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

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 Z

[gmx-users] deprotonated cys

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 d

[gmx-users] deprotonated cys (fw)

Original Message Date: Sun, 27 Jul 2008 17:58:20 + From: najwa drici <[EMAIL PROTECTED]> To: <[EMAIL PROTECTED]> 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 us