Hello Vitaly--
>
> I would like to evaluate the energy of the ordered regions of the
> calculated structure relative to the reference pdb. To do this, I have
> been trying the following approach:
>
> #start
> refRMSD = create_PosDiffPot("refRMSD","resi 6:63", pdbFile="reference.pdb")
> minim = IVM()
> protocol.initMinimize(minim)
> minim.potList().append(refRMSD)
> minim.group("resi 1:81") #move the protein as a rigid body
> minim.run()
> #end
You might try the helper script targetRMSD:
targetRMSD -diffSeq -selection "resid 6:63" reference.pdb file.pdb
Hopefully, this gives you what you're looking for.
Charles
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