[Chimera-users] FAD Topology/Parameter Files

Eric Pettersen pett at cgl.ucsf.edu
Mon Nov 22 13:09:48 PST 2021

Hi Zehra,
	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 <http://ambermd.org/MailingLists.php>).  That said, there is a parameterization for FAD at this site: AMBER parameter database <http://amber.manchester.ac.uk/>, though I don't know if its protonation state matches what you need.


	Eric Pettersen
	UCSF Computer Graphics Lab

> On Nov 20, 2021, at 8:59 AM, Zehra GÜNEŞ via Chimera-users <chimera-users at 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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