{"id":1174,"date":"2021-12-21T18:41:29","date_gmt":"2021-12-21T18:41:29","guid":{"rendered":"https:\/\/ccsb.scripps.edu\/adcp\/?page_id=1174"},"modified":"2022-01-13T03:51:24","modified_gmt":"2022-01-13T03:51:24","slug":"windows10","status":"publish","type":"page","link":"https:\/\/ccsb.scripps.edu\/adcp\/windows10\/","title":{"rendered":"Windows10"},"content":{"rendered":"<p class=\"last-modified\">This page was last updated on January 13th, 2022 at 03:51 am<\/p><div class=\"fusion-fullwidth fullwidth-box fusion-builder-row-1 nonhundred-percent-fullwidth non-hundred-percent-height-scrolling\" style=\"--awb-border-radius-top-left:0px;--awb-border-radius-top-right:0px;--awb-border-radius-bottom-right:0px;--awb-border-radius-bottom-left:0px;--awb-flex-wrap:wrap;\" ><div class=\"fusion-builder-row fusion-row\"><div class=\"fusion-layout-column fusion_builder_column fusion-builder-column-0 fusion_builder_column_1_1 1_1 fusion-one-full fusion-column-first fusion-column-last\" style=\"--awb-bg-size:cover;--awb-margin-bottom:0px;\"><div class=\"fusion-column-wrapper fusion-flex-column-wrapper-legacy\"><div class=\"fusion-text fusion-text-1\"><h2>Running AutoDock CrankPep on Windows 10 or above using WSL<\/h2>\n<\/div><div class=\"fusion-sep-clear\"><\/div><div class=\"fusion-separator fusion-no-medium-visibility fusion-full-width-sep\" style=\"margin-left: auto;margin-right: auto;width:100%;\"><div class=\"fusion-separator-border sep-shadow\" style=\"--awb-height:20px;--awb-amount:20px;background:radial-gradient(ellipse at 50% -50% , #e0dede 0px, rgba(255, 255, 255, 0) 80%) repeat scroll 0 0 rgba(0, 0, 0, 0);background:-webkit-radial-gradient(ellipse at 50% -50% , #e0dede 0px, rgba(255, 255, 255, 0) 80%) repeat scroll 0 0 rgba(0, 0, 0, 0);background:-moz-radial-gradient(ellipse at 50% -50% , #e0dede 0px, rgba(255, 255, 255, 0) 80%) repeat scroll 0 0 rgba(0, 0, 0, 0);background:-o-radial-gradient(ellipse at 50% -50% , #e0dede 0px, rgba(255, 255, 255, 0) 80%) repeat scroll 0 0 rgba(0, 0, 0, 0);\"><\/div><\/div><div class=\"fusion-sep-clear\"><\/div><div class=\"fusion-text fusion-text-2\"><p>Starting with Windows 10, it has become possible to run a Linux subsystem\u00a0 on windows (Windows Subsystem for Linux). Once enabled, it is possible to install the Linux 64 bit build of ADFRsuite to run ADCP on windows.<\/p>\n<p>This page provides information on how to enable WSL, install Ubuntu 20.04, install ADFRsuite1.0 to run ADCP.<\/p>\n<p>NOTE: this installation currently only allows to run command line programs. Graphical User Interfaces such as AGFRGUI will not work as they require a X server for windows.<\/p>\n<\/div><div class=\"accordian fusion-accordian\" style=\"--awb-border-size:1px;--awb-icon-size:24px;--awb-content-font-size:16px;--awb-icon-alignment:left;--awb-hover-color:#f9f9f9;--awb-border-color:#cccccc;--awb-background-color:#ffffff;--awb-divider-color:#e0dede;--awb-divider-hover-color:#e0dede;--awb-icon-color:#c1c1c1;--awb-title-color:#52a3bf;--awb-content-color:#747474;--awb-icon-box-color:#0262d1;--awb-toggle-hover-accent-color:#5c51d6;--awb-title-font-family:&quot;Montserrat&quot;;--awb-title-font-weight:400;--awb-title-font-style:normal;--awb-title-font-size:24px;--awb-title-line-height:1.4;--awb-content-font-family:&quot;Hind&quot;;--awb-content-font-style:normal;--awb-content-font-weight:400;\"><div