From: Kwee Hong (joyssstan0202_at_gmail.com)
Date: Sun Oct 24 2010 - 22:07:39 CDT
Hi.
I have my protein simulated for 5ns to see how each CYS behave across the
simulation.
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
minimization.
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.
Thanks.
Regards,
Joyce
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