{"id":1084,"date":"2017-04-21T10:26:55","date_gmt":"2017-04-21T01:26:55","guid":{"rendered":"https:\/\/www.ag.kagawa-u.ac.jp\/charlesy\/?p=1084"},"modified":"2017-04-21T10:28:19","modified_gmt":"2017-04-21T01:28:19","slug":"ambertools17%e3%81%b8%e3%81%ae%e3%82%a2%e3%83%83%e3%83%97%e3%82%b0%e3%83%ac%e3%83%bc%e3%83%89","status":"publish","type":"post","link":"https:\/\/www.ag.kagawa-u.ac.jp\/charlesy\/2017\/04\/21\/ambertools17%e3%81%b8%e3%81%ae%e3%82%a2%e3%83%83%e3%83%97%e3%82%b0%e3%83%ac%e3%83%bc%e3%83%89\/","title":{"rendered":"AmberTools17\u3078\u306e\u30a2\u30c3\u30d7\u30b0\u30ec\u30fc\u30c9"},"content":{"rendered":"<p><a href=\"http:\/\/ambermd.org\/\">AmberTools17<\/a>\u304c4\/17\u306b\u30ea\u30ea\u30fc\u30b9\u3055\u308c\u3066\u3044\u307e\u3057\u305f\uff08Amber\u672c\u4f53\u306f16\u306e\u307e\u307e\uff09\uff0e\u95a2\u5fc3\u306e\u3042\u308b\u5909\u66f4\u70b9\u306fLipid17\u529b\u5834\u306e\u5c0e\u5165\u3067\u3059\uff0e\u524d\u30d0\u30fc\u30b8\u30e7\u30f3 (<a href=\"http:\/\/ambermd.org\/tutorials\/advanced\/tutorial16\/\">Lipid14<\/a>) \u3067\u306fhead group\u304cPC\u3068PE\u306e2\u7a2e\u985e\u3057\u304b\u4f7f\u7528\u3067\u304d\u306a\u304b\u3063\u305f\u306e\u304c\uff0c<\/p>\n<ul>\n<li>Phosphatidylcholine (PC)<\/li>\n<li>Phosphatidylethanolamine (PE)<\/li>\n<li>Phosphatidylserine (PS)<\/li>\n<li>Phosphatidylglycerol (PGR)<\/li>\n<li>Phosphaditic acid (PH-)<\/li>\n<\/ul>\n<p>\u306e5\u7a2e\u985e\u306b\u306a\u308a\u307e\u3057\u305f\uff0e\u5074\u9396\u30825\u7a2e\u985e\u304b\u30897\u7a2e\u985e\u306b\u5897\u3048\uff08\u30a2\u30e9\u30ad\u30c9\u30f3\u9178\u3014AR\u3015\u3068\u30c9\u30b3\u30b5\u30d8\u30ad\u30b5\u30a8\u30f3\u9178\u3014DHA\u3015\u304c\u8ffd\u52a0\u3055\u308c\u305f\uff09\uff0c\u305d\u306e\u4ed6\u306e\u8102\u8cea\u3068\u3057\u3066cholesterol\u3082\u4f7f\u7528\u53ef\u80fd\u306b\u306a\u308a\u307e\u3057\u305f\uff0e<\/p>\n<p>\u3053\u308c\u3067\uff0cAmber\u529b\u5834\u3068\u7d44\u307f\u5408\u308f\u305b\u3066PS\u3092\u542b\u3080\u8102\u8cea\u4e8c\u91cd\u819c\u306etensionless\u30b7\u30df\u30e5\u30ec\u30fc\u30b7\u30e7\u30f3\uff08\u8868\u9762\u5f35\u529b\u3092\u304b\u3051\u306a\u304f\u3066\u3082\u3088\u3044\uff09\u304c\u53ef\u80fd\u306b\u306a\u308a\u307e\u3057\u305f\uff0e<\/p>\n<p>\u4f4e\u5206\u5b50\u7528\u529b\u5834\u306b\u95a2\u3057\u3066\u306f\u307e\u3060GAFF2\u304c\u958b\u767a\u9014\u4e0a\u306e\u3088\u3046\u3067\u3059\uff0e\u5c11\u306a\u304f\u3068\u3082\u3046\u3061\u3067\u8208\u5473\u306e\u3042\u308b\u30de\u30af\u30ed\u30e9\u30af\u30c8\u30f3\u3067\u306fGAFF\u529b\u5834\u3088\u308a\u3082Charmm\u306eCGenFF\u306e\u65b9\u304c\u30b3\u30f3\u30db\u30e1\u30fc\u30b7\u30e7\u30f3\u3084\u30a8\u30cd\u30eb\u30ae\u30fc\u306e\u518d\u73fe\u5ea6\u304c\u3088\u3044\uff08DFT\u3068\u3088\u304f\u4e00\u81f4\u3059\u308b\uff09\u306e\u3067\uff0cGAFF2\u306e\u9032\u5316\u306b\u671f\u5f85\u3057\u307e\u3059\uff0e<\/p>\n<h2>\u30a2\u30c3\u30d7\u30b0\u30ec\u30fc\u30c9<\/h2>\n<p>AmberTools16\u3092\u30a4\u30f3\u30b9\u30c8\u30fc\u30eb\u6e08\u307f\u306a\u306e\u3067\uff0c\u30a6\u30a7\u30d6\u30b5\u30a4\u30c8\u306e\u6307\u793a\u901a\u308a\u306b\u30b3\u30de\u30f3\u30c9\u30e9\u30a4\u30f3\u304b\u3089patch\u3092\u30c0\u30a6\u30f3\u30ed\u30fc\u30c9\u3057\u307e\u3057\u305f\uff0e<\/p>\n<pre class=\"command-line\"><code class=\"language-bash\" data-line=\"\">$ cd $AMBERHOME \n$ .