class=\"panel-group fusion-toggle-icon-boxed\" id=\"accordion-1174-1\"><div class=\"fusion-panel panel-default panel-f2cf425f1468b12f8 fusion-toggle-has-divider\"><div class=\"panel-heading\"><h4 class=\"panel-title toggle\" id=\"toggle_f2cf425f1468b12f8\"><a aria-expanded=\"false\" aria-controls=\"f2cf425f1468b12f8\" role=\"button\" data-toggle=\"collapse\" data-parent=\"#accordion-1174-1\" data-target=\"#f2cf425f1468b12f8\" href=\"#f2cf425f1468b12f8\"><span class=\"fusion-toggle-icon-wrapper\" aria-hidden=\"true\"><i class=\"fa-fusion-box active-icon awb-icon-minus\" aria-hidden=\"true\"><\/i><i class=\"fa-fusion-box inactive-icon awb-icon-plus\" aria-hidden=\"true\"><\/i><\/span><span class=\"fusion-toggle-heading\">Enabling WSL and installing Ubuntu<\/span><\/a><\/h4><\/div><div id=\"f2cf425f1468b12f8\" class=\"panel-collapse collapse \" aria-labelledby=\"toggle_f2cf425f1468b12f8\"><div class=\"panel-body toggle-content fusion-clearfix\">\n<p>Follow the instructions on <a href=\"http:\/\/se-the-linux-bash-shell-on-windows-10\/\" target=\"_blank\" rel=\"noopener\">this page to install enable WSL and install Ubuntu<\/a>.<\/p>\n<p>in summary:<\/p>\n<ol>\n<li>Control Panel &gt; Programs &gt; Turn Windows Features On Or Off. Enable the \u201cWindows Subsystem for Linux\u201d option in the list, and then click the \u201cOK\u201d button.<\/li>\n<li>Click &#8220;Restart&#8221; now to reboot windows<\/li>\n<li>open the Microsoft Store (Start menu, type store) and search for \u201cUbuntu\u201d. get Ubuntu 20.04<\/li>\n<li>Launch Ubuntu: (Start -&gt; Ubuntu). The first time you launch the Linux environment, you\u2019re be prompted to enter a UNIX username and password.<\/li>\n<\/ol>\n<p>At this point you have a working Ubuntu subsystem.<\/p>\n<p>NOTE: you can access files from the Windows OS through \/mnt\/c. So if you download software with the webrowser under windows you can copy it over from \/mnt\/c\/Users\/<em>yourname<\/em>\/Downloads<\/p>\n<\/div><\/div><\/div><div class=\"fusion-panel panel-default panel-8ded817541d2b13e4 fusion-toggle-has-divider\"><div class=\"panel-heading\"><h4 class=\"panel-title toggle\" id=\"toggle_8ded817541d2b13e4\"><a aria-expanded=\"false\" aria-controls=\"8ded817541d2b13e4\" role=\"button\" data-toggle=\"collapse\" data-parent=\"#accordion-1174-1\" data-target=\"#8ded817541d2b13e4\" href=\"#8ded817541d2b13e4\"><span class=\"fusion-toggle-icon-wrapper\" aria-hidden=\"true\"><i class=\"fa-fusion-box active-icon awb-icon-minus\" aria-hidden=\"true\"><\/i><i class=\"fa-fusion-box inactive-icon awb-icon-plus\" aria-hidden=\"true\"><\/i><\/span><span class=\"fusion-toggle-heading\">installing ADFRsuite Linux 64 bits<\/span><\/a><\/h4><\/div><div id=\"8ded817541d2b13e4\" class=\"panel-collapse collapse \" aria-labelledby=\"toggle_8ded817541d2b13e4\"><div class=\"panel-body toggle-content fusion-clearfix\">\n<p>Now we can download and install ADFRsuite1.0 for Linux<\/p>\n<p>in summary:<\/p>\n<ol>\n<li>Obtain the<a href=\"http:\/\/ccsb.scripps.edu\/adfr\/downloads\"> tarball installer for linux 64 bits here<\/a><\/li>\n<li>in the Ubuntu shell:\n<ul>\n<li>mv \/mnt\/c\/Users\/<em>myUserName<\/em>\/Downloads\/ADFRsuite_x86_64Linux_1.0.tar.gz .