[gmx-users] How to use deprotonated Cys
raja
raja_28 at fastmail.us
Fri Aug 25 06:43:13 CEST 2006
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.
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
> >>++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
> >>_______________________________________________
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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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