[Chimera-users] FAD Topology/Parameter Files

[Elaine Meng]

Hi Zehra,
If you mean you're trying to minimize (or even do short dynamics) inside of Chimera, it might not be possible.  If you tried to minimize this structure in Chimera, it will attempt to calculate partial charges and other force field parameters it needs for the FAD using Antechamber. 

However, charge calculation may fail on residues as large as FAD especially those with high charge density like phosphates.  You could try the Gasteiger option of the charge calculation for a more quick-and-dirty calculation, but it is not recommended for detailed/quantitative simulations of any kind.  Although it is possible to manually add specific charge values to use in Chimera, it is somewhat difficult.  Details about calculating or adding charges for ligand residues here:
<https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/minimize/minimize.html#nonstandard>

If you want to perform longer simulations or get quantitative results you should probably use some full-featured dynamics software like AMBER or GROMACS instead of Chimera.

I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Nov 22, 2021, at 1:09 PM, Eric Pettersen via Chimera-users <chimera-users at cgl.ucsf.edu> wrote:
> 
> 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).  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 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