From: Jim Phillips (jim_at_ks.uiuc.edu)
Date: Mon Oct 25 2010 - 13:21:03 CDT
This warning is not significant during the early stages of minimization.
It is a result of nonphysical deformations as the line minimizer takes
progressively larger steps trying to bracket a minimum.
On Mon, 25 Oct 2010, Kwee Hong wrote:
> I have my protein simulated for 5ns to see how each CYS behave across the
> Then I have 4 of the CYS in the protein bound to one cadmium ion using
> pymol. The distance between the Cd-S was long and I minimized it for 10000
> steps while expecting the Cd-S length would get to the length as defined in
> the force field.At the end of the minimization, the Cd-S length did shrink
> to the value defined in the force field yet I got this warning at the
> beginning of the minimization:
> *Warning: Bad global exclusion count, possible error!*
> *Warning: Increasing cutoff during minimization may avoid this.*
> though this warning disappear after appearing for a few times at the
> beginning of the simulation. After reading the mailing list, I believe this
> warning was generated due to the long Cd-S at the beginning of the
> So, is the warning significant since it has disappeared at the early stage
> of minimization? Would I still need to increase the cutoff as suggested and
> re-do the simulation.
> Here, I attached my .pdb, .psf and config file.
> Advices are welcomed.
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