remarks   build two-stranded DNA structure
{* one strand in dna1.pdb, other strand in dna2.pdb. *}

rtf  @TOPPAR:nucleic.top  end

parameter @TOPPAR:nucleic.par end


segment
   name="    "
   SETUP=TRUE
   chain

REMARKS  TOPH11.NUC  MACRO for RNA/DNA sequence
SET ECHO=FALSE END

! this is a macro to define standard DNA/RNA polynucleotide bonds
! and termini to generate a sequence.
! it should be added as @TOPTRNA8.NUC in the SEGMent SEQUence
! level.
! 
! Axel Brunger, 17-AUG-84
{* This tells the program what the ends of the oligonucleotide *}
{* have in the way of atoms and how nucleotides in the middle  *}
{* are joined. *}
{* The ends are defined by the first and last residues in the PDB file. *}
{* so if there are any errors, check there first. *}

LINK NUC  HEAD - *  TAIL + *  END

FIRST  5ter  TAIL + * END

LAST 3TER  HEAD - * END

SET ECHO=TRUE END

coor @dna1.pdb
coor @dna2.pdb
    end
end


{* now apply DNA patches to all residues *}
{* ===================================== *}

{====>}
{* Change the numbers in this loop to match resids in the PDBs? *}
for $1 in ( 1 2 3 4 5 6 7 8 9 10 11 12
            13 14 15 16 17 18 19 20 21 22 23 24 )
loop main
   patch DEOX  reference=NIL=( resid $1 ) end
end loop main


{* rename some atoms *}
{* ================= *}
vector do (name "HN'")  ( NAME H61 AND RESNAME ADE )
vector do (name "HN''")  ( name H62 and resname ADE )
vector do (name "HN'")  ( name H21 and resname GUA )
vector do (name "HN''")  ( name H22 and resname GUA )
vector do (name "HN'")  ( name H41 and resname CYT )
vector do (name "HN''")  ( name H42 and resname CYT )
vector do (name "CM")   ( name C5A and resname THY )
!vector do (segid "A") (resid 1:12)
!vector do (segid "B") (resid 13:24)
!vector do ( resid = encode ( decode ( resid ) + 100 ) ) ( segid " ")
! This allows you to renumber the nucleotides.

write psf output=dna.psf end


stop