{"id":350,"date":"2016-10-17T15:57:39","date_gmt":"2016-10-17T06:57:39","guid":{"rendered":"https:\/\/www.ag.kagawa-u.ac.jp\/charlesy\/wp\/?page_id=350"},"modified":"2017-12-06T14:54:47","modified_gmt":"2017-12-06T05:54:47","slug":"softwares","status":"publish","type":"page","link":"https:\/\/www.ag.kagawa-u.ac.jp\/charlesy\/memo\/softwares\/","title":{"rendered":"Softwares"},"content":{"rendered":"<p>\u4ee5\u4e0b\u306fmacOS Sierra\u74b0\u5883\u3067\u306e\u89e3\u8aac\u3067\u3059 (November 2, 2016)\uff0e\u74b0\u5883\uff1a macOS Sierra 10.12.1, 3.3 GHz Intel Core i5, \u30e1\u30e2\u30ea8 GB\uff0e<\/p>\n<p><del datetime=\"2017-01-17T00:34:26+00:00\">First, install <a href=\"https:\/\/www.xquartz.org\/\">Xquartz<\/a> (<span style=\"color: #ff0000;\">2.7.8<\/span>) on MacOS Sierra. Xquartz 2.7.11\u3067\u3082Openmotif\u3068\u306e\u554f\u984c\u304c\u89e3\u6c7a\u3055\u308c\u3066\u3044\u307e\u305b\u3093\u3067\u3057\u305f\uff0e<\/del>\uff08Homebrew\u306eopenmotif\u304c\u4fee\u6b63\u3055\u308c\uff0c\u554f\u984c\u304c\u89e3\u6c7a\u3055\u308c\u307e\u3057\u305f\uff09\uff0e<\/p>\n<p>\u307e\u305a\uff0c\u6700\u65b0\u306e<a href=\"https:\/\/www.xquartz.org\/\">Xquartz<\/a>\u3092\u30a4\u30f3\u30b9\u30c8\u30fc\u30eb\uff0e<\/p>\n<h3><span style=\"font-weight: bold;\"><a href=\"http:\/\/brew.sh\/index_ja.html\">Homebrew<\/a> (Package manager)<\/span><\/h3>\n<pre class=\"command-line\"><code class=\"language-bash\" data-line=\"\">$ \/usr\/bin\/ruby -e &quot;$(curl -fsSL https:\/\/raw.githubusercontent.com\/Homebrew\/install\/master\/install)&quot;<\/code><\/pre>\n<p>Paste that at a Terminal(.app) prompt. Xcode command line tools will be automatically installed.<\/p>\n<p>\u30b3\u30de\u30f3\u30c9\u30e9\u30a4\u30f3\u88dc\u5b8c\u306e\u305f\u3081\u306bbash-completion\u3092\u5165\u308c\u308b\u3068\u5e78\u305b\u306b\u306a\u308c\u308b (<a href=\"http:\/\/macwiki.osdn.jp\/wiki\/index.php\/bash\">bash- MacWiki<\/a>)\uff0e <\/p>\n<pre class=\"command-line\"><code class=\"language-bash\" data-line=\"\">$ brew install bash-completion<\/code><\/pre>\n<p>\u8a00\u308f\u308c\u305f\u901a\u308a\uff0c ~\/.bash_profile \u306b\u4ee5\u4e0b\u306e\u3088\u3046\u306b\u66f8\u304d\u8fbc\u3080\uff0e<\/p>\n<pre class=\"prettyprint\">&#091; -f &#47;usr&#47;local&#47;etc&#47;bash_completion &#093; && . &#47;usr&#47;local&#47;etc&#47;bash_completion<\/pre>\n<h2><span style=\"font-style: italic;\">Molecular Dynamics<\/span><\/h2>\n<h3><span style=\"font-weight: bold;\"><a href=\"http:\/\/www.gromacs.org\/\">GROMACS<\/a> (Molecular Dynamics Package)<\/span><\/h3>\n<p><a href=\"http:\/\/blog.livedoor.jp\/ag_plusplus\/archives\/68581553.html\">Gromacs 