CNS, ZN, missing Leonard Jones

Holly Berkovits holly at groucho.med.jhmi.edu
Fri Apr 21 13:24:09 EST 2000


Hi,
   I am trying to include a zinc ion in my structure using NOE type
restraints to the liganding residues, instead of declaring actual
bonds.   In attempting this, my files are the following:

zinc.seq file:

        ZN  ZN


zinc.top file:

    MASS ZN 65.37

    AUTOgenerate ANGLes=TRUE END

    RESIdue ZN
      GROUp
        ATOM ZN TYPE=ZN CHARge=0.60 end
    end
    GROUp
      MODIfy atom 1CB  charge=-0.00 END
      MODIfy atom 1SG type=S charge=-0.20 END
    GROUp
      MODIfy atom 2CB  charge=-0.00 END
      MODIfy atom 2SG type=S charge=-0.20 END
    GROUp
      MODIfy atom 3CB  charge=-0.00 END
      MODIfy atom 3SG type=S charge=-0.20 END
    END

zinc.param file:

    nonbonded ZN  0.25   1.942   0.25   1.942
    END

Using these files (and others), I use the generate_sequence.inp and the
generate_extended.inp in anneal.
Then I try to run anneal.inp and get the following error:

%NBUPDA-ERR: missing nonbonded Lennard-Jones parameters %%%%%%%
  ATOM: SEGId="    ",  RESId="1   ",  NAME="ZN  ",  CHEMical="ZN  "
 %NBUPDA-ERR: missing nonbonded Lennard-Jones parameters %%%%%%%
  ATOM: SEGId="    ",  RESId="2   ",  NAME="ZN  ",  CHEMical="ZN  "
 %NBUPDA error encountered: program will be aborted.


But haven't I included this parameter in my zinc.param file?   Can
someone please help me understand what is missing and how do I correct
it?  Thank you.      Holly


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