On Fri, Apr 27, 2012, Chris Chris wrote:
> I have an organic molecule (coelenterazine) that was generated in the
> molegro molecular viewer and then exported as a pdb. I want to put it
> into antechamber for processing so I can use in AMBER. The problem is
> that the pdb file looks like it has too many bonds to each atom. Can
> anyone tell me how to fix this problem.
All the bond distances in this molecule are way to short. Visualization
programs that bond by distance will find all these "extra" bonds. I'm not
familiar with molegro, so can't speculate on how this might have happened --
it's like there is some scaling factor that has been applied to the molecular
coordinates.
...good luck....dac
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Received on Sat Apr 28 2012 - 07:00:04 PDT
