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.
Chris.
-- 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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