[gmx-users] How to use deprotonated Cys

[David van der Spoel]

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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