[gmx-users] How to use deprotonated Cys

Alpay Temiz temiz+ at pitt.edu
Thu Aug 24 17:41:18 CEST 2006


Copy your forcefield rtp file to you working diecrtory and comment out the
CYSH entry

This way pdb2gmx will use CYS (deprotanated) topology,
It may give a warning as cant find CYSH trying to use CYS

Give it a try


Date: Thu, 24 Aug 2006 06:10:00 -0700
From: "raja" <raja_28 at fastmail.us>
To: gmx-users at gromacs.org
Message-ID: <1156425000.2288.269317922 at webmail.messagingengine.com>
Content-Type: text/plain; charset="iso-8859-1"

Hi all,
I have protein with cys in active site, and I want to use deprotonated
cys. In manual for pdb2gmx  clearly says on option of choosing Cys
protonated state possibility but why that option not appearing while
running pdb2gmx , just like for Arg, His, Asp and Glu. I read
quite a lot of mails regarding this issue most of them are in 2004
archives. Hope things are now changed and I can get some direct
solution for this from any of you. 
With thanks!
  raja_28 at fastmail.us

http://www.fastmail.fm - Same, same, but different

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