[gmx-users] deprotonated cys

Chris Neale chris.neale at utoronto.ca
Mon Jul 28 16:00:31 CEST 2008

But of course then you also need to parameterize it, which is not a trivial task. OPLS does not have parameters for a cys thiolate; I'm not sure about other ff's. If you go back to the opls paper, you can follow the route by which they parameterized other ionized sc's. I have been considering doing this myself, but it seems complicated for my slight experience level with qm. Remove the hydrogen from the rtp file and re-work the charge based on a guess at your own peril. I suppose that there are things that you could do with such a model, but if the cys is deeply relevant then you should really find consistent parameters or develop them yourself.


-- original message --

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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