[gmx-users] How to use deprotonated Cys
raja
raja_28 at fastmail.us
Fri Aug 25 07:10:30 CEST 2006
Dear David,
Thanks for your support as you are always.
Regards,
B.Nataraj
On Fri, 25 Aug 2006 06:46:19 +0200, "David van der Spoel"
<spoel at xray.bmc.uu.se> said:
> raja wrote:
> > Dear David,
> > Thanks again, yes Cys is having fourth ligand as water to complete the
> > tetrahedral geometry. So for, I used distance restraints to hold all
> > ligands intact with Zn at active site. All I want to do is trying to
> > simulate the structure to see the overall dynamics of protein; the
> > default Cys (protonated) in that case will affect the dynamics of
> > protein in big deal? Since I am not going to simulate any QM at active
> > site.
> >
> > So your feedback will help me to stick on the current setting and go
> > ahead for further simulation without further thinking of protonated
> > state of Cys.
>
>
> you need to have a good description of the Zn site. We previously used
> distance restraints for that (J. Comp. Aid. Mol. Des. 17 pp. 551-565
> (2003)), but it depends on the distance S-Zn (and other ligands). What
> is particularly important is the charge distribution. You can not leave
> the proton on if it shouldn't be there.
> >
> > With thanks!
> > B.Nataraj
> >
> >
> >
> > On Fri, 25 Aug 2006 06:24:58 +0200, "David van der Spoel"
> > <spoel at xray.bmc.uu.se> said:
> >
> >>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 “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!
> >>>>>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
> >>>>++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
> >>>>_______________________________________________
> >>>>gmx-users mailing list gmx-users at gromacs.org
> >>>>http://www.gromacs.org/mailman/listinfo/gmx-users
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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
> >>++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
> >>_______________________________________________
> >>gmx-users mailing list gmx-users at gromacs.org
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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
> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
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--
raja
raja_28 at fastmail.us
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