Hello Diego--
>
> 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.
protocol.addUnknownAtoms() should be the correct approach, but I
suspect that something is wrong with the parameters. Let's go through
your script:
>
> xplor.parseArguments()
>
> import protocol
>
> protocol.loadPDB("t28_extended.pdb")
>
> import psfGen
>
these lines should not be needed:
> protocol.initTopology("toppar/toph19.ion")
>
> protocol.initTopology("toppar/toph19.his")
>
> protocol.initParams("toppar/param19.ion")
>
> protocol.initParams("toppar/parhcsdx.pro")
If you want to use nondefault topology and parameters, there is an
alternate setup involving setting the variables protocol.topology and
protocol.parameters.
>
> xplor.command("""
>
> topology
>
> AUTO ANGLe=False DIHEdral=False END
>
> end
>
This next command is not necessary because this is the default HIS
protonation state- initialized in loadPDB above.
> 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
>
> """)
Here you would call protocol.addUnknownAtoms, but first you will need
zinc cluster parameters. In the past I've used this parameter set:
param
bond s zn+2 500.0 2.30
bond NB zn+2 500.0 2.30 !FIX!
bond NA zn+2 500.0 2.30 !FIX!!!
angle s zn+2 s 500.0 109.0
angle NB zn+2 NB 500.0 109.0
! angle NB zn+2 S 500.0 109.0
! angle NA zn+2 NA 500.0 109.0 !FIX!
angle NA zn+2 S 500.0 109.0 !FIX!
end
But you may need something else. Please let me know if you'd like
further help at this point.
>
> xplor.command("write psf output=t28_zn.psf end")
>
> from pdbTool import PDBTool
>
> PDBTool("test.pdb").write()
>
best regards--
Charles
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