[Chimera-users] Ligand structure minimization

Jean-Didier Marechal jeandidier.marechal at uab.es
Fri Apr 27 09:39:27 PDT 2007

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
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? 


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