[gmx-users] How to use deprotonated Cys
David van der Spoel
spoel at xray.bmc.uu.se
Fri Aug 25 06:46:19 CEST 2006
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
>>>>Please don't post (un)subscribe requests to the list. Use the
>>>>www interface or send it to gmx-users-request at gromacs.org.
>>>>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
>>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
>>Please don't post (un)subscribe requests to the list. Use the
>>www interface or send it to gmx-users-request at gromacs.org.
>>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
spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
More information about the gromacs.org_gmx-users
mailing list