remarks  file  generate/generatedna.inp 
 remarks  Generate structure file for a dodecamer

 topology  @TOPPAR:toph11.dna  end            {*Read topology file for dna.*}
                                             {*This file is in subdirectory*}
                                             {*TOPPAR.                     *}
 parameter 
  
   @TOPPAR:param11bx.dna                     {*This file is in subdirectory*}
                                             {*TOPPAR.                     *}
          
   nbonds                                    {*This statement specifies the*}
      atom cdie shift eps=1.0  e14fac=0.4    {*nonbonded interaction energy*}
      cutnb=7.5 ctonnb=6.0 ctofnb=6.5        {*options.  Note the reduced  *}
      nbxmod=5 vswitch                       {*nonbonding cutoff to save   *}
   end                                       {*CPU time.                   *}
 end
                           
                                             {*We are generating one strand*}
                                             {*at a time.                  *}
 segment                            
   name="    "                             {*This name has to match the    *}
                                           {*four characters in columns 73-*}
                                           {*76 in the coordinate          *}
                                           {*file; in XPLOR this name is   *}
   chain                                   {*referred to as SEGId.         *}
       LINK NUC  HEAD - *  TAIL + *  END
       FIRST  5TER  TAIL + * END            {*5-terminus without phosphate.*}
       LAST 3TER  HEAD - * END              {*3-terminus.                  *}

       coordinates @strand1.pdb              {*Interpret coordinate file to*}
   end                                       {*obtain sequence.            *}
 end

                                             {*It comes as RNA; now we have*}
                                             {*to apply deoxy patches for  *}
                                             {*each residue.               *}
 
for $1 in ( 402 403 404 405 406 407 408 409 410 411 
                      412 413 414 415 416 417 418 419) loop main
    patch deox reference=nil=( resid $1 ) end
 end loop main


 coordinates @strand1.pdb                       {*Here we actually read the*}
                                                {*coordinates.             *}

{---------------------------------------------------------------------------}
 segment                                          {*Generate second strand.*}

   name="    " 
   chain
       LINK NUC  HEAD - *  TAIL + *  END
       FIRST  5TER  TAIL + * END
       LAST 3TER  HEAD - * END
       coordinates @strand2.pdb 
   end
 end

 for $1 in ( 421 422 423 424 425 426 427 428 429 430 
                    431 432 433 434 435 436 437 438) loop main
    patch deox reference=nil=( resid $1 ) end
 end loop main


 coordinates @strand2.pdb  


{---------------------------------------------------------------------------}

 flags exclude vdw elec end                  {*Do hydrogen building w/o vdw*}
                                             {*and elec.                   *} 

 hbuild                                     {*This statement builds missing*}
    selection=( hydrogen )                  {*hydrogens, which are needed  *}
    phistep=45                              {*for the force field.         *} 
 end

 constraints fix=( not hydrogen ) end      {* Minimize hydrogen positions. *}
 flags include vdw elec end
 minimize powell 
    nstep=40 
 end
 constraints fix=( not all ) end 

 write coordinates output=generatedna.pdb end      {*Write out coordinates.*} 

 write structure output=generatedna.psf end     {*Write the structure file.*}

          {* Oligonucleotides usually require additional restraints during *}
          {* refinement.  The following file must be included in all       *}
          {* subsequent files.                                             *} 

 @brestraints.inp 

 stop