[gmx-users] deprotonated cys (fw)

David van der Spoel spoel at xray.bmc.uu.se
Sun Jul 27 23:01:02 CEST 2008

-------- Original Message --------
Date: 	Sun, 27 Jul 2008 17:58:20 +0000
From: 	najwa drici <dricinajwa at hotmail.fr>
To: 	<spoel at xray.bmc.uu.se>

i want to ask you question about how can i deprotonate or use
deprotonated cysteine because I have protein with “cys” in active site,
and I want to use deprotonated
“cys”. when i run “pdb2gmx “  no option appearing of choosing Cys
deprotonated state possibility

That's correct. You can edit the rtp file to add support for CYS-, e.g. 
name it CYM and then name the residue in your pdb file CYS instead of 
CYS as well.

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David van der Spoel, Ph.D., Professor of Biology
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se

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