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<p>Hi guys!</p>
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<p>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.</p>
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<p>I detailed my adventure in a post in OpenMM forums, so if somebody is experiencing the same issue, go to: <a href="https://simtk.org/forums/viewtopic.php?f=161&t=6158&p=15787#p15787" id="LPlnk713491" title="https://simtk.org/forums/viewtopic.php?f=161&t=6158&p=15787#p15787
Ctrl+Haga clic o puntee para seguir el vínculo">https://simtk.org/forums/viewtopic.php?f=161&t=6158&p=15787#p15787</a></p>
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<p>Thanks again!</p>
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<p>PS: Eric, yes, I did know about MMTK in Chimera, but I am trying to do some GPU accelerated calculations. Thanks anyway! :)</p>
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<div id="divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" color="#000000" style="font-size:11pt"><b>De:</b> Eric Pettersen <pett@cgl.ucsf.edu><br>
<b>Enviado:</b> martes, 1 de diciembre de 2015 2:36<br>
<b>Para:</b> Jaime Rodríguez-Guerra Pedregal<br>
<b>Cc:</b> chimera-users@cgl.ucsf.edu<br>
<b>Asunto:</b> Re: [Chimera-users] Installing OpenMM in Chimera</font>
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<div>Hi Jaime,
<div class=""><span class="Apple-tab-span" style="white-space:pre"></span>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…</div>
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<div class="">—Eric</div>
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<div class=""><span class="Apple-tab-span" style="white-space:pre"></span>Eric Pettersen</div>
<div class=""><span class="Apple-tab-span" style="white-space:pre"></span>UCSF Computer Graphics Lab</div>
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<div class="">On Nov 30, 2015, at 9:04 AM, Jaime Rodríguez-Guerra Pedregal <<a href="mailto:Jaime.RodriguezGuerra@uab.cat" class="">Jaime.RodriguezGuerra@uab.cat</a>> wrote:</div>
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<div class="" style="margin-top:0px; margin-bottom:0px">Hello,</div>
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<div class="" style="margin-top:0px; margin-bottom:0px">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:</div>
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<div class="">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 class="">g++: error: unrecognized command line option ‘-R’</div>
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which is probably not related to Chimera at all.
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<div class="" style="margin-top:0px; margin-bottom:0px">What I've done so far:</div>
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<div class="" style="margin-top:0px; margin-bottom:0px">1. Download precompiled binaries for Linux from their site: <a 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" class="">https://simtk.org/project/xml/downloads.xml?group_id=161</a></div>
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<div class="" style="margin-top:0px; margin-bottom:0px">2. Extract that file and merge the contents of the directories "include" and "lib" with those in Chimera root path.</div>
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<div class="" style="margin-top:0px; margin-bottom:0px">3. Cd into the python directory of the extracted file and run: chimera --nogui --script "setup.py install". </div>
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<div class="" style="margin-top:0px; margin-bottom:0px">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.</div>
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<div class="" style="margin-top:0px; margin-bottom:0px">Thank you in advance,</div>
<div class="" style="margin-top:0px; margin-bottom:0px">Jaime.</div>
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