<\/li>\n<li>tar zxvf ADFRsuite_x86_64Linux_1.0.tar.gz<\/li>\n<li>\u00a0cd ADFRsuite_x86_64Linux_1.0<\/li>\n<li>bash .\/install.sh -d ..\/ADFR10 -c 0 # NOTE you have to type &#8220;bash&#8221; for this to work<\/li>\n<li>cd ..<\/li>\n<li>sudo apt-get install libgomp1<\/li>\n<li>sudo apt-get install unzip<\/li>\n<li>repalce reduce with a 64 bit version\n<ul>\n<li><a href=\"https:\/\/ccsb.scripps.edu\/adcp\/wp-content\/uploads\/sites\/38\/2021\/12\/reduce64Bit.exe\">download reduce here<\/a><\/li>\n<li>mv reduce64bits.exe \/$WHERE_YOU_INSTALLED\/bin\/reduce<\/li>\n<\/ul>\n<\/li>\n<\/ul>\n<\/li>\n<\/ol>\n<p>At this point you can download tutorial files for ADFR and ADCP and try to run dockings<\/p>\n<\/div><\/div><\/div><div class=\"fusion-panel panel-default panel-b687ad988b3447bc9 fusion-toggle-has-divider\"><div class=\"panel-heading\"><h4 class=\"panel-title toggle\" id=\"toggle_b687ad988b3447bc9\"><a aria-expanded=\"false\" aria-controls=\"b687ad988b3447bc9\" role=\"button\" data-toggle=\"collapse\" data-parent=\"#accordion-1174-1\" data-target=\"#b687ad988b3447bc9\" href=\"#b687ad988b3447bc9\"><span class=\"fusion-toggle-icon-wrapper\" aria-hidden=\"true\"><i class=\"fa-fusion-box active-icon awb-icon-minus\" aria-hidden=\"true\"><\/i><i class=\"fa-fusion-box inactive-icon awb-icon-plus\" aria-hidden=\"true\"><\/i><\/span><span class=\"fusion-toggle-heading\">Docking with ADFR<\/span><\/a><\/h4><\/div><div id=\"b687ad988b3447bc9\" class=\"panel-collapse collapse \" aria-labelledby=\"toggle_b687ad988b3447bc9\"><div class=\"panel-body toggle-content fusion-clearfix\">\n<p>from https:\/\/ccsb.scripps.edu\/adfr\/tutorial-redocking\/<\/p>\n<ol>\n<li>download data <a href=\"http:\/\/ccsb.scripps.edu\/adfr\/documentation\">here<\/a><\/li>\n<li>\n<blockquote><p>mv\u00a0\/mnt\/c\/Users\/<em>myUserName<\/em>\/Downloads\/ADFRsuite-1.0_tutorial_data.zip .<\/p><\/blockquote>\n<\/li>\n<li>\n<blockquote><p>unzip ADFRsuite-1.0_tutorial_data.zip<\/p><\/blockquote>\n<\/li>\n<li>\n<blockquote><p>.\/ADFR10\/bin\/agfr -r data\/4EK3_rec.pdbqt -l data\/4EK4_lig.pdbqt -o ligPocket -ng<\/p><\/blockquote>\n<\/li>\n<li>\n<blockquote><p>.\/ADFR10\/bin\/adfr -l data\/4EK4_random.pdbqt -t ligPocket.trg -J rigid -n 8 -e 20000 -O -s 1<\/p><\/blockquote>\n<\/li>\n<\/ol>\n<\/div><\/div><\/div><div class=\"fusion-panel panel-default panel-fadb7326a3f6e21fe fusion-toggle-has-divider\"><div class=\"panel-heading\"><h4 class=\"panel-title toggle\" id=\"toggle_fadb7326a3f6e21fe\"><a aria-expanded=\"false\" aria-controls=\"fadb7326a3f6e21fe\" role=\"button\" data-toggle=\"collapse\" data-parent=\"#accordion-1174-1\" data-target=\"#fadb7326a3f6e21fe\" href=\"#fadb7326a3f6e21fe\"><span class=\"fusion-toggle-icon-wrapper\" aria-hidden=\"true\"><i class=\"fa-fusion-box active-icon awb-icon-minus\" aria-hidden=\"true\"><\/i><i class=\"fa-fusion-box inactive-icon awb-icon-plus\" aria-hidden=\"true\"><\/i><\/span><span class=\"fusion-toggle-heading\">Docking with ADCP<\/span><\/a><\/h4><\/div><div id=\"fadb7326a3f6e21fe\" class=\"panel-collapse collapse \" aria-labelledby=\"toggle_fadb7326a3f6e21fe\"><div class=\"panel-body toggle-content fusion-clearfix\">\n<ol>\n<li>The version of reduce provided by the installer is 32 bit and will fail.