5.1.4\u3092Mac Yosemite\u4e0a\u306b\u30a4\u30f3\u30b9\u30c8\u30fc\u30eb (Ag++)<\/a>&nbsp;\u3092\u53c2\u8003\u306b\u3057\u3066\u30b3\u30f3\u30d1\u30a4\u30eb\uff0e<\/p>\n<pre class=\"command-line\"><code class=\"language-bash\" data-line=\"\">$ brew tap homebrew\/versions\n$ brew install gcc5 cmake boost fftw\n$ ln -s \/usr\/local\/bin\/gcc-5 \/usr\/local\/bin\/gcc\n$ ln -s \/usr\/local\/bin\/g++-5 \/usr\/local\/bin\/g++\n$ curl ftp:\/\/ftp.gromacs.org\/pub\/gromacs\/gromacs-5.1.4.tar.gz -o gromacs-5.1.4.tar.gz\n$ tar xvzf gromacs-5.1.4.tar.gz\n$ cd gromacs-5.1.4\n$ mkdir build\n$ cd build\n$ ccmake ..<\/code><\/pre>\n<p>ccmake\u304c\u8d77\u52d5\u3057\u305f\u3089\uff0c \u3092\u62bc\u3057\u307e\u3059\uff0eGCC\u304cOpenMP\u306b\u5bfe\u5fdc\u3057\u3066\u3044\u306a\u3044\u3068\u8a00\u308f\u308c\u307e\u3059\uff0e[e] \u3092\u62bc\u3057\u307e\u3059\uff0eBUILD_SHARED_LIBS OFF\u306b\uff0cBUILD_TESTING OFF\u306b\uff0cCMAKE_INSTALL_PREFIX\u306f \/opt\/gromacs-5.1.4\u306b\u3057\u307e\u3057\u305f\uff0eGMX_SIMD\u306fAVX2_256\u306e\u307e\u307e\u3067\uff0e\u30de\u30b7\u30f3\u306b\u3088\u3063\u3066\u9055\u3046\u3068\u601d\u3044\u307e\u3059\u304c\uff0cSSE4.1\u306b\u3057\u3066\u3044\u305f\u6642\u3088\u308a\u3082\u8a08\u7b97\u304c2\u500d\u901f\u304f\u306a\u308a\u307e\u3057\u305f\uff0e \u3092\u62bc\u3057\u3066\u3082\u3046\u4e00\u5ea6configure\u3057\u3066\uff0c[g] \u3067Makefile\u3092\u751f\u6210\u3057\u307e\u3059\uff0e<\/p>\n<pre class=\"command-line\"><code class=\"language-bash\" data-line=\"\">$ make -j 8\n$ sudo make install<\/code><\/pre>\n<p>~\/.bash_profile\u306b\uff0c<\/p>\n<pre class=\"prettyprint\">source &#47;opt&#47;gromacs-5.1.4&#47;bin&#47;GMXRC.bash<\/pre>\n<p>\u3068\u66f8\u304d\u8fbc\u3093\u3067\u304a\u304d\u307e\u3059\uff0e<\/p>\n<p>GPU\u7248\u306e\u30a4\u30f3\u30b9\u30c8\u30fc\u30eb\u65b9\u6cd5\u306f<a href=\"https:\/\/www.ag.kagawa-u.ac.jp\/charlesy\/2016\/11\/02\/gpu%E5%AF%BE%E5%BF%9Cgromacs%E3%81%AE%E3%82%A4%E3%83%B3%E3%82%B9%E3%83%88%E3%83%BC%E3%83%AB\/\">\u3053\u3061\u3089<\/a>\uff0e<\/p>\n<h3><span style=\"font-weight: bold;\"><a href=\"http:\/\/www.ks.uiuc.edu\/Research\/vmd\/\">VMD &#8212; Visual Molecular Dynamics<\/a><\/span><\/h3>\n<p>Download version 1.9.2 for MacOS X OpenGL (32-bit Intel x86) and put it into \/Applications folder. Set command-line alias and VMD_PLUGIN_PATH environment variable in your .bashrc file as follow.