Re: undefined loops

From: Brian Bennion (
Date: Thu Mar 18 2004 - 12:16:58 CST

Hi Julie

You will have to identify the separate peptides explicitly as segments in
your psf file.


On Thu, 18 Mar 2004, Stern, Julie wrote:

> Hello,
> 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?
> Thanks.
> Sincerely,
> Julie Stern
> Biology
> Brookhaven

**Brian Bennion, Ph.D. **
**Computational and Systems Biology Division **
**Biology and Biotechnology Research Program **
**Lawrence Livermore National Laboratory **
**P.O. Box 808, L-448 **
**7000 East Avenue phone: (925) 422-5722 **
**Livermore, CA 94550 fax: (925) 424-6605 **

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