\n<ol>\n<li>download <a href=\"https:\/\/ccsb.scripps.edu\/adcp\/wp-content\/uploads\/sites\/38\/2021\/12\/reduce64Bit.exe\">this 64 bit version for Linux<\/a>.<\/li>\n<li>\n<blockquote><p>mv\u00a0\/mnt\/c\/Users\/<em>myUserName<\/em>\/Downloads\/reduce64Bit.exe ADFR10\/bin\/reduce<\/p><\/blockquote>\n<\/li>\n<\/ol>\n<\/li>\n<li>download the <a href=\"https:\/\/ccsb.scripps.edu\/adcp\/download\/1063\/\">tutorial data<\/a><\/li>\n<li>\n<blockquote><p>mv\u00a0\/mnt\/c\/Users\/<em>myUserName<\/em>\/Downloads\/ADCP_tutorial_data.zip .<\/p><\/blockquote>\n<\/li>\n<li>from https:\/\/ccsb.scripps.edu\/adcp\/tutorial-redocking\/\n<ol>\n<li>\n<blockquote><p>unzip ADCP_tutorial_data.zip<\/p><\/blockquote>\n<\/li>\n<li>\n<blockquote><p>cd ADCP_tutorial_data\/3Q47<\/p><\/blockquote>\n<\/li>\n<li>\n<blockquote><p>..\/..\/ADFR10\/bin\/reduce 3Q47_rec.pdb &gt; 3Q47_recH.pdb<\/p><\/blockquote>\n<\/li>\n<li>\n<blockquote><p>..\/..\/ADFR10\/bin\/reduce\u00a03Q47_pep.pdb &gt; 3Q47_pepH.pdb<\/p><\/blockquote>\n<\/li>\n<li>\n<blockquote><p>..\/..\/ADFR10\/bin\/prepare_receptor -r 3Q47_recH.pdb<\/p><\/blockquote>\n<\/li>\n<li>\n<blockquote><p>..\/..\/ADFR10\/bin\/prepare_ligand -l 3Q47_pepH.pdb<\/p><\/blockquote>\n<\/li>\n<li>\n<blockquote><p>..\/..\/ADFR10\/bin\/agfr -r 3Q47_recH.pdbqt -l 3Q47_pepH.pdbqt -asv 1.1 -o 3Q47 -ng<\/p><\/blockquote>\n<\/li>\n<li>\n<blockquote><p>..\/..\/ADFR10\/bin\/adcp -t 3Q47.trg -s npisdvd -N 20 -n 1000000 -o 3Q47_redocking -ref 3Q47_pepH.pdb<\/p><\/blockquote>\n<\/li>\n<\/ol>\n<\/li>\n<\/ol>\n<\/div><\/div><\/div><\/div><\/div><div class=\"fusion-clearfix\"><\/div><\/div><\/div><\/div><\/div>\n","protected":false},"excerpt":{"rendered":"<p>This page was last updated on January 13th, 2022 at  [&#8230;]<\/p>\n","protected":false},"author":13,"featured_media":0,"parent":0,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"footnotes":""},"class_list":["post-1174","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"https:\/\/ccsb.scripps.edu\/adcp\/wp-json\/wp\/v2\/pages\/1174","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/ccsb.scripps.edu\/adcp\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/ccsb.scripps.edu\/adcp\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/ccsb.scripps.edu\/adcp\/wp-json\/wp\/v2\/users\/13"}],"replies":[{"embeddable":true,"href":"https:\/\/ccsb.scripps.edu\/adcp\/wp-json\/wp\/v2\/comments?post=1174"}],"version-history":[{"count":20,"href":"https:\/\/ccsb.scripps.edu\/adcp\/wp-json\/wp\/v2\/pages\/1174\/revisions"}],"predecessor-version":[{"id":1179,"href":"https:\/\/ccsb.scripps.edu\/adcp\/wp-json\/wp\/v2\/pages\/1174\/revisions\/1179"}],"wp:attachment":[{"href":"https:\/\/ccsb.scripps.edu\/adcp\/wp-json\/wp\/v2\/media?parent=1174"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}