From: Jim Pfaendtner (jpfaendt_at_hec.utah.edu)
Date: Thu Aug 02 2007 - 15:56:18 CDT
I have built a system from a pdb which contains several protein
segments. Using psfgen I read them in separately and created
separate segments for them. Next I solvated and neutralized it using
the vmd solvate/ionize plugins. When I am doing a minimization I am
getting this error:
Warning: Bad global exclusion count, possible error!
Warning: Increasing cutoff during minimization may avoid this.
Warning: Bad global bond count!
Warning: Bad global angle count!
Warning: Bad global dihedral count!
Warning: Bad global improper count!
And after the minimization finishes I am getting this error when I
try to heat the crystal structure:
REASSIGNING VELOCITIES AT STEP 0 TO 20 KELVIN.
FATAL ERROR: Bad global exclusion count!
FATAL ERROR: See http://www.ks.uiuc.edu/Research/namd/bugreport.html
And then the job crashes completely. This is occurring at the
"temperature 20.0" line in my NAMD file. I normally start the
heating run with the temperature set to 0.0 K but I was trying
slightly above 0 K just in case that was the problem (the crash
happens no matter what I set the "temperature XX" value to.
I saw a previous note about this error and added the line:
"regenerate angles dihedrals" to my psfgen script, but that did not
seem to help.
Can anyone suggest how I can find the source of this error?
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