[Chimera-users] how to guess ligand's net charge?

Eric Pettersen pett at cgl.ucsf.edu
Wed Aug 21 09:31:04 PDT 2019

Hi Thomas,
	Chimera does its own charge estimation, based on the atom types it’s computed for the ligand.  The routine is called estimateNetCharge and it’s found in the AddCharge module in your Chimera distribution.  It’s a fairly complicated routine.
	Specifically the file you will find estimateNetCharge in is:


	<Chimera install location>/share/AddCharge/__init__.py


	Eric Pettersen
	UCSF Computer Graphics Lab

> On Aug 21, 2019, at 9:00 AM, Thomas Evangelidis <tevang3 at gmail.com> wrote:
> Greetings,
> How does Chimera guess the net charge of a ligand when prompted to select the charge type (AM1-bcc or Gasteiger)? I am doing high throughput protein-ligand MD simulations and would like to know which open source library Chimera uses for this task.
> Thanks in advance.
> Thomas 
> -- 
> ======================================================================
> Dr. Thomas Evangelidis
> Research Scientist
> IOCB - Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences <https://www.uochb.cz/web/structure/31.html?lang=en>, Prague, Czech Republic
>   & 
> CEITEC - Central European Institute of Technology <https://www.ceitec.eu/>, Brno, Czech Republic 
> email: tevang3 at gmail.com <mailto:tevang3 at gmail.com>, Twitter: tevangelidis <https://twitter.com/tevangelidis>, LinkedIn: Thomas Evangelidis <https://www.linkedin.com/in/thomas-evangelidis-495b45125/>
> website: https://sites.google.com/site/thomasevangelidishomepage/ <https://sites.google.com/site/thomasevangelidishomepage/>
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