{"id":917,"date":"2019-04-18T17:46:54","date_gmt":"2019-04-18T17:46:54","guid":{"rendered":"https:\/\/ccsb.scripps.edu\/adfr\/?page_id=917"},"modified":"2019-04-18T18:02:21","modified_gmt":"2019-04-18T18:02:21","slug":"tutorial-_redockingex1","status":"publish","type":"page","link":"https:\/\/ccsb.scripps.edu\/adfr\/tutorial-_redockingex1\/","title":{"rendered":"tutorial _redockingEx1"},"content":{"rendered":"<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;\"><div class=\"fusion-column-wrapper fusion-flex-column-wrapper-legacy\"><div class=\"fusion-text fusion-text-1\"><p>The command line used in the tutorial lead to all searches ending while they where still actively optimizing their solutions. Therefore the first natural step is to increase the number of evaluations to allow each search to converge. Using the default value of 2.5M evals is a good idea because, unlike <em>AutoDock4<\/em>, <em>ADFR<\/em> will not only use up as long as improvements are seen and can be hoped for.<\/p>\n<p>Additionally, providing the crystal structure as a reference\u00a0(-r\/&#8211;reference option) will results in the RMSD between the docked pose and crystal structure to be reported.<\/p>\n<p>Finally, we name the job rigid1 to avoid <em>adfr<\/em> complaining that output files with the same name already exist and stopping the calculation. The -O option could be used to tell <em>adfr<\/em> to overwrite existing files silently.<\/p>\n<style type=\"text\/css\" scopped=\"scopped\">.fusion-syntax-highlighter-1 > .CodeMirror, .fusion-syntax-highlighter-1 > .CodeMirror .CodeMirror-gutters {background-color:var(--awb-color1);}<\/style><div class=\"fusion-syntax-highlighter-container fusion-syntax-highlighter-1 fusion-syntax-highlighter-theme-light\" style=\"opacity:0;margin-top:0px;margin-right:0px;margin-bottom:15px;margin-left:0px;font-size:14px;border-width:1px;border-style:solid;border-color:var(--awb-color3);\"><div class=\"syntax-highlighter-copy-code\"><span class=\"syntax-highlighter-copy-code-title\" data-id=\"fusion_syntax_highlighter_1\" style=\"font-size:14px;\">Copy to Clipboard<\/span><\/div><label for=\"fusion_syntax_highlighter_1\" class=\"screen-reader-text\">Syntax Highlighter<\/label><textarea class=\"fusion-syntax-highlighter-textarea\" id=\"fusion_syntax_highlighter_1\" data-readOnly=\"nocursor\" data-lineNumbers=\"\" data-lineWrapping=\"\" data-theme=\"default\" data-mode=\"text\/x-sh\">adfr -l data\/4EK4_random.pdbqt -t ligPocket.trg --reference data\/4EK4_lig.pdbqt --jobName rigid1 --nbRuns 8 -O --seed 1<\/textarea><\/div>\n<p>The run takes longer now but all runs converge as seen below<\/p>\n<style type=\"text\/css\" scopped=\"scopped\">.fusion-syntax-highlighter-2 > .CodeMirror, .fusion-syntax-highlighter-2 > .CodeMirror .CodeMirror-gutters {background-color:var(--awb-color1);}.fusion-syntax-highlighter-2 > .CodeMirror .CodeMirror-gutters { background-color: var(--awb-color2); }.fusion-syntax-highlighter-2 > .CodeMirror .CodeMirror-linenumber { color: var(--awb-color8); }<\/style><div class=\"fusion-syntax-highlighter-container fusion-syntax-highlighter-2 fusion-syntax-highlighter-theme-light\" style=\"opacity:0;margin-top:0px;margin-right:0px;margin-bottom:15px;margin-left:0px;font-size:14px;border-width:1px;border-style:solid;border-color:var(--awb-color3);\"><label for=\"fusion_syntax_highlighter_2\" class=\"screen-reader-text\">Syntax Highlighter<\/label><textarea class=\"fusion-syntax-highlighter-textarea\" id=\"fusion_syntax_highlighter_2\" data-readOnly=\"nocursor\" data-lineNumbers=\"1\" data-lineWrapping=\"\" data-theme=\"default\" data-mode=\"text\/x-sh\">0%   10   20   30   40   50   60   70   80   90   100%\n|----|----|----|----|----|----|----|----|----|----|\n***************************************************\nTermination status\n    0\/   8  0.0% runs failed\n    0\/   8  