remarks  file  generate/generatemetal.inp 
 remarks  Sample: generate protein structure with metal cluster 

 topology  
    @TOPPAR:tophcsdx.pro
                                                 {*Append the metal cluster*}
    autogenerate angles=true end                 {*topology.               *}

    mass SC 32.0600                           
    mass FE 55.847                           
                                             

    RESIdue FS4                            {*Generate the cluster itself.  *}
                                           {*The name FS4 has to match what*}
                                           {*you are using for the residue *}
     GROUP                                 {*name in the coordinate file.  *}
       ATOM FE1    type FE  charge  2.5 end
       ATOM FE2    type FE  charge  2.5 end
       ATOM FE3    type FE  charge  2.5 end
       ATOM FE4    type FE  charge  2.5 end
       ATOM S1     type SC   charge -2.0 end
       ATOM S2     type SC   charge -2.0 end
       ATOM S3     type SC   charge -2.0 end
       ATOM S4     type SC   charge -2.0 end

       bond FE1 S1  bond FE1 S2  bond FE1 S3    {*These are connectivities.*}
       bond FE2 S1  bond FE2 S2  bond FE2 S4
       bond FE3 S1  bond FE3 S3  bond FE3 S4
       bond FE4 S2  bond FE4 S3  bond FE4 S4
              
    END
                                             {*Generate the patch topology,*}
                                             {*which will be used in the   *}
    PREsidue PFS4                            {*PATCh command.              *}
      GROUp
        MODIfy ATOM 1CB           CHARge=0.00  END 
        MODIfy ATOM 1SG  TYPE=SC  CHARge=-1.00 END
      GROUp
        MODIfy ATOM 2CB           CHARge=0.00  END
        MODIfy ATOM 2SG  TYPE=SC  CHARge=-1.00 END
      GROUp
        MODIfy ATOM 3CB           CHARge=0.00  END
        MODIfy ATOM 3SG  TYPE=SC  CHARge=-1.00 END
      GROUp
        MODIfy ATOM 4CB           CHARge=0.00  END
        MODIfy ATOM 4SG  TYPE=SC  CHARge=-1.00 END
                     
      ADD BOND 5FE1  1SG                     {*These are the covalent bonds*}
      ADD BOND 5FE2  2SG                     {*between the CYSs and the    *}
      ADD BOND 5FE3  3SG                     {*cluster.                    *} 
      ADD BOND 5FE4  4SG

                                           {*Autogenerate does not work yet*}
                                           {*for patch residues.           *}

      ADD ANGLe  1CB 1SG 5FE1          ADD ANGLe  2CB 2SG 5FE2
      ADD ANGLe  3CB 3SG 5FE3          ADD ANGLe  4CB 4SG 5FE4

      ADD ANGLe  1SG 5FE1 5S2          ADD ANGLe  1SG 5FE1 5S1   
      ADD ANGLe  1SG 5FE1 5S3

      ADD ANGLe  2SG 5FE2 5S2          ADD ANGLe  2SG 5FE2 5S1
      ADD ANGLe  2SG 5FE2 5S4

      ADD ANGLe  3SG 5FE3 5S3          ADD ANGLe  3SG 5FE3 5S1
      ADD ANGLe  3SG 5FE3 5S4

      ADD ANGLe  4SG 5FE4 5S2          ADD ANGLe  4SG 5FE4 5S3
      ADD ANGLe  4SG 5FE4 5S4
  END
 end 
                     
 parameter                                     

   @TOPPAR:parhcsdx.pro 
                                                {*Append parameters for metal*}
   bonds SC FE   1000.0 2.33                    {*cluster.                   *}
   bonds FE FE   1000.0 2.75
   bonds SC SC   1000.0 3.60   
   bonds CH2E SC 1000.0 1.81                
                                            
                                            
   angle SC FE SC    500.0 112.0
   angle FE SC FE    500.0 75.0
   angle FE SC CH2E  500.0 109.5
   angle CH1E CH2E SC 500.0 114.400 


 !                  eps     sigma       eps(1:4) sigma(1:4)
 !                  (kcal/mol) (A)
 !                  ---------------------------------------
   nonbonded FE     0.1     1.15        0.1      1.15
   nonbonded SC     0.0430  3.3676      0.0430   3.3676

   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
                                           {*Split the coordinate file into*}
                                           {*two files, one containing the *}
                                           {*protein coordinates, the other*}
                                           {*the metal cluster             *}
                                           {*coordinates.                  *}

                                                 {*First, generate protein.*}
 segment 
   name="2FXB" 
   chain
     @TOPPAR:toph19.pep 
     coordinates @test_2fxb_protein.pdb 
   end
 end
 coordinates @test_2fxb_protein.pdb 

                                              {*Now generate metal cluster.*}
 segment 
   name="2FXB" 
   chain
     coordinates @test_2fxb_metal.pdb 
   end
 end
 coordinates @test_2fxb_metal.pdb 
                                               {*Now generate the          *}
                                               {*covalent links between the*}
 patch  PFS4                                   {*cluster and the protein.  *}
     reference=1=( resid 11 )
     reference=2=( resid 14 )
     reference=3=( resid 17 )
     reference=4=( resid 61 )
     reference=5=( resid 82 )
 end

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