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:

Mac:
Chimera.app/Contents/Resources/share/AddCharge/__init__.py

Linux/Windows:
<Chimera install location>/share/AddCharge/__init__.py

—Eric

Eric Pettersen
UCSF Computer Graphics Lab


On Aug 21, 2019, at 9:00 AM, Thomas Evangelidis <tevang3@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, Prague, Czech Republic

  & 
CEITEC - Central European Institute of Technology, Brno, Czech Republic 

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