AMBER Archive (2006)

Subject: RE: AMBER: Amber: disufide bond

From: hayden (s0237717_at_sms.ed.ac.uk)
Date: Sun Nov 05 2006 - 07:03:23 CST

Hi Fenghui

It's not possible at this moment to have mobile cysteine bonds that form and
break during a single simulation. I suffer from the same problem with 3
cysteine bridges. I have some code that I wrote which performs cys-cys bond
breaking and forming, which you're welcome to, though it hasn't been tested
or peer-reviewed (other than by my supervisor). In essence it bonds cys to
cys via a distant dependent probabilistic function. I'm in the process of
upgrading it, the new bug-free version should be ready in a couple of weeks
if you're interested....

Best

Hayden

 
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