* This file is inten.inp.
* Calculates interaction energy between residues 7-20 and 24-167. 
* Usage, charmm <inten.inp >inten.out. 
*

! Open and read amino acid topology and parameter files
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

!open and read psf file
open read card name "fullprot.psf" unit 20
read psf card unit 20
close unit 20

open write card name "energy.tst" unit 52

open read file name sim.dcd unit 51

trajectory query unit 51
trajectory iread 51 begin ?start skip ?skip

set i 1
label loop

trajectory read
!update
!interaction select segid prot .and. resid 7 : 20 end -
! select segid prot .and. resid 24 : 167 end unit 52

open write card name dyn@{i}.pdb unit 15
write coordinate pdb select all end unit 15
* Coordinates of protein 
*

increment i
!if i le ?nfile goto loop
if i le 11 goto loop
stop