[gmx-users] CYS deprotonated!
malvezzi at iq.usp.br
Mon Dec 27 17:28:33 CET 2004
I have a depronated CYS in my protein.
Is there a way to tell this to gromacs?
Has anyone done this before?
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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