<\/p>\n<pre class=\"prettyprint\">alias vmd=&#34;&#47;Applications&#47;VMD\\ 1.9.2.app&#47;Contents&#47;vmd&#47;vmd_MACOSXX86&#34;\r\nexport VMD_PLUGIN_PATH=&#47;Applications&#47;VMD\\ 1.9.2.app&#47;Contents&#47;vmd&#47;plugins&#47;MACOSXX86&#47;molfile<\/pre>\n<h3><span style=\"font-weight: bold;\"><a href=\"http:\/\/ambermd.org\/\">AmberTools16<\/a><\/span><\/h3>\n<p>\u53c2\u8003\u30b5\u30a4\u30c8:&nbsp;<a href=\"http:\/\/blog.livedoor.jp\/ag_plusplus\/archives\/68540711.html\">Mac OS\u306bAmberTools 16\u3092\u30a4\u30f3\u30b9\u30c8\u30fc\u30eb (Ag++) <\/a><\/p>\n<p>\/opt\/amber16 \u306b\u30a4\u30f3\u30b9\u30c8\u30fc\u30eb\u3057\u305f\uff0e<\/p>\n<pre class=\"command-line\"><code class=\"language-bash\" data-line=\"\">$ tar xvjf AmberTools16.tar.bz2\n$ sudo mv amber16 \/opt\/\n$ cd \/opt\/amber16\n$ brew install gcc5 python\n$ ln -s \/usr\/local\/bin\/gcc-5 \/usr\/local\/bin\/gcc\n$ ln -s \/usr\/local\/bin\/g++-5 \/usr\/local\/bin\/g++\n$ ln -s \/usr\/local\/bin\/gfortran-5 \/usr\/local\/bin\/gfortran\n$ pip install numpy scipy matplotlib\n$ export AMBERHOME=\/opt\/amber16\n$ .\/configure gnu\n$ source \/opt\/amber16\/amber.sh\n$ make -j8 install<\/code><\/pre>\n<p>~\/.bash_profile\u306b\uff0c<\/p>\n<pre class=\"prettyprint\">source &#47;opt&#47;amber16&#47;amber.sh<\/pre>\n<p>\u3068\u66f8\u304d\u8fbc\u3093\u3067\u304a\u304d\u307e\u3059\uff0e<\/p>\n<h3><span style=\"font-weight: bold;\"><a href=\"https:\/\/code.google.com\/archive\/p\/acpype\/\">Acpype<\/a><\/span><\/h3>\n<p>A tool based on Python to use Antechamber to generate topologies for chemical compounds.<\/p>\n<pre class=\"command-line\"><code class=\"language-bash\" data-line=\"\">$ cd \/opt\n$ svn checkout http:\/\/svn.code.sf.net\/p\/ccpn\/code\/branches\/stable\/ccpn\/python\/acpype acpype\n$ ln -s \/opt\/acpype\/acpype.py \/usr\/local\/bin\/acpype<\/code><\/pre>\n<p><a href=\"http:\/\/blog.livedoor.jp\/ag_plusplus\/archives\/68154284.html\">Ag++: ACPYPE.py\u3092\u4f7f\u3063\u305fAMBER\u2192Gromacs topology\u306e\u5909\u63db\u3068\u6ce8\u610f\u70b9\uff08\u30d0\u30b0\uff1f\uff09<\/a>\u306e\u30b3\u30e1\u30f3\u30c8\u3092\u53c2\u8003\u306b\uff0cacpype.py\u306e2389\u884c\u76ee\u306e%12.6f\u3092%12.5f\u3078\u4fee\u6b63\u3057\u305f\uff0e<\/p>\n<h3><span style=\"font-weight: bold;\"><a href=\"http:\/\/plasma-gate.weizmann.ac.il\/Grace\/\">Grace<\/a><\/span><\/h3>\n<p>A WYSIWYG 2D plotting tool.<\/p>\n<p><del datetime=\"2017-01-17T00:34:26+00:00\">XQuartz 2.7.9\u3067\u306f\u30a8\u30e9\u30fc\u3067\u8d77\u52d5\u3067\u304d\u305a<a href=\"https:\/\/www.xquartz.org\/releases\/XQuartz-2.7.8.html\">2.7.8<\/a>\u306b<a href=\"https:\/\/gist.github.com\/tonymtz\/714e73ccb79e21c4fc9c\">\u30c0\u30a6\u30f3\u30b0\u30ec\u30fc\u30c9<\/a>\u3057\uff0copenmotif\u3068grace\u3092\u518d\u30a4\u30f3\u30b9\u30c8\u30fc\u30eb\u3059\u308b (<a href=\"https:\/\/github.com\/Homebrew\/brew\/issues\/1189\">\u53c2\u8003<\/a>) \u3068\u8d77\u52d5\u3067\u304d\u307e\u3057\u305f\uff0e<\/del>\uff08\u4fee\u6b63\u3055\u308c\u307e\u3057\u305f\uff09\uff0e<\/p>\n<pre class=\"command-line\"><code class=\"language-bash\" data-line=\"\">$ brew install homebrew\/X11\/grace<\/code><\/pre>\n<h3><span style=\"font-weight: bold;\"><a href=\"http:\/\/www.poissonboltzmann.org\/\">APBS<\/a><\/span><\/h3>\n<p>Version 1.5 \u3092<a href=\"http:\/\/blog.livedoor.jp\/ag_plusplus\/archives\/68544187.html\">Homebrewed PyMOL 1.8.2 + APBS plugin work on Mac El Capitan (Ag++) <\/a>\u3092\u53c2\u8003\u306b\u3057\u3066<a href=\"https:\/\/www.ag.kagawa-u.ac.jp\/charlesy\/\">compile<\/a>\uff0c\/opt\/apbs-1.5 \u3078\u30a4\u30f3\u30b9\u30c8\u30fc\u30eb\u3057\u3066\uff0c\/opt\/apbs-1.5\/bin\u3078PATH\u3092\u901a\u3059\uff0e<a href=\"http:\/\/blog.livedoor.jp\/ag_plusplus\/archives\/68544187.html\">\u4e0a\u8a18\u30b5\u30a4<\/a>\u30c8\u3067\u516c\u958b\u3055\u308c\u3066\u3044\u308b\u4fee\u6b63\u3055\u308c\u305fPymol plugin\u3067\u53ef\u8996\u5316\uff0ePQR file\u306fGROMACS\u306etpr\u30d5\u30a1\u30a4\u30eb\u304b\u3089\u4f5c\u6210\uff0e<\/p>\n<pre class=\"command-line\"><code class=\"language-bash\" data-line=\"\">$ gmx editconf -f hoge.tpr -mead<\/code><\/pre>\n<p>mead.pqr\u304c\u4f5c\u6210\u3055\u308c\u308b\uff0e<\/p>\n<h2><span style=\"font-style: italic;\">Molecular structure editing and visualisation<\/span><\/h2>\n<h3><span style=\"font-weight: bold;\"><a href=\"http:\/\/www.pymol.org\/\">PyMOL<\/a> (Molecular viewer)<\/span><\/h3>\n<p>For OS X native PyMOL, visit pymol website, register an academic license, and download MacPyMOL 1.3r1. If you want the latest version (1.8.2.1) with X11,<\/p>\n<pre class=\"command-line\"><code class=\"language-bash\" data-line=\"\">$ brew install homebrew\/science\/pymol<\/code><\/pre>\n<h3><span style=\"font-weight: bold;\">Open Babel (Molecular File Converter)<\/span><\/h3>\n<pre class=\"command-line\"><code class=\"language-bash\" data-line=\"\">$ brew install open-babel<\/code><\/pre>\n<h3><span style=\"font-weight: bold;\"><a href=\"http:\/\/avogadro.cc\/wiki\/Main_Page\">Avogadro<\/a> (Molecular Editor)<\/span><\/h3>\n<p>Free cross-platform molecular editor.<\/p>\n<pre class=\"command-line\"><code class=\"language-bash\" data-line=\"\">$ brew tap caskroom\/cask\n$ brew cask install avogadro<\/code><\/pre>\n<h3><span style=\"font-weight: bold;\"><a href=\"http:\/\/spdbv.vital-it.ch\/disclaim.html#\">Swiss PDB Viewer<\/a><\/span><\/h3>\n<p>Swiss PDB Viewer can build and edit protein structure.