[Chimera-users] Help Generating Spheres

Repic Matej matej.repic at epfl.ch
Fri Aug 7 02:07:49 PDT 2015

Dear Daniel,

The error you are getting only says that the sphgen program is not in your $PATH and therefore the shell cannot find the executable to run. Make sure you have installed DOCK6, which is not bundled with Chimera. You need to apply for the DOCK6 license (free for academia) and the "sphgen" program will be bundled with it. Apply here:

After you have made sure DOCK6 is properly installed by following the instructions below, you can follow all the tutorials available online.


Dr. Matej Repic
Ecole Polytechnique Fédérale de Lausanne
Laboratory of Computational Chemistry and Biochemistry
BCH 4108
CH - 1015 Lausanne

From: <chimera-users-bounces at cgl.ucsf.edu<mailto:chimera-users-bounces at cgl.ucsf.edu>> on behalf of "Flaherty, Daniel P" <dflaher at purdue.edu<mailto:dflaher at purdue.edu>>
Date: Friday, August 7, 2015 at 04:38
To: "chimera-users at cgl.ucsf.edu<mailto:chimera-users at cgl.ucsf.edu>" <chimera-users at cgl.ucsf.edu<mailto:chimera-users at cgl.ucsf.edu>>
Subject: [Chimera-users] Help Generating Spheres


I’m teaching myself to perform molecular modeling and docking using your tutorials.   I am trying to prepare a protein for a vHTS and I have run into a snag during the sphere generation tutorial (http://dock.compbio.ucsf.edu/DOCK_6/tutorials/sphere_generation/generating_spheres.htm).

In the section where it says,"To generate the spheres, simply use the command "sphgen"  in the same folder that contains the INSPH and the rec.ms files. The output will be two files: rec.sph<http://dock.compbio.ucsf.edu/DOCK_6/tutorials/sphere_generation/rec.sph>, which contains the spheres in clusters, and OUTSPH<http://dock.compbio.ucsf.edu/DOCK_6/tutorials/sphere_generation/OUTSPH>, which contains general information about the calculation.”

I am getting an error that says Unrecognized command: “sphgen”.   I downloaded the INSPH text file but I have no idea what to do with it.  I don’t know what “folder” the tutorial refers to when it says,”use the command ‘sphgen’ in the same folder that contains the INSPH and rec.ms files."

Any help would be greatly appreciated!


-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/attachments/20150807/4cf7027c/attachment.html>

More information about the Chimera-users mailing list