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]]
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