AMBER Archive (2002)

Subject: Re: SS bond

From: David A. Case (case_at_scripps.edu)
Date: Wed Jul 24 2002 - 15:00:44 CDT

On Wed, Jul 24, 2002, Masaki Tomimoto wrote:
>
> (2) I tried to add hydrogen atoms to a protein which has SS bonds with
> tleap. In that process, all cystein residues gets hydrogen atoms even if
> some of them make SS-bonds. Could anybody give me a way how tackle with a
> protein which has SS-bond?

Cysteines that are involved in SS bonds need to be labelled "CYX" in the
pdb file, so that LEaP will know that they are not "free" cysteines for which
a proton is needed.

..good luck...dac 

-- 

==================================================================
David A. Case                     |  e-mail:      case_at_scripps.edu
Dept. of Molecular Biology, TPC15 |  fax:          +1-858-784-8896
The Scripps Research Institute    |  phone:        +1-858-784-9768
10550 N. Torrey Pines Rd.         |  home page:                   
La Jolla CA 92037  USA            |    http://www.scripps.edu/case
==================================================================