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

From: Frances Leung (
Date: Thu Jan 29 2004 - 21:20:54 CST


I think it's a little different for my case. Previously I successfully
minimized my protein complex. I even finished equilibrating it.
However, the process took so long and I expected the SMD would take even
longer and due to time constraints, I decided to do just half of the
protein (the protein has two chains, now I'm trying to do simulation on
just one of the chains to save time since both chains are essentially
identical). I didn't get warnings like these when I was minimizing the
complete protein complex, but now that I'm doing just half of it, I get
problems. I wonder what I need to do to get through the minimization
part by simulating just one chain?


-----Original Message-----
From: [] On
Behalf Of Brian Bennion
Sent: Thursday, January 29, 2004 3:47 PM
To: Uday Chippada
Subject: Re: namd-l: minimization problem - "Bad global exclusion count,
possible error!"


After having a problem in my topology file cause the same error I would
highly advise looking at the HYP residue you created and make sure the
bonding is corect. Just checking the psf file in vmd didn't catch my
mistake. It sounds like a bond is actually missing in your case.


On Thu, 29 Jan 2004, Uday Chippada wrote:

> Hi,
> 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
> 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
> 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
> fine.
> Any help would be greatly appreciated. Thank you
> Sincerely
> Uday Chippada.
> > Hi,
> >
> > I'm trying to do the minimization for a protein complex and keep
> getting
> > 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
> >

**Brian Bennion, Ph.D. **
**Computational and Systems Biology Division **
**Biology and Biotechnology Research Program **
**Lawrence Livermore National Laboratory **
**P.O. Box 808, L-448 **
**7000 East Avenue phone: (925) 422-5722 **
**Livermore, CA 94550 fax: (925) 424-6605 **

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