[Chimera-users] Installing OpenMM in Chimera

Jaime Rodríguez-Guerra Pedregal Jaime.RodriguezGuerra at uab.cat
Tue Dec 1 06:34:28 PST 2015

Hi guys!

Thanks for those tips! I managed to install it after patching unixccompiler.py in Chimera's distutils. I was using Chimera 1.10.2 with Python 2.7.8 so maybe that's already fixed in a more recent version, but I had installed a lot of packages a didn't feel like going through that hassle again.

I detailed my adventure in a post in OpenMM forums, so if somebody is experiencing the same issue, go to: https://simtk.org/forums/viewtopic.php?f=161&t=6158&p=15787#p15787

Thanks again!

PS: Eric, yes, I did know about MMTK in Chimera, but I am trying to do some GPU accelerated calculations. Thanks anyway! :)

De: Eric Pettersen <pett at cgl.ucsf.edu>
Enviado: martes, 1 de diciembre de 2015 2:36
Para: Jaime Rodríguez-Guerra Pedregal
Cc: chimera-users at cgl.ucsf.edu
Asunto: Re: [Chimera-users] Installing OpenMM in Chimera

Hi Jaime,
You don't say exactly what your goal is with the MD, but I feel like I should point out that in the daily build you can run MD via the included MMTK library.  The code is in the "md" module and the interface in the the MD/Ensemble Analysis category of tools.  Of course, OpenMM offers different capabilties and maybe you need those specifically...


Eric Pettersen
UCSF Computer Graphics Lab

On Nov 30, 2015, at 9:04 AM, Jaime Rodríguez-Guerra Pedregal <Jaime.RodriguezGuerra at uab.cat<mailto:Jaime.RodriguezGuerra at uab.cat>> wrote:


I am trying to install OpenMM in Chimera to script some molecular dynamics. However, I am struggling to make it work, since the build fails with this error:

g++ -pthread -fPIC -mtune=generic -m64 -I/home/chimera/chimeraBuild_X11/build/build/include -L/home/chimera/chimeraBuild_X11/build/build/lib -DUSE_DYLD_GLOBAL_NAMESPACE -shared -Wl,--hash-style=both build/temp.linux-x86_64-2.7/src/swig_doxygen/OpenMMSwig.o -L/lib -R/lib -lOpenMM -lOpenMMAmoeba -lOpenMMRPMD -lOpenMMDrude -o build/lib.linux-x86_64-2.7/simtk/openmm/_openmm.so
g++: error: unrecognized command line option '-R'

which is probably not related to Chimera at all.

What I've done so far:

1. Download precompiled binaries for Linux from their site: https://simtk.org/project/xml/downloads.xml?group_id=161

2. Extract that file and merge the contents of the directories "include" and "lib" with those in Chimera root path.

3. Cd into the python directory of the extracted file and run: chimera --nogui --script "setup.py install".

Has somebody been successful with this package? I know it seems more of a compiler issue, but maybe Chimera is doing some trickery with the build mechanism too.

Thank you in advance,
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