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

From: Frances Leung (frances_leung_at_rogers.com)
Date: Fri Jan 30 2004 - 02:52:09 CST

Hi,

It may have to do with the missing residues in the protein? When I was
generating the psf file using psfgen, I got warnings like:

extracted 26 residues from pdb file
generating structure at end of segment
no residue 1 before GLU:698 of segment SEG0
Warning: add improper failed in residue GLU:698
no residue 1 before GLU:698 of segment SEG0
Warning: add conformation C-N-CA-C failed in residue GLU:698
no residue 1 before GLU:698 of segment SEG0
Warning: add conformation C-CA-N-HN failed in residue GLU:698
.....
the log file is attached.

what should I do to get rid of these warnings? Do I need to use the
patch command, I don't think there are disulfide bonds in the protein
however. If there are, how can I find out?

Frances

-----Original Message-----
From: Harindar Keer [mailto:hkeer_at_uci.edu]
Sent: Thursday, January 29, 2004 4:21 PM
To: Frances Leung
Cc: namd-l_at_ks.uiuc.edu
Subject: RE: namd-l: minimization problem - "Bad global exclusion
count,possible error!"

 Hi,

     Check if some bonds in complex are crossing the periodic cell
boundary, fixing the complex such that nothing crosses the boundary
before minimization might help. Although I am not sure but reason might
lie in way interactions are calculated under boundary conditions, as one
atom leaves one side of cell it appears in the cell from opposite side.
Being part of same bond but now more than cutoff distance away might
cause the warning.
Please correct if someone knows the reason.

Regards,

On Thu, 2004-01-29 at 19:20, Frances Leung wrote:
> Hello,
>
> 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?
>
> Frances
>
> -----Original Message-----
> From: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] On
> Behalf Of Brian Bennion
> Sent: Thursday, January 29, 2004 3:47 PM
> To: Uday Chippada
> Cc: namd-l_at_ks.uiuc.edu
> Subject: Re: namd-l: minimization problem - "Bad global exclusion
count,
> possible error!"
>
> Hello,
>
> 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.
>
> Regards,
> Brian
>
>
> 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
> 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
> > 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 bennion1_at_llnl.gov **
> **7000 East Avenue phone: (925) 422-5722 **
> **Livermore, CA 94550 fax: (925) 424-6605 **
> *****************************************************************
>


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