AMBER Archive (2003)

Subject: Re: question about lysine?

From: Guanglei Cui (cuigl_at_morita.chem.sunysb.edu)
Date: Wed Feb 26 2003 - 21:20:43 CST

Hi,
     If you are trying to do constant pH simulation, you can find LYN in
amber force field for the deprotonated LYS. But it seems parameters
(charges) for all titratable groups in amber force field are not
complete. I had to calcuate charges for deprotonated TYR a while ago.

Guanglei Cui

Lishan Yao wrote:

>Hi:
> I want to change my lysine from protonated form to deprotonated form to run
>MD. How can I do that? Do I need to generate force parameters for it, just like
>an organic molecule, or can I find a easy way to do it?
>
>Thanks.
>
>Lishan
>
>
>