*File
*





set 1 ../lib
! pdb or pdb.crd file name
set 4 mini_helix_allh_final
! file name 
set 2 helix_2_zwit
! number of steps
set 3 1500000     

open read unit 11 card name @1/toph19_eef1.1.inp
read rtf card unit 11
close unit 11

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

open read unit 12 card name ../coor/@4.crd
read sequ coor unit 12
close unit 12

gene prot first nter last cter setu

patch disu prot 90 prot 122
!patch disu prot 28 prot 111
!patch disu prot 61 prot 77
!patch disu prot 73 prot 91



open read unit 12 card name ../coor/@4.crd
read coor card unit 12
close unit 12

ic param
ic build
coor init sele type H* end
hbuild



coor orient           !this aligns it with x axis
coor rotate xdir 1. ydir 0. zdir 0. phi 180.0
coor trans zdir 40


open write unit 2 card name ../coor/@2.crd
write coor card unit 2
close unit 2


open write unit 2 form name ../coor/@2.pdb
write coor pdb unit 2

                                                                                                   
! write out the protein structure file (psf)
                                                                                                   
open unit 1 name ../lib/@2.psf write formatted
write psf card unit 1
* Human phospholipid scramblase 1 from human_plscr1_B99990001.pdb
*
                                                                                                   
                                                                                                   
                                                                                                   
open unit 1 name ../lib/@2.xplor.psf write formatted
write psf xplor card unit 1
* Human phospholipid scramblase 1 from human_plscr1_B99990001.pdb
*

!stop


eef1 setup membrane slvt water slv2 chex nsmth 10 width 23.0 temp 298.15 -
              unit 93 name @1/solvpar.inp  aemp 0.85 -
     !gouy anfr 0.50 area 70. conc 0.03 offset 3.0 valence 1
update ctonnb 7. ctofnb 9. cutnb 10. group rdie
                                                                                
!cons harm sele (atom * * ca) .or. (atom * * c) -
!      .or. (atom * * o) .or. (atom * * n) end force 1.0
                                                                                
mini abnr nstep 300
                                                                                
open write unit 2 card name ../coor/@2min.crd
write coor card unit 2
        
open write unit 2 form name ../coor/@2min.pdb
write coor pdb unit 2
                                                                                
shake bonh

open write unit 31 card name ../rst/@2.rst
open write unit 32 file name ../dcd/@2.dcd
dynamics verlet - 
      timestep 0.002 nstep @3 nprint 100 iprfrq 1000 -
      ieqfrq 200 ichecw 1 -
      firstt 240 finalt 300 twindh 2.0 -
      iasors 0 iasvel 1 nsavc  500 inbfrq 20 -
      iunrea -1 iunwri 31 iuncrd 32


open write unit 2 card name ../coor/@2dyn.crd
write coor card unit 2
               
open write unit 2 form name ../coor/@2dyn.pdb
write coor pdb unit 2
                                                                                
mini abnr nstep 300
                                                                                
open write unit 2 card name ../coor/@2dynmin.crd
write coor card unit 2
     
open write unit 2 form name ../coor/@2dynmin.pdb
write coor pdb unit 2


                                                                                 
prnlev 10
energy
coor trans zdir 500
energy ! will calculate the energy of the protein solvated in water ! 

stop