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" <[EMAIL PROTECTED]> 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" > > <[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 > >>>>++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ > >>>>_______________________________________________ > >>>>gmx-users mailing list [email protected] > >>>>http://www.gromacs.org/mailman/listinfo/gmx-users > >>>>Please don't post (un)subscribe requests to the list. Use the > >>>>www interface or send it to [EMAIL PROTECTED] > >>>>Can't post? Read http://www.gromacs.org/mailing_lists/users.php > >> > >> > >>-- > >>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 > >>++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ > >>_______________________________________________ > >>gmx-users mailing list [email protected] > >>http://www.gromacs.org/mailman/listinfo/gmx-users > >>Please don't post (un)subscribe requests to the list. Use the > >>www interface or send it to [EMAIL PROTECTED] > >>Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > > -- > 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 > ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ > _______________________________________________ > gmx-users mailing list [email protected] > http://www.gromacs.org/mailman/listinfo/gmx-users > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- raja [EMAIL PROTECTED]
-- http://www.fastmail.fm - Choose from over 50 domains or use your own _______________________________________________ gmx-users mailing list [email protected] http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
