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Hello Ryan--
> I was working with a protein-ligand complex using CNS, way back when,
> and have moved my calculations over to Xplor-NIH, in part to make use
> of its facilities for multiple conformer interpretation of NOEs and
> other refinement goodies.
>
> I generated my ligand parameters using Xplo2D. When implemented in
> CNS I had no problems with the ligand's naphthalene ring deviating
> from planarity. After scrutinizing the parameter file (and consulting
> with Xplo2D's author, Gerard Kleywegt) I am quite certain the
> planarity ought to be maintained in Xplor-NIH. Nonetheless, the
> naphthalene ring is puckering in my current calculations.
How is planarity maintained? Is it using the DIHE potential term? This
term is unused in the Python protocols -- the IMPR term should be used
instead.
To maintain strict planarity, a call to the IVM can be used, assuming
planarity is correct initiallly:
ivm.group("planar atom selection")
where "planar atom selection" selects all atoms which should be
planar. Note that this should be called for each IVM object used
[e.g. for the dyn and minc objects in eginput.gb1_rdc/anneal.py]
hope this helps--
Charles
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