From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Tue Jun 12 2007 - 20:48:31 CDT
Please also have a look at the Troubleshooting section of the namd wiki
(http://www.ks.uiuc.edu/Research/namd/wiki/index.cgi?NamdTroubleshooting).
Peter
Huy N. Ha wrote:
>
> I'm assuming you have a psf file with that? Also, did you use psfgen
> to generate it? If so, chances are you are missing some dihedral
> parameters if you patched the different residues. You might need to
> use 'regenerate angles dihedrals' immediately after the patch, in your
> configuration file. See if that helps.
>
> Mr. Huy Ha
> B. Med. Chem. Honours Student
> Dept. of Medicinal Chemistry
> Victorian College of Pharmacy
> Monash University
> 381 Royal Parade,
> Parkville, VIC, 3052
> Phone No: 99039136
> Ext: #39136
> Email: Huy.Ha_at_vcp.monash.edu.au
>
>
>
> -----Original Message-----
> From: owner-namd-l_at_ks.uiuc.edu on behalf of Idit Buch
> Sent: Wed 6/13/2007 12:04 AM
> To: namd-l_at_ks.uiuc.edu
> Subject: namd-l: FATAL ERROR: Bad global exclusion count
>
> Hello all,
>
> While running equilibration on a protein, using periodic boundary
> conditions, I received
> the following crash:
>
> FATAL ERROR: Bad global exclusion count!
>
> FATAL ERROR: See http://www.ks.uiuc.edu/Research/namd/bugreport.html
> ------------- Processor 0 Exiting: Called CmiAbort ------------
> Reason: FATAL ERROR: Bad global exclusion count!
> FATAL ERROR: See http://www.ks.uiuc.edu/Research/namd/bugreport.html
>
> Stack Traceback:
> [0] _ZN10Controller9algorithmEv+0x4e8 [0x81f46a8]
> [1] _ZN10Controller9threadRunEPS_+0xc [0x8200a06]
> [2] /usr/local/namd/namd2.i686 [0x82eddb5]
> [3] Charm++ Runtime: Converse thread (qt_args+0x72 [0x83722ee])
> Fatal error on PE 0> FATAL ERROR: Bad global exclusion count!
>
> FATAL ERROR: See http://www.ks.uiuc.edu/Research/namd/bugreport.html
>
> The input pdb file looks OK, i.e., the protein is well inside the box of
> water.
>
> Does anyone have a clue?
>
> Thanks
>
> Idit Buch
>
> Ph.D. student of Bio-nanotechnology
>
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