Re: minimization problem - "Bad global exclusion count, possible error!"

From: Uday Chippada (
Date: Thu Jan 29 2004 - 17:05:54 CST


I am getting the same error too. Also in the end the error that is
shown is something like

ERROR: Constraint failure in RATTLE algorithm for atom 231!
ERROR: Constraint failure; simulation has become unstable.
ERROR: Exiting prematurely.

I recieved the same error while working with the 1QSU molecule which
had a HYP residue, for which there was no entries in topology file or
the parameter file. So I included these values for HYP, and got the
error. So I attributed it to the HYP residue.

But when I tried for the 1A3J chain from the protein data bank, I still
got the same error, this one has just PRO and GLY residues.

I read in some previous messages that it could be because of the sphere
radius, but I checked it and even varied it drastically to no avail.

When I try the 1UBQ given in the tutorial on the NAMD site, it works

Any help would be greatly appreciated. Thank you
Uday Chippada.

> Hi,
> I'm trying to do the minimization for a protein complex and keep
> these warnings:
> Warning: Bad global exclusion count, possible error!
> Warning: Increasing cutoff during minimization may avoid this.
> Does anyone know what this means? The log file is attached.
> Regards,
> Frances

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