AMBER Archive (2007)

Subject: AMBER: Disulfide Bonds

From: Beale, John (jbeale_at_stlcop.edu)
Date: Wed Feb 28 2007 - 06:56:55 CST

I have a problem that I hope is fairly simple. I am working with a small
peptide that has a single disulfide bond. I do the correct "bond"
procedure in LEaP, and when I view the structure with "Edit" in LEaP
the disulfide bond is intact. When I do a minimization on the structure
and examine the pdb file generated with ambpdb from the *.rst file, I
find that the disulfide bond is no longer intact and the two sulfur
atoms have moved away from each other.

 

Can someone tell me what I can do to be certain that the disulfide bond
remains intact after LEaP?

 

John

 

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