0.0% runs exhausted their evaluations\n    0\/   8  0.0% runs stopped converged 1 or 2 clusters\n    8\/   8 100.0% runs stopped after no improvement in clusters\n    0\/   8  0.0% runs stopped because GA ran out of choices\n    0\/   8  0.0% runs stopped because GA population converged\n<\/textarea><\/div>\n<p>Furthermore, all runs converge to the same solution<\/p>\n<style type=\"text\/css\" scopped=\"scopped\">.fusion-syntax-highlighter-3 > .CodeMirror, .fusion-syntax-highlighter-3 > .CodeMirror .CodeMirror-gutters {background-color:var(--awb-color1);}.fusion-syntax-highlighter-3 > .CodeMirror .CodeMirror-gutters { background-color: var(--awb-color2); }.fusion-syntax-highlighter-3 > .CodeMirror .CodeMirror-linenumber { color: var(--awb-color8); }<\/style><div class=\"fusion-syntax-highlighter-container fusion-syntax-highlighter-3 fusion-syntax-highlighter-theme-light\" style=\"opacity:0;margin-top:0px;margin-right:0px;margin-bottom:15px;margin-left:0px;font-size:14px;border-width:1px;border-style:solid;border-color:var(--awb-color3);\"><label for=\"fusion_syntax_highlighter_3\" class=\"screen-reader-text\">Syntax Highlighter<\/label><textarea class=\"fusion-syntax-highlighter-textarea\" id=\"fusion_syntax_highlighter_3\" data-readOnly=\"nocursor\" data-lineNumbers=\"1\" data-lineWrapping=\"\" data-theme=\"default\" data-mode=\"text\/x-sh\">mode |  affinity  | clust. | ref. | clust. | rmsd | energy | best |\n     | (kcal\/mol) | rmsd   | rmsd |  size  | stdv |  stdv  | run  |\n-----+------------+--------+------+--------+------+--------+------+\n   1         -7.2     0.0     0.3       8     0.2     0.1    004\n<\/textarea><\/div>\n<p>The <em>ref. rmsd<\/em> column shows that the docked pose is within 0.3 Angstroms of the crystal structure, indicating that for this simple ligand, 8 independent searches are sufficient to reliably identify the crystal structure pose.<\/p>\n<p>The default values of 50 searches is reasonable for docking most small molecules.<\/p>\n<p>We can inspect the content of the .dro file to find out how many evaluations have been used up by each search.<\/p>\n<p>First unpack the file<\/p>\n<style type=\"text\/css\" scopped=\"scopped\">.fusion-syntax-highlighter-4 > .CodeMirror, .fusion-syntax-highlighter-4 > .CodeMirror .CodeMirror-gutters {background-color:var(--awb-color1);}<\/style><div class=\"fusion-syntax-highlighter-container fusion-syntax-highlighter-4 fusion-syntax-highlighter-theme-light\" style=\"opacity:0;margin-top:0px;margin-right:0px;margin-bottom:15px;margin-left:0px;font-size:14px;border-width:1px;border-style:solid;border-color:var(--awb-color3);\"><div class=\"syntax-highlighter-copy-code\"><span class=\"syntax-highlighter-copy-code-title\" data-id=\"fusion_syntax_highlighter_4\" style=\"font-size:14px;\">Copy to Clipboard<\/span><\/div><label for=\"fusion_syntax_highlighter_4\" class=\"screen-reader-text\">Syntax Highlighter<\/label><textarea class=\"fusion-syntax-highlighter-textarea\" id=\"fusion_syntax_highlighter_4\" data-readOnly=\"nocursor\" data-lineNumbers=\"\" data-lineWrapping=\"\" data-theme=\"default\" data-mode=\"text\/x-sh\">tar -xvof 4EK4_random_rigid1.dro\n<\/textarea><\/div>\n<p>Next, extract the ending summary line from the log file of each search.<\/p>\n<p><style type=\"text\/css\" scopped=\"scopped\">.fusion-syntax-highlighter-5 > .CodeMirror, .fusion-syntax-highlighter-5 > .CodeMirror .CodeMirror-gutters {background-color:var(--awb-color1);}<\/style><div class=\"fusion-syntax-highlighter-container fusion-syntax-highlighter-5 fusion-syntax-highlighter-theme-light\" style=\"opacity:0;margin-top:0px;margin-right:0px;margin-bottom:15px;margin-left:0px;font-size:14px;border-width:1px;border-style:solid;border-color:var(--awb-color3);\"><div class=\"syntax-highlighter-copy-code\"><span class=\"syntax-highlighter-copy-code-title\" data-id=\"fusion_syntax_highlighter_5\" style=\"font-size:14px;\">Copy