Re: (No subject)

From: Mark Abraham (
Date: Mon Jul 10 2006 - 18:52:23 CDT

> After the minimization, the protein (in a water box) looks terrible in
> VMD! And in the log file it
> keeps saying "Warning: Bad global exclusion count, possible error!
> Warning: Increasing cutoff during minimization may avoid this.".
> Is the small cutoff value responsible for such a poor representation or
> can I do something else to
> change it?

Yes, probably. Please give some details about what you're doing - like the
size of your cutoffs... If you're new to this, please try some of the
tutorial exercises available on the NAMD website.


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