*  ========================================= 
*  JOB: 
*

bomb -2

! { parameters passed }
set i 0  ! counter
$SET$

! get parameters
!par and top files
open unit 1 card read name lib/top_all27_prot_na.rtf
read RTF card unit 1
close unit 1

open unit 1 card read name lib/par_all27_prot_na.prm
read PARA card unit 1
close unit 1

stream lib/aco.rtf

calc stopdyna = @{conf_n} * @skip

! { psf }
open unit 1 read formatted name @path/scr/@pdb.dyna_@etat.psf
read psf card unit 1
close unit 1

! { coordinates }
OPEN UNIT 1 READ FORMatted NAME @path/scr/@pdb.dyna_@etat.crd
READ COORdinate CARD  UNIT 1
CLOSE UNIT 1

stream @path/inp/all-traj.dat

trajectory iread 21  nread 1 skip 1 begin 0 stop 20005


LABEL conditions 

incr i by 1

traj read

$IF$
if @i LT @{conf_n} GOTO conditions
if @i EQ @{conf_n} GOTO stop


LABEL writing

NBONDS  cutnb 13.5 ctonnb 8.5 ctofnb 12.5 -
vswitch shift cdie eps 1 !-
SKIPe  ALL EXCLude ELECtrostatic VDW
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
!puts the good keyword to select the 2 parts of the system!
!the order of the selection isn't important               !
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
inte sele @fp end sele @sp end

! this is also the total int. energy, for consistency check
set a = ?ENER
set b = ?VDW
set c = ?ELEC

open write formatted unit 10 name @path/scr/@pdb.conf_@i/@pdb.conf_@i.pdb 
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
!puts the good keyword to select the 2 parts of the system!
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
write coor pdb sele (@fp .or. @sp) end unit 10 
* pdb for @pdb
* conformation  = @i TOTAL energy = @a
* Van der Waals   =  @b      Electrostatic = @c
*
close unit 10

! Let's keep a record of the radii
scalar radius store 1
scalar wmain recall 1
! Let's write the radii in a crd file
open unit 11 write formatted name @path/scr/@pdb.conf_@i/@pdb.conf_@i-rad.crd.his
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
!puts the good keyword to select the 2 parts of the system!
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
write coor card sele (@fp .or. @sp) end unit 11
* crd with radii in WMAIN for @pdb
* conformation  = @i TOTAL energy = @a
* Van der Waals   =  @b      Electrostatic = @c
*
close unit 11
open unit 12  write formatted name @path/scr/@pdb.conf_@i/@{fc_n}.conf_@i-rad.crd.his
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
!puts the good keyword to select the first part of the    !
!system (the first in crd)                                !
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
write coor card sele @fp end unit 12
* crd with radii in WMAIN for @{fc_n}
* conformation  = @i TOTAL energy = @a
* Van der Waals   =  @b      Electrostatic = @c
*
close unit 12
open unit 13 write formatted name @path/scr/@pdb.conf_@i/@{sc_n}.conf_@i-rad.crd.his
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
!puts the good keyword to select the second part of the   !
!system (the second in crd)                               !
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
write coor card sele @sp end unit 13
* crd with radii in WMAIN for @{sc_n}
* conformation  = @i TOTAL energy = @a
* Van der Waals   =  @b      Electrostatic = @c
*
close unit 13

open unit 12  write formatted name @path/scr/@pdb.conf_@i/@{fc_n}.conf_@i.pdb
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
!puts the good keyword to select the first part of the    !
!system (the first in crd)                                !
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
write coor pdb sele @fp  end unit 12
close unit 12

open unit 13 write formatted name @path/scr/@pdb.conf_@i/@{sc_n}.conf_@i.pdb
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
!puts the good keyword to select the second part of the   !
!system (the second in crd)                               !
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
write coor pdb sele @sp end unit 13
close unit 13

! Let's keep a record of the charges
scalar charges store 2
scalar wmain recall 2 
! Let's write the radii in a crd file
open unit 14 write formatted name @path/scr/@pdb.conf_@i/@pdb.conf_@i-cha.crd.his
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
!puts the good keyword to select the 2 parts of the system!
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
write coor card sele (@fp .or. @sp) end unit 14
* crd with radii in WMAIN for @pdb
* conformation  = @i TOTAL energy = @a
* Van der Waals   =  @b      Electrostatic = @c
*
close unit 14
open unit 15 write formatted name @path/scr/@pdb.conf_@i/@{fc_n}.conf_@i-cha.crd.his
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
!puts the good keyword to select the first part of the    !
!system (the first in crd)                                !
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
write coor card sele @fp end unit 15
* crd with radii in WMAIN for @{fc_n}
* conformation  = @i TOTAL energy = @a
* Van der Waals   =  @b      Electrostatic = @c
*
close unit 15
open unit 16 write formatted name @path/scr/@pdb.conf_@i/@{sc_n}.conf_@i-cha.crd.his
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
!puts the good keyword to select the second part of the   !
!system (the second in crd)                               !
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
write coor card sele @sp end unit 16
* crd with radii in WMAIN for @{sc_n}
* conformation  = @i TOTAL energy = @a
* Van der Waals   =  @b      Electrostatic = @c
*
close unit 16

if @i EQ @{conf_n} GOTO stop
if @i LT @{conf_n} GOTO conditions
                                                                                                                  


LABEL stop
stop