to Clipboard<\/span><\/div><label for=\"fusion_syntax_highlighter_5\" class=\"screen-reader-text\">Syntax Highlighter<\/label><textarea class=\"fusion-syntax-highlighter-textarea\" id=\"fusion_syntax_highlighter_5\" data-readOnly=\"nocursor\" data-lineNumbers=\"\" data-lineWrapping=\"\" data-theme=\"default\" data-mode=\"text\/x-sh\">grep END 4EK4_random_rigid1_dro\/dockingDetails\/rigid1000*.dlg<\/textarea><\/div>\n<style type=\"text\/css\" scopped=\"scopped\">.fusion-syntax-highlighter-6 > .CodeMirror, .fusion-syntax-highlighter-6 > .CodeMirror .CodeMirror-gutters {background-color:var(--awb-color1);}.fusion-syntax-highlighter-6 > .CodeMirror .CodeMirror-gutters { background-color: var(--awb-color2); }.fusion-syntax-highlighter-6 > .CodeMirror .CodeMirror-linenumber { color: var(--awb-color8); }<\/style><div class=\"fusion-syntax-highlighter-container fusion-syntax-highlighter-6 fusion-syntax-highlighter-theme-light\" style=\"opacity:0;margin-top:0px;margin-right:0px;margin-bottom:0px;margin-left:0px;font-size:14px;border-width:1px;border-style:solid;border-color:var(--awb-color3);\"><label for=\"fusion_syntax_highlighter_6\" class=\"screen-reader-text\">Syntax Highlighter<\/label><textarea class=\"fusion-syntax-highlighter-textarea\" id=\"fusion_syntax_highlighter_6\" data-readOnly=\"nocursor\" data-lineNumbers=\"1\" data-lineWrapping=\"\" data-theme=\"default\" data-mode=\"text\/x-sh\">4EK4_random_rigid1_dro\/dockingDetails\/rigid10001.dlg:END bestScore: -7.986 RMSD: 0.63 nbgen: 132 nbEvals   750868 time 11.534\n4EK4_random_rigid1_dro\/dockingDetails\/rigid10002.dlg:END bestScore: -7.803 RMSD: 0.74 nbgen: 246 nbEvals  1374668 time 22.495\n4EK4_random_rigid1_dro\/dockingDetails\/rigid10003.dlg:END bestScore: -8.095 RMSD: 0.56 nbgen: 168 nbEvals   833674 time 14.200\n4EK4_random_rigid1_dro\/dockingDetails\/rigid10004.dlg:END bestScore: -8.106 RMSD: 0.33 nbgen: 149 nbEvals   861056 time 13.679\n4EK4_random_rigid1_dro\/dockingDetails\/rigid10005.dlg:END bestScore: -8.054 RMSD: 0.59 nbgen: 135 nbEvals   752220 time 10.907\n4EK4_random_rigid1_dro\/dockingDetails\/rigid10006.dlg:END bestScore: -8.058 RMSD: 0.59 nbgen:  72 nbEvals   371400 time 5.874\n4EK4_random_rigid1_dro\/dockingDetails\/rigid10007.dlg:END bestScore: -7.798 RMSD: 0.75 nbgen: 162 nbEvals   881594 time 11.150\n4EK4_random_rigid1_dro\/dockingDetails\/rigid10008.dlg:END bestScore: -7.994 RMSD: 0.60 nbgen:  54 nbEvals   258364 time 2.693\n<\/textarea><\/div><\/p>\n<p>The nbEvals column shows that searches use up different number of evals, ranging from 258&#8217;364 to 1&#8217;374&#8217;668 with the run leading to the best solution (run 004) using up 861&#8217;056 evals.<\/p>\n<\/div><div class=\"fusion-clearfix\"><\/div><\/div><\/div><\/div><\/div>\n","protected":false},"excerpt":{"rendered":"","protected":false},"author":1,"featured_media":0,"parent":0,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"footnotes":""},"class_list":["post-917","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"https:\/\/ccsb.scripps.edu\/adfr\/wp-json\/wp\/v2\/pages\/917","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/ccsb.scripps.edu\/adfr\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/ccsb.scripps.edu\/adfr\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/ccsb.scripps.edu\/adfr\/wp-json\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/ccsb.scripps.edu\/adfr\/wp-json\/wp\/v2\/comments?post=917"}],"version-history":[{"count":4,"href":"https:\/\/ccsb.scripps.edu\/adfr\/wp-json\/wp\/v2\/pages\/917\/revisions"}],"predecessor-version":[{"id":924,"href":"https:\/\/ccsb.scripps.edu\/adfr\/wp-json\/wp\/v2\/pages\/917\/revisions\/924"}],"wp:attachment":[{"href":"https:\/\/ccsb.scripps.edu\/adfr\/wp-json\/wp\/v2\/media?parent=917"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}