[Chimera-users] Installing OpenMM in Chimera

Greg Couch gregc at cgl.ucsf.edu
Mon Nov 30 17:06:33 PST 2015

This is probably a bug in OpenMM's build script, but it could be in the 
Python distutils package that comes with Chimera (you don't say which 
version you're using).  Try again with the Chimera daily build, since 
that comes with Python 2.7.10, the latest revision of Python 2.7.

If that doesn't fix it, you will need to patch the appropriate source 
code -- OpenMM's build script or the Python distutils module.

 From the ld documentation:
> For compatibility with other ELF linkers, if the -R option is followed 
> by a directory name, rather than a file name, it is treated as the 
> -rpath option.
So, you should change the -R/lib to be -Wl,-Rlib or -Wl,-rpath,/lib.  I 
suspect that the -R is from SunOS, but as you found out, that is not 

If the above information is insufficient to get it to install, let me 
know, and I'll dig further.

     -- Greg

On 11/30/2015 09:04 AM, Jaime Rodríguez-Guerra Pedregal 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
> 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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> Chimera-users at cgl.ucsf.edu
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