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"
<[EMAIL PROTECTED]> 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"
<[EMAIL PROTECTED]> 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
[EMAIL PROTECTED] [EMAIL PROTECTED] 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
[EMAIL PROTECTED] [EMAIL PROTECTED] 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
[EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se
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