[gmx-users] deprotonated Cys in Zn ion binding site

Tomek Wlodarski tomek.wlodarski at gmail.com
Wed Aug 3 23:58:33 CEST 2011

Hi all!

I would like to carry out a simulation of protein with Zn ion
coordinated by 2 Cys and 2 His in Gromos ff.
So I would need a deprotonated Cys however I know that it is present
only in Amber ff...
Do any of You have some experience with deprotonated Cys in Gromos ff?
especially bounded to Zn ion like in case of zinc finger?
I could use position restrain for Zn ion but still Cys would have
wrong protonation and this would influence the simulation.
Maybe someone has succeeded in parametrization or could help with it.
I have checked mailing list and found some ideas but would be very
grateful for some suggestions.
Thank you.


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