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@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 _______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users