*File
*



!bomlev -10
!wrnlev 10
!prnlev 10


set 1 ../../lib/helix_surface_3_zwit.psf      ! PSF
set 2 ../../coor/helix_surface_3_zwit.crd     ! coord file, reference
                                                                                                                   
set 3 ../../dcd/helix_surface_3_zwit.dcd               ! traj. file #1
                                                                                                                   
set 4 ../../lib
                                                                                                                   
                                                                                                                   
open read unit 11 card name @4/toph19_eef1.1.inp
read rtf card unit 11
close unit 11

open read unit 12 card name @4/param19_eef1.1.inp
read para card unit 12
close unit 12


! Read in structure and psf file of the Nter-ss
!______________________________________________

open read unit 9 card name @1
read psf card unit 9  ! card ? file ?
close unit 9

open read unit 10 card name @2 ! card if crd file if pdb
read coor card unit 10   ! CARD INSTEAD OF PDB if we have a .crd !
close unit 10

coor copy comp
!print coor comp

stream @4/prot.def


! setup the 1/2anionic membrane

eef1 setup membrane slvt water slv2 chex nsmth 10 width 23.0 temp 298.15 -
              unit 93 name @4/solvpar.inp  aemp 0.85 -
     !gouy anfr 1.0 area 70. conc 0.03 offset 3.0 valence 1
update ctonnb 7. ctofnb 9. cutnb 10. group rdie


!! Read trajectory file
!_____________________

open read file unit 10 name @3


! Read the trajectory file(s)
!____________________________



!trajectory query unit 10

trajectory iread 10 nread 1 ! begin stop skip ?

set n = 1

label loop

traj read
prnlev 10
energy

coor trans zdir 500

energy 
! will calculate the energy of the protein solvated in water ! 
! and the second column will substract it to the energy in model membrane ! 

coor trans zdir -500
! put back the protein at origin ! 


incr n by 1

goto loop ! and wait for crash


stop