Jerome,
Yes, I did rename the CyS into CYX.
John
-----Original Message-----
From: owner-amber.scripps.edu [mailto:owner-amber.scripps.edu] On Behalf Of Jerome.GOLEBIOWSKI.unice.fr
Sent: Wednesday, February 28, 2007 7:27 AM
To: amber.scripps.edu
Subject: Re: AMBER: Disulfide Bonds
Did you rename your cysteine residues (CYS) into CYX in your pdb ?
Jerome
Selon "Beale, John" <jbeale.stlcop.edu>:
> 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
France
tel: +33 (0)4 92 07 61 03
http://www.unice.fr/lcmba
http://www.unice.fr/lcmba/golebiowski
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Received on Sun Mar 04 2007 - 06:07:07 PST
