[chimerax-users] chimerax python module - LigParGen tutorial

[Elaine Meng]

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
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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 at 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 I have found chimera (0.4.7) as pip module, but it's written in python2 and therefore no longer maintained.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