<\/p>\n<p><span style=\"color: #ff0000;\">Fatal Error: The folder \u2018usrstuff\u2019 is missing \u3068\u30d7\u30ed\u30f3\u30d7\u30c8\u304c\u51fa\u3066\u8d77\u52d5\u4e0d\u53ef\uff0e<\/span><\/p>\n<h3><span style=\"font-weight: bold;\"><a href=\"https:\/\/salilab.org\/modeller\/\">MODELLER<\/a> (version 9.17)<\/span><\/h3>\n<p>\u30bf\u30f3\u30d1\u30af\u8cea\u306e\u30db\u30e2\u30ed\u30b8\u30fc\u30e2\u30c7\u30ea\u30f3\u30b0\u30d7\u30ed\u30b0\u30e9\u30e0\uff0e<\/p>\n<pre class=\"command-line\"><code class=\"language-bash\" data-line=\"\">$ brew tap salilab\/salilab\n$ brew install modeller<\/code><\/pre>\n<p>Edit \/usr\/local\/Cellar\/modeller\/9.17\/modlib\/modeller\/config.py<br \/>\nand replace XXXX with your Modeller license key<\/p>\n<h3><span style=\"font-weight: bold;\"><a href=\"http:\/\/www.rdkit.org\/\">RDkit<\/a><\/h3>\n<p>Chemoinformatics\u30bd\u30d5\u30c8\u30a6\u30a7\u30a2\uff0e\u53c2\u8003URL: http:\/\/qiita.com\/mojaie\/items\/2113274201038b29af3d<\/p>\n<pre class=\"command-line\"><code class=\"language-bash\" data-line=\"\">$ brew tap edc\/homebrew-rdkit\n$ brew install rdkit --with-python3 --with-pycairo<\/code><\/pre>\n<h2><span style=\"font-style: italic;\">Docking Simulation<\/span><\/h2>\n<h3><span style=\"font-weight: bold;\"><a href=\"http:\/\/autodock.scripps.edu\/\">AutoDock<\/a><\/span><\/h3>\n<p>Free docking simulation tools. Register and download AutoDock 4.2.6.<\/p>\n<h3><span style=\"font-weight: bold;\"><a href=\"http:\/\/mgltools.scripps.edu\/\">MGLTools<\/a><\/span><\/h3>\n<p>Python Molecular Viewer (PMV) and AutoDockTools (AutoDock front-end).&nbsp; Install the latest release candidate (RC).&nbsp; Add \u201c\/Library\/MGLTools\/1.5.7rc1\/bin\u201d to PATH.<\/p>\n<h2><span style=\"font-style: italic;\">MO Calculation<\/span><\/h2>\n<h3><span style=\"font-weight: bold;\"><a href=\"http:\/\/www.msg.ameslab.gov\/gamess\/\">GAMESS (US)<\/a> (quantum chemistry program)<\/span><\/h3>\n<p>Register, download, and install latest GAMESS package (version August 18, 2016 R1) for Mac OS X. Gamess can perform&nbsp;ab initio MO calculations and semi-empirical MO calculations (AM1, PM3, MNDO).<\/p>\n<h3><span style=\"font-weight: bold;\"><a href=\"http:\/\/openmopac.net\/\">MOPAC<\/a> (semi-empirical quantum chemistry program)<\/span><\/h3>\n<p>MOPAC2016 executables are available FREE for academic, not-for-profit use. PM6 and PM7 hamiltonians are available. Set command-line alias in your .bashrc file as follow.