[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
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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