[2Fe-2S] cluster in protein

Hong Yu Liu hong at tracer.chem.uh.edu
Mon Dec 8 18:01:00 EST 1997


Hi, Dear X-Plor newsgroup readers:

	I'm new here, but have questions no the less. Thanks in advance.
I'm generateing a molecular structure which have a [2Fe-2S] cluster 
bonding to 4 Cys S's of the protein. I'm using an modified version of
the generatemetal.inp_new attached to the x-plor 3.1 manual. It works
fine and generate a .pdb file, but when I try to see the .pdb file in
quanta, the Fe-S connectivities and some other bonds are missing or
wrong bonds are added in the CYS bond to it. What's wrong? Is it b/c
the .pdb and .psf files I generated are wrong or quanta has some 
special requirements? I'm changing the following:

	1) parallhdg.pro and topallhdg.pro are used for NMR.
	2) FES residue are modified as the following:

GROUP                                 {*name in the coordinate file.  *}
       ATOM FE1    type FE  charge  2.5 end
       ATOM FE2    type FE  charge  2.5 end
       ATOM S1     type SC   charge -2.0 end
       ATOM S2     type SC   charge -2.0 end

       bond FE1 S1  bond FE1 S2                {*These are
connectivities.*}
       bond FE2 S1  bond FE2 S2

    END
 RESIdue CYSM                                   {singlt out the four Cys
bound }
  GROUp                                         {to the metal cluster}
    atom N   type=NH1 charge=-0.36 end
    atom HN  type=H   charge= 0.26 end
    atom CA  type=CT  charge= 0.00 end
    atom HA  type=HA  charge= 0.10 end
    atom CB  type=CT  charge=-0.20 end
    atom HB1 type=HA  charge= 0.10 end
    atom HB2 type=HA  charge= 0.10 end
    atom SG  type=S   charge=-0.05 end
    atom C   type=C   charge= 0.48 end
    atom O   type=O   charge=-0.48 end  bond CA CB     bond CB HB1    
bond CB HB2
  bond CB SG
  bond CA C
  bond C  O

  improper HA N C CB   !stereo CA
  improper HB1 HB2 CA SG  !stereo CB

  dihedral SG  CB  CA  N

  ic N C  *CA CB  0.0 0.0  120.0  0.0 0.0
  ic N CA CB  SG  0.0 0.0  180.0  0.0 0.0

end
                                            {*Generate the patch
topology,*}
                                             {*which will be used in
the   *}
    PREsidue PFES                             {*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      ADD BOND 5FE1 
1SG                     {*These are the covalent bonds*}
      ADD BOND 5FE1  2SG                     {*between the CYSs and
the    *}
      ADD BOND 5FE2  3SG                    
{*cluster.                    *}
      ADD BOND 5FE2  4SG

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

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

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

      ADD ANGLe  2SG 5FE1 5S2          ADD ANGLe  2SG 5FE1 5S1

      ADD ANGLe  3SG 5FE2 5S1          ADD ANGLe  3SG 5FE2 5S2

      ADD ANGLe  4SG 5FE2 5S1          ADD ANGLe  4SG 5FE2 5S2
  END
 end

 parameter

   @toppar/parallhdg.pro
                                                {*Append parameters for
metal*}
   bonds SC FE   1000.0 2.33                   
{*cluster.                   *}
   bonds CT SC 1000.0 1.81

   angle SC FE SC    500.0 105.0
   angle FE SC FE    500.0 75.0
   angle FE SC CT    500.0 109.5
   angle CT CT SC    500.0 114.4
   angle HA CT SC    500.0 109.5
   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

   improper HA HA CT SC 500 0 -73.230

        MODIfy ATOM 4SG  TYPE=SC  CHARge=-1.00 END


  bond N  HN
  bond N  CA     bond CA HA



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