<\/p>\n<pre class=\"prettyprint\">alias mopac=&#34;&#47;opt&#47;mopac&#47;MOPAC2016.exe&#34;<\/pre>\n<h3><span style=\"font-weight: bold;\"><a href=\"https:\/\/www.webmo.net\/\">WebMO<\/a><\/span><\/h3>\n<p>A free WWW-based interface to computational chemistry. WebMO can be used as a front-end for GAMESS and MOPAC. To set up Web-server (Apache) with PHP on MacOS Sierra, see &#8220;<a href=\"https:\/\/getgrav.org\/blog\/macos-sierra-apache-multiple-php-versions\">macOS 10.12 Sierra Apache Setup: Multiple PHP Versions | Grav<\/a>&#8220;.<\/p>\n","protected":false},"excerpt":{"rendered":"<p>\u4ee5\u4e0b\u306fmacOS Sierra\u74b0\u5883\u3067\u306e\u89e3\u8aac\u3067\u3059 (Novem &#8230;<\/p>\n","protected":false},"author":1,"featured_media":0,"parent":346,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"om_disable_all_campaigns":false,"_uag_custom_page_level_css":"","_monsterinsights_skip_tracking":false,"_monsterinsights_sitenote_active":false,"_monsterinsights_sitenote_note":"","_monsterinsights_sitenote_category":0,"_uf_show_specific_survey":0,"_uf_disable_surveys":false,"_locale":"","_original_post":"","footnotes":""},"class_list":["post-350","page","type-page","status-publish","hentry","ja"],"aioseo_notices":[],"uagb_featured_image_src":{"full":false,"thumbnail":false,"medium":false,"medium_large":false,"large":false,"1536x1536":false,"2048x2048":false,"onepress-blog-small":false,"onepress-small":false,"onepress-medium":false},"uagb_author_info":{"display_name":"RCY","author_link":"https:\/\/www.ag.kagawa-u.ac.jp\/charlesy\/author\/charlesy\/"},"uagb_comment_info":0,"uagb_excerpt":"\u4ee5\u4e0b\u306fmacOS Sierra\u74b0\u5883\u3067\u306e\u89e3\u8aac\u3067\u3059 (Novem ...","_links":{"self":[{"href":"https:\/\/www.ag.kagawa-u.ac.jp\/charlesy\/wp-json\/wp\/v2\/pages\/350","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/www.ag.kagawa-u.ac.jp\/charlesy\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/www.ag.kagawa-u.ac.jp\/charlesy\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/www.ag.kagawa-u.ac.jp\/charlesy\/wp-json\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/www.ag.kagawa-u.ac.jp\/charlesy\/wp-json\/wp\/v2\/comments?post=350"}],"version-history":[{"count":57,"href":"https:\/\/www.ag.kagawa-u.ac.jp\/charlesy\/wp-json\/wp\/v2\/pages\/350\/revisions"}],"predecessor-version":[{"id":1384,"href":"https:\/\/www.ag.kagawa-u.ac.jp\/charlesy\/wp-json\/wp\/v2\/pages\/350\/revisions\/1384"}],"up":[{"embeddable":true,"href":"https:\/\/www.ag.kagawa-u.ac.jp\/charlesy\/wp-json\/wp\/v2\/pages\/346"}],"wp:attachment":[{"href":"https:\/\/www.ag.kagawa-u.ac.jp\/charlesy\/wp-json\/wp\/v2\/media?parent=350"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}