[Chimera-users] using scripts to prepare ligands

Elaine Meng meng at cgl.ucsf.edu
Sat Mar 30 08:12:43 PDT 2019

Hi Prasad,
(I changed the subject line to something more descriptive)

First use the Chimera GUI and try using commands on a few example molecules, to figure out what commands you want to use.  See command “minimize” with “nogui true” option (which will include adding hydrogens and charges) and command “write” (to save as mol2). 

Make sure to read the instructions carefully, especially for the “nogui” option of minimize:

Then if you need to loop through multiple inputs, you would put the commands into a script.

Make sure your SDF are 3D molecules.  Sometimes SDF files only have flat 2D diagrams that are not suitable for processing with Chimera.

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

> On Mar 30, 2019, at 3:23 AM, prasad ssv <prasad.ssva at gmail.com> wrote:
> hi,
> i had sdf file which contain a library of molecules,may be in thousands.
> and i want to minimize all those compounds for dockig,when i am adding hydrogen it showing some reply log as attached below.
> could you please help me to sort it out.i would like assign charges also for those molecules and save as mol2 files in single file.
> thanking you,

More information about the Chimera-users mailing list