[Chimera-users] Adding charges to insulin receptor

[Saousen Diaf]

Thank you Elaine for the information, glycans are important for the
receptor that I am working on and I want to remove steric clashes, that
might have developed during their addition, I will try and see if CHRMM GUI
will work, thank you again.

Best
Saousen

On Tue, Feb 15, 2022 at 5:05 PM Elaine Meng <meng at cgl.ucsf.edu> wrote:

> 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
>
>
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