[gmx-users] How to use deprotonated Cys

raja raja_28 at fastmail.us
Fri Aug 25 05:59:08 CEST 2006

Dear david,
Thanks for your reply. There are two forms exist for the protein of my
interest and one is native form and other is with ligand bound in it. In
later form of crystal structure, Cys is found to be as CSD [side chain
as -C-S(2OH)] and physically  attached to the Zn ion (as per pdb
connection record) at the active site. In native form, the Cys is as
such but not connected with Zn (in pdb no connection record is found). I
use the native form for the simulation; here I want to use Cys, as
deprotonated Cys since I believe is the right way to treat Cys which is
electorstaticaly ligating Zn along with other two partners,( 2 His NE2

Now please tell me how to treat this Cys in opls force field.

With thanks!

On Thu, 24 Aug 2006 17:21:22 +0200, "David van der Spoel"
<spoel at xray.bmc.uu.se> said:
> raja wrote:
> > Hi all,
> > I have protein with &#8220;cys&#8221; in active site, and I want to use deprotonated
> > &#8220;cys&#8221;. In manual for &#8220;pdb2gmx &#8220; clearly says on option of choosing Cys
> > protonated state possibility but why that option not appearing while
> > running &#8220;pdb2gmx&#8221; , just like for &#8220;Arg&#8221;, &#8220;His&#8221;, &#8220;Asp&#8221; and &#8220;Glu&#8221;. I read
> > quite a lot of mails regarding this issue most of them are in &#8220;2004
> > archives&#8221;. Hope things are now changed and I can get some direct
> > solution for this from any of you. 
> > With thanks!
> > B.Nataraj
> There is no support for a charged Cys in OPLS or GROMOS ffs, but in 
> GROMOS you can have deprotonated CYS (cys1) with zero charge. Is the CYS 
> not bound to anything?
> -- 
> David.
> ________________________________________________________________________
> David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
> Dept. of Cell and Molecular Biology, Uppsala University.
> Husargatan 3, Box 596,          75124 Uppsala, Sweden
> phone:  46 18 471 4205          fax: 46 18 511 755
> spoel at xray.bmc.uu.se    spoel at gromacs.org   http://folding.bmc.uu.se
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