[Chimera-users] Adding charges to insulin receptor

[Elaine Meng]

Hi Saousen,
If you are using CHARMM GUI to add residues, it might make more sense to use CHARMM to minimize the structure.

If trying to use Chimera: You have to use your own chemical knowledge of these glycan residues and specify their net charges as requested.  If the residue is neutral, then net charge is 0, of course.  Chimera does not "know" the glycan residues so it has to calculate partial charges for all the atoms using Antechamber, which requires specifying net charges, and also might take a long time. Chimera does not know the GLYCAM force field which already has partial charges for the glycan residues, for example.  Chimera guesses the net charges, so you could just use those guesses, but it would be best if you checked to be sure.

Are the glycans important to the minimization?  Maybe you could minimize the protein part before adding them.

Also remember that minimization will not change the structure much, and has very limited power to "rescue" poorly built areas.  
Good luck,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco


> On Feb 15, 2022, at 1:45 PM, Saousen Diaf via Chimera-users <chimera-users at cgl.ucsf.edu> wrote:
> 
> Hello Elaine,
> 
> I want to energy minimize a model of insulin receptor using chimera, but it is asking me to specify the net charges of some residues, which most of them are glycans that I added using CHARMM GUI, would you please help me with that?
> 
> Thank you in advance for your help.
> 
> Best
> Saousen