[Chimera-users] Ligand structure minimization

Conrad Huang conrad at cgl.ucsf.edu
Wed May 2 09:49:08 PDT 2007

That's definitely a bug.  I missed a Numeric reference in MMTK when I 
did the Numeric->numpy conversion.  It will be fixed in the next 
release, which should be up in a couple weeks.  We will also try to get 
more recent snapshots with the bug fix up in the mean time.  Sorry about 


Jean-Didier Marechal wrote:
> Dear all,
> I don't know whether my problem falls in "bug" or "user request"
> category, pcorry if I use the wrong list.
> I am preparing a course where students will perform some protein-ligand
> dockings. I was thinking in minimizing the ligand in chimera using the
> "minimize structure" tool. 
> I have installed the 1.2356 (that's what I thought but the message in
> the "About UCSF Chimera" pop up window says 1.2376 actually)  version of
> chimera on ubuntu 6.10 and when I try to minimize my ligand (a HIV
> protease inhibitor), I am stopped at the PARMCHK run. Chimera seems to
> have compatibility problems with numpy. I join here the message given in
> the reply log file:
> ....
> Charges for residue U0E determined
> Total charge for #0: 1.0000
> Running PARMCHK for U0E1.pdb
> command: /usr/local/chimera/bin/antechamber/exe/parmchk
> -i /tmp/tmpc6R8F8/parmchk.in.0 -f mol2 -o /tmp/tmpc6R8F8/frcmod.0
> -p /usr/local/chimera/share/MMMD/parm/gaff.dat
> Finished PARMCHK for U0E1.pdbThis version of Chimera uses numpy for
> calculations.
> Numeric is only available in Chimera 1.2318 and earlier.
> Is there an easy way to move around this problem or should I install a
> earlier version of chimera for the moment? 
> cheers,
> JD
> _______________________________________________
> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu
> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users

More information about the Chimera-users mailing list