AMBER Archive (2002)

Subject: SS bond

From: Masaki Tomimoto (masaki_at_stromix.com)
Date: Wed Jul 24 2002 - 14:04:21 CDT

Hi, All

   I have two questions. I think these are FAQ, but I could not find them.

(1) What I want to do is just minimizing only hydrogen atoms.

        * * S *
        * * B *
        * * 3 *
        * * M *

    With the above options, heavy atoms which directly attach to hydrogen atoms can move. Is there any way to fix ALL heavy atoms?

(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?

Thank you in advance

Masaki Tomimoto
Sr. Scientist
Computational Chemistry Department
Structural GenomiX, Inc