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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.<br>
<br>
If that doesn't fix it, you will need to patch the appropriate
source code -- OpenMM's build script or the Python distutils module.<br>
<br>
From the ld documentation:<br>
<blockquote type="cite">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.</blockquote>
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 portable.<br>
<br>
If the above information is insufficient to get it to install, let
me know, and I'll dig further.<br>
<br>
-- Greg<br>
<br>
<div class="moz-cite-prefix">On 11/30/2015 09:04 AM, Jaime
Rodríguez-Guerra Pedregal wrote:<br>
</div>
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<p>Hello,</p>
<p><br>
</p>
<p>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:</p>
<p><br>
</p>
<div>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</div>
<div>g++: error: unrecognized command line option ‘-R’</div>
<div><br>
</div>
which is probably not related to Chimera at all.
<p><br>
</p>
<p>What I've done so far:</p>
<p><br>
</p>
<p>1. Download precompiled binaries for Linux from their site: <a
moz-do-not-send="true"
href="https://simtk.org/project/xml/downloads.xml?group_id=161"
id="LPlnk393679"
title="https://simtk.org/project/xml/downloads.xml?group_id=161
Ctrl+Haga clic o puntee para seguir el vínculo"><a class="moz-txt-link-freetext" href="https://simtk.org/project/xml/downloads.xml?group_id=161">https://simtk.org/project/xml/downloads.xml?group_id=161</a></a></p>
<p><br>
</p>
<p>2. Extract that file and merge the contents of the
directories "include" and "lib" with those in Chimera root
path.</p>
<p><br>
</p>
<p>3. Cd into the python directory of the extracted file and
run: chimera --nogui --script "setup.py install". </p>
<p><br>
</p>
<p>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.</p>
<p><br>
</p>
<p>Thank you in advance,</p>
<p>Jaime.</p>
</div>
<br>
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