Chimera does not include any explicit parameterization of FAD. If necessary, it estimates parameters on the fly. If you are doing a serious simulation you would want the most accurate parameters you can obtain, so perhaps you could ask for help on the AMBER mailing list (http://ambermd.org/MailingLists.php). That said, there is a parameterization for FAD at this site: AMBER parameter database, though I don't know if its protonation state matches what you need.

--Eric

Eric Pettersen

UCSF Computer Graphics Lab

On Nov 20, 2021, at 8:59 AM, Zehra GÜNEŞ via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:

Dear all,

I am working on a research protein that contains FAD. I have tried to prepare it for simulation but unfortunately I have neither trajectory nor parameter file of FAD. Would it be possible to share with me these files if you have?

Thanks in advance,

Zehra Güneş
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