remarks  file generate/csa_generate.inp 
 remarks  Generate structure file and hydrogens for Cylcosporin A 

 topology  
    @TOPPAR:topallhdg.pro                    {*Read standard all-h topology*}
                                             {*file.                       *}
    pres m                                   {*Define methylation patch for*}
                                             {*amides.                     *}
      modify ATOM N    TYPE=NH1 CHARge=-0.360  END
      add atom CN  charge=-0.3 type=CT end
      add atom HN1 charge=0.1 type=HA end
      add atom HN2 charge=0.1 type=HA end
      add atom HN3 charge=0.1 type=HA end
      delete atom HN  end

      bond N CN      bond CN HN1        bond CN HN2        bond CN HN3

      angles N CN HN1       angles N CN HN2        angles N CN HN3
      angles HN1 CN HN2     angles HN1 CN HN3      angles HN2 CN HN3
   end

   RESI ABU                                   {*Define special residue ABU.*} 
      ATOM N    TYPE=NH1 CHARge=-0.360 END
      ATOM HN   TYPE=H   CHARge=0.260  END
      ATOM CA   TYPE=CT  CHARge=0.000  END
      ATOM HA   TYPE=HA  CHARge=0.100  END
      ATOM CB   TYPE=CT  CHARge=-0.200 END
      ATOM HB1  TYPE=HA  CHARge=0.100  END
      ATOM HB2  TYPE=HA  CHARge=0.100  END
      ATOM CG   TYPE=CT  CHARge=-0.100 END
      ATOM HG1  TYPE=HA  CHARge=0.100  END
      ATOM HG2  TYPE=HA  CHARge=0.100  END
      ATOM HG3  TYPE=HA  CHARge=0.100  END
      ATOM C    TYPE=C   CHARge=0.480  END
      ATOM O    TYPE=O   CHARge=-0.480 END

      BOND CB CA     BOND CG CB    
      BOND N HN      BOND N CA     BOND O C       BOND C CA 
      BOND CA HA     BOND CB HB1   BOND CB HB2    BOND CG HG1
      BOND CG HG2    BOND CG HG3

   END
    
   residue bmt                                {*Define special residue BMT.*}
      ATOM N    TYPE=NH1 CHARge=-0.360 END
      ATOM HN   TYPE=H   CHARge=0.260  END
      ATOM CA   TYPE=CT  CHARge=0.000  END
      ATOM HA   TYPE=HA  CHARge=0.100  END
      ATOM CB   TYPE=CT  CHARge=0.180  END
      ATOM HB   TYPE=HA  CHARge=0.100  END
      ATOM OG1  TYPE=OH  CHARge=-0.680 END
      ATOM HG1  TYPE=H   CHARge=0.400  END  
      ATOM CG2  TYPE=CT  CHARge=-0.300 END
      ATOM HG2  TYPE=HA  CHARge=0.100  END
      ATOM CD1  TYPE=CT  CHARge=-0.300 END
      atom hd11 type=ha  charge=0.1 end
      atom hd12 type=ha  charge=0.1 end
      atom hd13 type=ha  charge=0.1 end
      atom cd2 type=ct  charge=0.0 end
      atom hd21 type=ha  charge=0.0 end
      atom hd22 type=ha  charge=0.0 end
      atom ce type=ct charge=0.0 end
      atom he type=ha charge=0.0 end
      atom ch type=ct charge=0.0 end
      atom hh type=ha charge=0.0 end
      atom cp type=ct charge=-0.3 end
      atom hp1 type=ha  charge=0.1 end
      atom hp2 type=ha  charge=0.1 end
      atom hp3 type=ha  charge=0.1 end
      ATOM C    TYPE=C   CHARge=0.480  END
      ATOM O    TYPE=O   CHARge=-0.480 END

      BOND CB CA    BOND OG1 CB    BOND CG2 CB     BOND N HN
      BOND N CA     BOND O C       BOND C CA       BOND CA HA
      BOND CB HB    BOND OG1 HG1   bond cg2 hg2    bond cg2 cd1
      bond cd1 hd11 bond cd1 hd12  bond cd1 hd13   bond cg2 cd2
      bond cd2 hd21 bond cd2 hd22  bond cd2 ce     bond ce he
      bond ce  ch   bond ch  hh    bond ch cp  bond cp hp1
      bond cp hp2   bond cp hp3

      IMPROPER ch  cd2 he   ce 
      IMPROPER ce  hh  cp  ch  

   end
end

 parameter 
   @TOPPAR:parallhdg.pro                   {*Read all-h parameters, append.*}

   improper ct ct ha ct 250.0 0 0.0        {*Parameters that are needed for*}
                                           {*special residues.             *}
 end

 segment 
   name="    "   
   chain                                  {*Definition for peptide linkage.*}

      LINK PEPP    HEAD - *     TAIL + PRO     END           {*LINK to PRO.*}
      LINK PEPT    HEAD - *     TAIL + *       END

      coordinates @csa_ini.pdb 
   end
 end

                                                     {*Make cyclic peptide.*}
 patch pept 
    reference="-"=( resid 11 ) 
    reference="+"=( resid 1 ) 
 end
                                                              {*Make D-ALA.*}
 patch ltod 
    reference=nil=( resid 8 )
 end

                                                   {*Make CIS-peptide bond.*}
 patch CISP
    reference=-=( resid 3 )
    reference=+=( resid 4 ) 
 end
                                                        {*Methylate groups.*}
 patch m reference=nil=( resid 1 )  end
 patch m reference=nil=( resid 3 )  end
 patch m reference=nil=( resid 4 )  end 
 patch m reference=nil=( resid 6 )  end
 patch m reference=nil=( resid 9 )  end
 patch m reference=nil=( resid 10 ) end
 patch m reference=nil=( resid 11 ) end

 coordinates @csa_ini.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 for*}
    phistep=45                            {*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=csa_gen.pdb end          {*Write out coordinates.*} 

 write structure output=csa_gen.psf end   {*This writes the structure file.*}
 
 stop