[gmx-users] CYS deprotonated!

Alberto Malvezzi malvezzi at iq.usp.br
Mon Dec 27 17:28:33 CET 2004

Dear all,
I have a depronated CYS in my protein.
Is there a way to tell this to gromacs?
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...

Marc Lensink              http://www.biochem.oulu.fi/~lensink/
SCMBB, Université Libre de Bruxelles   lensink at scmbb.ulb.ac.be
Boulevard du Triomphe - CP 263, B-1050 Brussels, Belgium
tel: +32 2 650 5411  secr: +32 2 650 2013  fax: +32 2 650 5425

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