mass @N,CA,C out rmsd.dat

strip :WAT

trajout prod_noWAT.nc netcdf nobox
eof

cat tmp.ptraj tmp > strip_traj.ptraj