Hi Mark--
>
> I would like to refine the structure of a Zn finger peptide (Cys2, His2) I
> calculated in CYANA, in xplor. I modified a script with the CYS/HIS patches
> from 2019 I found on the xplor Listserver to test the patches (bottom). I get
> some errors (below), is there something I should do differently?
>
I've made some comments interspersed in your script below. In short,
you need to be careful in specifying how to apply the patch.
best regards--
Charles
>
> xplor.parseArguments()
>
> import protocol
> protocol.loadPDB("model.pdb")
> protocol.initTopology('ion')
> import psfGen
> xplor.command("""
> topology
> AUTO ANGLe=False DIHEdral=False END
>
> ! patch to create Zn (Cys)2 (His)2
> !
> ! 1 and 2 should be CYS
> !
> ! 3 and 4 should be HIS
> presidue ZnC2H2
> delete atom 1hg end
> delete atom 2hg end
> delete atom 3he2 end
> delete atom 4he2 end
> add bond 5ZN+2 1sg
> add bond 5ZN+2 2sg
> add bond 5ZN+2 3ne2
> add bond 5ZN+2 4ne2
> add angle 1SG 5ZN+2 2SG
> add angle 1SG 5ZN+2 3ne2
> add angle 1SG 5ZN+2 4ne2
> add angle 2SG 5ZN+2 3ne2
> add angle 2SG 5ZN+2 4ne2
> add angle 3SG 5ZN+2 4ne2
> end
> end
>
> !add the Zn2 atom
>
> segment
> setup=true
> !number=401
^
uncomment this: you want to specify a unique resid for the ion.
> chain
> sequence ZN2 end
> end
> end
> !do patch
> patch ZnC2H2 reference=1=(resid 8)
^ incorrect resid, should specify a CYS
> reference=2=(resid 3)
> reference=3=(resid 6)
^ incorrect resid, should specify a HIS
> reference=4=(resid 19)
> reference=5=(resid 23)
^^ incorrect resid. should be 401 (Zn2+)
> end
>
> """)
> xplor.command("write psf output=test.psf end")
> from pdbTool import PDBTool
> PDBTool("test.pdb").write()
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