[gmx-users] CYS deprotonated!

[David van der Spoel]

On Mon, 2004-12-27 at 14:28 -0200, Alberto Malvezzi wrote:
> Dear all,
> I have a depronated CYS in my protein.
> Is there a way to tell this to gromacs?
check recent mailing lists.
> Has anyone done this before?
> Thank You
> Alberto Malvezzi
> Universidade de São Paulo
> Brazil
> 
> On Thu, Dec 16, 2004 at 03:54:44PM +0000, Osmany Guirola Cruz wrote:
>  > >>
>  > Does not work :-( , my problem is this i have a peptide C-XXXXXXX-C (not
>  > ciclic)  but
>  > i dont want CYSH in mi gro file(i want it deprotonated and in the rtp
>  > files i found CYS1
>  > and CYS2). i probed pdb2gmx -ss and pdb2gmx -ss -inter and does not work
>  > always pdb2gmx
>  > put CYSH.
> 
> i have a topology for a deprotonated cys, made from some quantum
> calculations a while ago.  it's best that you contact me off-list.
> it will require some searching through my archives...
> 
> Marc
-- 
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://xray.bmc.uu.se/~spoel
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++