[Chimera-users] Installing OpenMM in Chimera

Eric Pettersen pett at cgl.ucsf.edu
Mon Nov 30 17:36:11 PST 2015

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> wrote:
> Hello,
> 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 <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,
> Jaime.
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