[gmx-users] CYS deprotonated!
David van der Spoel
spoel at xray.bmc.uu.se
Mon Dec 27 18:59:51 CET 2004
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
> 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...
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
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