\/update_amber --upgrade \n<\/code><\/pre>\n<p>\u5fc5\u8981\u306a\u30d5\u30a1\u30a4\u30eb\u304c\u30c0\u30a6\u30f3\u30ed\u30fc\u30c9\u3055\u308c\uff0c\u53e4\u3044\u30d5\u30a1\u30a4\u30eb\u304c\u524a\u9664\u3055\u308c\u307e\u3057\u305f\uff0e\u6b21\u306b\u6307\u793a\u901a\u308a\uff0cconfigure\u3092\u5b9f\u884c\u3057\u307e\u3057\u305f\uff0e<\/p>\n<pre class=\"command-line\"><code class=\"language-bash\" data-line=\"\">$ .\/configure gnu\n<\/code><\/pre>\n<pre class=\"prettyprint\">We highly recommend to let AMBER install Python with all prerequisites inside\r\n&#47;opt&#47;amber16 via a Continuum Miniconda distribution. <\/pre>\n<p>\u3068\u8a00\u308f\u308c\u305f\u306e\u3067\uff0cy\u3092\u9078\u629e\u3059\u308b\u3068Amber\u5c02\u7528\u306epython\u74b0\u5883\u304c\u81ea\u52d5\u7684\u306b\u69cb\u7bc9\u3055\u308c\u307e\u3057\u305f\uff0eConfigure\u306f\u7a0b\u306a\u304f\u7d42\u4e86\u3057\u305f\u306e\u3067\uff0c\u6b21\u306bcompile\u3092\u5b9f\u884c\u3057\u307e\u3057\u305f\uff08GCC\u306e\u30d0\u30fc\u30b8\u30e7\u30f3\u306fHomebrew\u3067\u30a4\u30f3\u30b9\u30c8\u30fc\u30eb\u3057\u305f6.3.0\uff09\uff0e<\/p>\n<pre class=\"command-line\"><code class=\"language-bash\" data-line=\"\">$ make install\n<\/code><\/pre>\n<pre class=\"prettyprint\">cp: &#47;opt&#47;amber16&#47;bin&#47;FEW.pl and &#47;opt&#47;amber16&#47;AmberTools&#47;src&#47;FEW&#47;FEW.pl are identical (not copied).<\/pre>\n<p>\u3068\u8a00\u308f\u308c\u3066\u30a8\u30e9\u30fc\u3067\u9014\u4e2d\u3067\u6b62\u307e\u3063\u305f\u306e\u3067\uff0c\u305d\u306e\u30d5\u30a1\u30a4\u30eb\u3092rename\u3057\u3066\u304b\u3089\uff0cmake install\u3092\u518d\u958b\u3057\u307e\u3057\u305f\uff0e\u554f\u984c\u306a\u304f\u7d42\u4e86\u3057\u307e\u3057\u305f\uff0e<\/p>\n<p>(\u4e86)<\/p>\n","protected":false},"excerpt":{"rendered":"<p>AmberTools17\u304c4\/17\u306b\u30ea\u30ea\u30fc\u30b9\u3055\u308c\u3066\u3044\u307e\u3057\u305f\uff08 &#8230;<\/p>\n","protected":false},"author":1,"featured_media":0,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","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":""},"categories":[5],"tags":[],"class_list":["post-1084","post","type-post","status-publish","format-standard","hentry","category-5","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":"AmberTools17\u304c4\/17\u306b\u30ea\u30ea\u30fc\u30b9\u3055\u308c\u3066\u3044\u307e\u3057\u305f\uff08 ...","_links":{"self":[{"href":"https:\/\/www.ag.kagawa-u.ac.jp\/charlesy\/wp-json\/wp\/v2\/posts\/1084","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/www.ag.kagawa-u.ac.jp\/charlesy\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/www.ag.kagawa-u.ac.jp\/charlesy\/wp-json\/wp\/v2\/types\/post"}],"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=1084"}],"version-history":[{"count":4,"href":"https:\/\/www.ag.kagawa-u.ac.jp\/charlesy\/wp-json\/wp\/v2\/posts\/1084\/revisions"}],"predecessor-version":[{"id":1088,"href":"https:\/\/www.ag.kagawa-u.ac.jp\/charlesy\/wp-json\/wp\/v2\/posts\/1084\/revisions\/1088"}],"wp:attachment":[{"href":"https:\/\/www.ag.kagawa-u.ac.jp\/charlesy\/wp-json\/wp\/v2\/media?parent=1084"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/www.ag.kagawa-u.ac.jp\/charlesy\/wp-json\/wp\/v2\/categories?post=1084"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/www.ag.kagawa-u.ac.jp\/charlesy\/wp-json\/wp\/v2\/tags?post=1084"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}