On Wed, Apr 23, 2014, Valentina Romano wrote:
>
> I ran an easy and short minimization of the 6-aminopurine-PknG kinase
> complex, but something went wrong.
>
>
> When i saved the pdb file after the minimization, the 6-aminopurine has
> lost is planarity.
Try a minimization of just 6-amino purine by itself; see what you get then.
Saying "lost its planarity" is pretty vague, and you will probably have to
debug this yourself. A ligand could correctly become non-planar when bound to
a protein. Or, antechamber might be underestimating the penalty for non-planar
behavior. Or, (we don't know any of this) you could be visually reacting to a
small amount of non-planarity that is really not important. Or, something
else.
...dac
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Received on Wed Apr 23 2014 - 11:00:02 PDT
