[gmx-users] How to use deprotonated Cys

David van der Spoel spoel at xray.bmc.uu.se
Thu Aug 24 17:21:22 CEST 2006

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 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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