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. Best!
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