From: Huy N. Ha (Huy.Ha_at_vcp.monash.edu.au)
Date: Tue Jun 12 2007 - 19:24:27 CDT
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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