[gmx-users] How to use deprotonated Cys

[David van der Spoel]

raja wrote:
> 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
> atoms).
> 
> Now please tell me how to treat this Cys in opls force field.
you will have to generate a specbond.dat entry for Cys-Zn linkage, and 
also a Cys residue entry in rtp/hdb with appropriate charges.  For this 
  you may need to do quantum calculations or check the literature. I 
assume the Zn has other ligands too, so these should be taken into 
account as well.

> 
> With thanks!
> B.Nataraj
> 
> 
> 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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-- 
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
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++