On Apr 7, 2021, at 8:59 AM, Elaine Meng <meng@cgl.ucsf.edu> wrote:

Dear Marco,
The instructions in the LigParGen tutorial are about using the Chimera program, not ChimeraX.  ChimeraX is a different program and does not (yet) have a Dock Prep tool.  Both programs are available, so you could certainly just get Chimera and try it according to the instructions.
I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Apr 7, 2021, at 12:30 AM, mdigennaro@uliege.be wrote:

Dear ChimeraX users,

I am trying to follow this tutorial to get the proper residues:
http://zarbi.chem.yale.edu/ligpargen/gmx_tutorial.html

I have found chimera (0.4.7) as pip module, but it's written in python2 and therefore no longer maintained.
Is there a chimerax module I can import?
Pychimera is also available and could install it with python2, but it also show compatibility problems with python3
Is DockPrep a separate module?

I have found this thread on the chimera forum which doesn't really answer the question:
http://plato.cgl.ucsf.edu/pipermail/chimera-users/2014-July/010115.html

Generally, how do I get unknown/custom residues (from LigParGen in this case) for Gromacs input files.

Thank you for your support

Marco

_______________________________________________
ChimeraX-users mailing list
ChimeraX-users@cgl.ucsf.edu
Manage subscription:
https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users