Re: AMBER: Disulfide Bonds

From: <>
Date: Wed, 28 Feb 2007 14:27:23 +0100

Did you rename your cysteine residues (CYS) into CYX in your pdb ?

Selon "Beale, John" <>:

> 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

Jérôme Golebiowski, Ph D.
Lab CMBA, University of Nice Sophia Antipolis
06108 nice cedex 2
tel: +33 (0)4 92 07 61 03
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Received on Sun Mar 04 2007 - 06:07:07 PST
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