undefined loops

From: Stern, Julie (jvstern_at_bnl.gov)
Date: Thu Mar 18 2004 - 11:47:39 CST

    My program crashed giving back a "BUG ALERT error:
Bad global exclusion count! " The only thing I did differently
than previously working programs was that the new structure
I was working with had some undefined loops which are basically
not there in the file creating about 10 residue gaps each in the
pdb file. Wouldn't this just be treated as separate chains? Is this
potentially a problem with how the inpcrd and prmtop files were
generated from the pdb file? Do I need to add in residues where the loops
are supposed to be and just put in a 0.0 occupancy number?
I was told the protonation program that is applied to the pdb
file fixes any gaps in atom numberings so that shouldn't have
been the problem.
     What does the BUG ALERT signify and does anyone have any
suggestions regarding how to handle the undefined loop situation?

Julie Stern

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