Dear All,

I am trying to generate a zinc finger protein with two Zn2+ atoms. One 
coordinated by 4 CYS and the other by 3 CYS and 1 His (ND is the coordinating 
atom for the histidine).
I am using the file and the patches for the ions below. When I run the file I 
get the position of the zinc atoms undefined (coordinates 9999.9). I have tried 
to add the line protocol.addUnknownAtoms() but I get all sorts of error 
messages. Does anyone have experience with Zn-finger proteins? Thank you

PRESidue ZNK
GROUP
  delete atom 1HG      end
  MODIfy ATOM 1CB           CHARge= 0.19  END
  MODIfy ATOM 1SG  TYPE=S   CHARge=-0.19  END
  ATOM 1ZN         TYPE=ZN  CHARGE=+2.0 END
GROUP
  delete atom 2HG     end
  MODIfy ATOM 2CB           CHARge= 0.19  END
  MODIfy ATOM 2SG  TYPE=S   CHARge=-0.19  END
GROUP
  delete atom 3HG     end
  MODIfy ATOM 3CB           CHARge= 0.19  END
  MODIfy ATOM 3SG  TYPE=S   CHARge=-0.19  END
GROUP
  delete atom 4HG   end
  MODIfy ATOM 4CB           CHARge= 0.19  END
  MODIfy ATOM 4SG  TYPE=S   CHARge=-0.19  END

ADD BOND 1ZN 1SG
ADD BOND 1ZN 2SG
ADD BOND 1ZN 3SG
ADD BOND 1ZN 4SG

ADD ANGLe  1CB 1SG 1ZN
ADD ANGLe  2CB 2SG 1ZN
ADD ANGLe  3CB 3SG 1ZN
ADD ANGLe  4CB 4SG 1ZN
ADD ANGLe  1SG 2SG 1ZN
ADD ANGLe  1SG 3SG 1ZN
ADD ANGLe  1SG 4SG 1ZN
ADD ANGLe  2SG 3SG 1ZN
ADD ANGLe  2SG 4SG 1ZN
ADD ANGLe  3SG 4SG 1ZN

END {DISU}

PRESidue C1HD
    GROUP
        delete atom 1HG end
        MODIfy ATOM 1CB           CHARge= 0.19  END
        MODIfy ATOM 1SG  TYPE=S   CHARge=-0.19  END
        ATOM 1ZN         TYPE=ZN  CHARGE=+2.0 END
    GROUP
        delete atom 2HG  end
        MODIfy ATOM 2CB           CHARge= 0.19  END
        MODIfy ATOM 2SG  TYPE=S   CHARge=-0.19  END
    GROUP
        delete atom 3HG   end
        MODIfy ATOM 3CB           CHARge= 0.19  END
        MODIfy ATOM 3SG  TYPE=S   CHARge=-0.19  END
    GROUP
    MODIFY ATOM  4ND1 TYPE=NR  CHARge=-0.40  END

  add bond 1ZN 1SG
  add bond 1ZN 2SG
  add bond 1ZN 3SG
  add bond 1ZN 4ND1

  add angle 1SG 1ZN 2SG
  add angle 1SG 1ZN 3SG
  add angle 1SG 1ZN 4ND1
  add angle 2SG 1ZN 3SG
  add angle 2SG 1ZN 4ND1
  add angle 3SG 1ZN 4ND1
  add angle 1ZN 1SG  1CB
  add angle 1ZN 2SG  2CB
  add angle 1ZN 3SG  3CB
  add angle 1ZN 4ND1 4CG
  add angle 1ZN 4ND1 4CE1

END

And the script:

xplor.parseArguments()

import protocol
protocol.loadPDB("t28_extended.pdb")

import psfGen

protocol.initTopology("toppar/toph19.ion")
protocol.initTopology("toppar/toph19.his")
protocol.initParams("toppar/param19.ion")
protocol.initParams("toppar/parhcsdx.pro")

xplor.command("""
topology
AUTO ANGLe=False DIHEdral=False END
end
patch HISE
   reference=nil=( resid 85 )
end
patch ZNK
        reference=1=( resid 65  )
        reference=2=( resid 68  )
        reference=3=( resid 88  )
        reference=4=( resid 91  )
end
patch C1HD
        reference=1=( resid 83  )
        reference=2=( resid 117 )
        reference=3=( resid 120 )
        reference=4=( resid 85  )
end
""")

xplor.command("write psf output=t28_zn.psf end")

from pdbTool import PDBTool
PDBTool("test.pdb").write()


Dr Diego Esposito
Principal Laboratory Research Scientist
Molecular Structure of Cell Signalling Laboratory
The Francis Crick Institute
1 Midland Road
London
NW1 1AT

T: +44 (0)20379 62272
E: [email protected]<mailto:[email protected]>
W: www.crick.ac.uk<http://www.crick.ac.uk/>

[cid:[email protected]]


The Francis Crick Institute Limited is a registered charity in England and 
Wales no. 1140062 and a company registered in England and Wales no. 06885462, 
with its registered office at 1 Midland Road London NW1 1AT
_______________________________________________
Xplor-nih mailing list
[email protected]
https://dcb.cit.nih.gov/mailman/listinfo/xplor-nih

Reply via email to