* set up a wwl
* truncated 
* hemchandra
* This file: setup.inp
* No di-sulphide bridges


BOMLEV -5
WRNLEV  5 
     

!prot 					
set a top_all36_prot.rtf
set b par_all36_prot.prm

!set c top_all36_cgenff.rtf
set d par_all36_cgenff.prm

		! file 2
set e boc.str



! read the protein topology
!---------------------------
read rtf card name @a

! read the protein parameters
!----------------------------
read para card flex name @b

! read the cgneff topology
!---------------------------
!read rtf card name @c

! read the cgneff parameters
!----------------------------
read para card flex name @d
stream @e



! Chain A 
!----------
open unit 3 read form name "wwl.pdb"
read sequ pdb unit 3 
close unit 3
GENERATE A setup warn first BOC last CT1  
open read card unit 3 name "wwl.pdb"
read coor pdb unit 3 resid





! build missing part
!-------------------
ic param
ic build

! build hydrogens; do this twice for improved performance
!------------------------------------------
hbuild select type h* end
hbuild select type h* end

COOR ORIENT  

! write out psf
!-----------------------
OPEN WRITE CARD UNIT 9 NAME "protein.psf"
WRITE PSF CARD  UNIT 9
* SPHERE WITH TRIMMED BOUNDARY
*


! write out starting coordinates
!---------------------------------
open write card unit 10 name "proteinH.crd"
write coor cards unit 10
* protein + ligand + crystal water
*

! write out coordinates
open write card unit 10 name "setup.pdb"
write coor pdb unit 10
* protein + water
*


stop