[gmx-users] How to use deprotonated Cys
David van der Spoel
spoel at xray.bmc.uu.se
Fri Aug 25 06:24:58 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.
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!
> On Thu, 24 Aug 2006 17:21:22 +0200, "David van der Spoel"
> <spoel at xray.bmc.uu.se> said:
>>>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.
>>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 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 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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