Hello Doug--
>
> I am refining a peptide but XPLOR is outputting a structure with what appears
> to
> be randomized stereochemistry. Is there a way to get XPLOR to stick to the
> stereochemistry specified by the input molecule? Run directory is attached.
>
Which stereocenters are randomized? Usually, stereochemistry is
specified by the improper dihedral angle energy term, and if it's not
correct, it usually means that one or more impropers is missing. I see
that your script does not use the standard Xplor-NIH parameter values,
so this may be an issue. Also, after you load coordinates with
protocol.initCoords('aS_k2c4_psfgen.pdb')
you call
protocol.genExtendedStructure(maxFixupIters=1000)
which does randomize the coordinates. You might leave this line out if
you wish to keep some characteristics of your input structure.
best regards--
Charles
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