sulphate ions

S.Ravichandran ravi at cmb2.saha.ernet.in
Wed Nov 25 21:45:48 EST 1998


Hi all,

We are using XPLOR 3.851 for refinement.

We wanted to refine sulphate ions present in the solvent channel.

But, after generating the 'psf' file (using generate) and incorporating
proper topology and parameter files for sulphates, we find that R-values
shooting up!!. This happens, even when we put 1 sulphate in the structure.
Without sulphates, the R-values are reasonable. 

So, we are thinking that some parameter have to be incorporated in the
input file?

Can anyone please help us??

Thanks in advance.

Sincerely,
Ravi.

P.S:- the following is the PDB and *generate* script incorporated in the
XPLOR program.



----------------------- so4.pdb------------------------------------

ATOM   1447  S   SO4   197      12.534 -19.291  10.154  1.00 55.87
ATOM   1448  O1  SO4   197      13.814 -19.359   9.381  1.00 54.65
ATOM   1449  O2  SO4   197      11.390 -19.045   9.212  1.00 52.09
ATOM   1450  O3  SO4   197      12.325 -20.572  10.873  1.00 53.49
ATOM   1451  O4  SO4   197      12.665 -18.199  11.193  1.00 54.67
ATOM   1452  S   SO4   198      16.165 -26.553   6.387  1.00 60.79
ATOM   1453  O1  SO4   198      16.297 -27.859   5.752  1.00 54.25
ATOM   1454  O2  SO4   198      17.286 -25.546   6.129  1.00 65.13
ATOM   1455  O3  SO4   198      14.935 -25.802   5.941  1.00 67.67
ATOM   1456  O4  SO4   198      16.253 -26.728   7.876  1.00 69.72


--------------------------generate.inp-----------------------------
 remarks  file  generate/generatewater.inp 
 topology  
    @TOPPAR:tophcsdx.pro
    @TOPPAR:toph19.sol 
    @TOPPAR:top.so4      
     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}
     autogenerate angles=true end

    MASS   OS    15.99940 ! sulfate oxygen
    MASS   SS    32.06000 ! sulfate sulfur
    RESIdue SO4
      GROUp
         ATOM S    TYPE=SS   CHARge= +2.000  END
         ATOM O1   TYPE=OS   CHARge= -1.000  END
         ATOM O2   TYPE=OS   CHARge= -1.000  END
         ATOM O3   TYPE=OS   CHARge= -1.000  END
         ATOM O4   TYPE=OS   CHARge= -1.000  END
      BOND S  O1
      BOND S  O2
      BOND S  O3
      BOND S  O4
     ACCEptor O1 S
     ACCEptor O2 S
     ACCEptor O3 S
     ACCEptor O4 S
 END {SO4} 
end
 parameter                                     
   @TOPPAR:protein_rep.param
   @TOPPAR:param.so4         
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 @frag1.pdb
   end
end
                                                 {*Sometimes different atom*}
 vector do (name="O") ( name OT1 )               {*names are used.         *}
 vector do (name="OT") ( name OT2 )
 vector do (name="CD1") ( name CD and resname ile )


end
delete
    selection=(resid 176 and name OT)
 end


 coordinates @frag1.pdb 
end

 segment                                         {* generate sulphate.*}

   name="    "                              {*Should match columns 73-76 in*}
                                            {*test.pdb_pro.                *}
   chain
     coordinates @so4.pdb   
   end
end
 coordinates @so4.pdb  

 segment                                         {*Generate water and zinc.*}

   name="    "                              {*Should match columns 73-76 in*}
                                            {*test.pdb_water.              *}
   chain
     coordinates @wat.pdb
   end
 end
delete
    selection=(resid 201 and name HT1)
 end

delete
    selection=(resid 201 and name HT2)
 end

delete
    selection=(resid 201 and name HT3)
 end

delete
    selection=(resid 387 and name OT1)
 end
delete
    selection=(resid 387 and name OT2)
 end

 coordinates @wat.pdb

  patch disu
    reference=1=( resid 41 )
    reference=2=( resid 85 )
  end
  patch disu
    reference=1=( resid 135 )
    reference=2=( resid 144 )
  end

 {===>} {set hydrogen flag: must be TRUE for NMR, atomic resolution X-ray }
        { crystallography or modelling.  Set the FALSE for most X-ray     }
        { crystallographic applications at resolution > 1. A              }
 evaluate ($hydrogen_flag=TRUE)
 
        
 if ($hydrogen_flag=TRUE) then
    flags exclude vdw elec end                {*Do QUICK hydrogen building w/o*}
                                              {*vdw and elec terms.           *}

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

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

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


------------------------------------------------------------------------------
------------------------------------------------------------------------------ 
         			   S. RAVICHANDRAN

        __              Crystallography & Molecular Biology Division
       / /\             Saha Institute of Nuclear Physics           
      / /  \            Sector I, Block-AF, Bidhan Nagar
     / / /\ \           Calcutta- 700 064, INDIA.
    / / /\ \ \                                                             
   / /_/__\ \ \         E-MAIL:- ravi at cmb2.saha.ernet.in   
  /________\ \ \        FAX:-  (91)(033)-337-4637
  \___________\/        TEL:-   91-033-3375345-49 (5 lines) Ext.308                   
                                033-337 4632 (Hostel)
______________________________________________________________________________
------------------------------------------------------------------------------
==============================================================================
"There is always one more bug"   -     Law of Cybernetic Entomology.         
==============================================================================



More information about the X-plor mailing list