[Chimera-users] user-defined charges

[Elaine Meng]

Hi Jay,
Add Ions needs Amber/GAFF atom types (not just charges), and Add Charge is called to assign both those things.  You would need to run Add Charge first to get the GAFF types, then use define attribute to overwrite the charges with your own charges, then run Add Ions.  

Add Charge can be run separately by choosing it from the menu under Tools… Structure Editing, or as command "addcharge"
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/addcharge/addcharge.html>
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/addcharge.html>

I hope this helps,
Elaine
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Elaine C. Meng, Ph.D. 
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Jun 16, 2014, at 12:37 PM, "Eifler, Jay Q. (UMKC-Student)" <jqewt2 at mail.umkc.edu> wrote:

> Wanting to know if we can use charges assigned by define attribute in a file
> for the purpose of adding ions.  Seems like the Add Ions feature will not do
> this and will only use the built in methods Gasteigter, etc.  I have a HYP
> residue that the Add Charge feature won't do.