remarks  file  generate/generatewater.inp 
 remarks  Sample: generate protein structure with waters and zinc ions

 topology  
    @TOPPAR:tophcsdx.pro

                                                         {*Append topology.*}

    autogenerate angles=true end

    MASS   HT     1.00800                                 {*Water hydrogen.*}
    MASS   OT    15.99940                                   {*Water oxygen.*}
    RESIdue H2O                                       {*TIPS3P water model.*} 
       GROUp
          ATOM OH2  TYPE=OT   CHARge= -0.834  END
          ATOM H1   TYPE=HT   CHARge=  0.417  END
          ATOM H2   TYPE=HT   CHARge=  0.417  END
       BOND OH2  H1
       BOND OH2  H2
    END {H2O} 

    MASS   ZN    65.37000                                           {*Zinc.*}
    RESIdue ZN                                   {*Zinc ion with +2 charge.*}
       GROUp
           ATOM ZN TYPE=ZN    CHARGE=2.00   END
    END {ZN}
 end 
       
 parameter                                     

   @TOPPAR:parhcsdx.pro 
                                            {*Append parameters for waters.*}
   BOND HT   OT     450.0       0.9572    
   ANGLE HT   OT   HT      55.0     104.52    

                                           {*For solute-water interactions.*}
   NONBONDED OT        0.1591   2.8509     0.1591   2.8509   
   NONBONDED HT        0.0498   1.4254     0.0498   1.4254   

                                            {*For water-water interactions.*}
   !---------------A--------------B--------------A14-----------B14-----
   nbfix ot  ot  581980.4948  595.0436396     581980.4948  595.0436396
   nbfix ht  ht  3.085665E-06 7.533363E-04    3.085665E-06 7.533363E-04
   nbfix ht  ot  327.8404792  10.47230620     327.8404792  10.47230620 
   
                                              {*Append parameters for zinc.*}
   nonbonded ZN        0.1000   1.1500       0.1000 1.1500  

   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                                       {*some CPU time.              *}
 end
                                           {*Split the coordinate file into*}
                                           {*two files, one containing the *}
                                           {*protein coordinates, the other*}
                                           {*all the water and             *}
                                           {*zinc coordinates.             *}

 segment                                         {*First, generate protein.*}

   name="    "                              {*Should match columns 73-76 in*}
                                            {*test.pdb_pro.                *}
   chain
     @TOPPAR:toph19.pep 
     coordinates @test.pdb_protein 
   end
 end
 coordinates @test.pdb_protein 

 segment                                         {*Generate water and zinc.*}

   name="    "                              {*Should match columns 73-76 in*}
                                            {*test.pdb_water.              *}
   chain
     coordinates @test.pdb_water 
   end
 end
 coordinates @test.pdb_water 

 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=generate.pdb end
 
 write structure output=generate.psf end 
 stop