AMBER Archive (2004)

Subject: Re: AMBER: about the parameter of the cystein pair in MD simulation

From: Thomas E. Cheatham, III (cheatham_at_chpc.utah.edu)
Date: Sun Jul 25 2004 - 22:07:44 CDT

> When I use "CYX" to describle CYS-CYS pair in my
> research project, the S-S bond always was broken even
> in my gradually equilibrium process. The distance

Have you added a bond between the CYX pairs using the bond command in
LEaP? The programs are not smart enough to automatically infer what
CYS-CYS bonds are present; it is your responsibility to make sure it is
set. If you have added a bond and it is deviated, this is most
unexpected...

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