* This file is rotate.inp.
* Usage, charmm <rotate.inp >rotate.out.
* Testing need for setup
*

! Open and read amino acid topology and parameter files in the same directory
open read card name "top_all27_prot_na.rtf" unit 20
read rtf card unit 20
close unit 20

open read card name "par_all27_prot_na.prm" unit 20
read parameter card unit 20
close unit 20

! Read sequence and coordinates 
open read card name "protein.pdb" unit 21
read sequence pdb unit 21
generate prot setup
rewind unit 21


read coordinate pdb offset -6 unit 21
close unit 21

coordinate rotate matrix select all end
1 0 0
0 1 0
0 0 -1

open write card name rotated.pdb unit 40
write coordinates pdb select all end unit 40
* Coordinates after simulation of all atoms in protein, pdb format
*

system "echo didn"'"t crash > /dev/tty"

stop