{"id":223,"date":"2019-03-08T00:08:47","date_gmt":"2019-03-08T00:08:47","guid":{"rendered":"https:\/\/ccsb.scripps.edu\/autodock\/?page_id=223"},"modified":"2019-08-01T14:40:38","modified_gmt":"2019-08-01T14:40:38","slug":"faq","status":"publish","type":"page","link":"https:\/\/ccsb.scripps.edu\/autodocksuite\/faq\/","title":{"rendered":"FAQ"},"content":{"rendered":"<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-title title fusion-title-1 fusion-sep-none fusion-title-text fusion-title-size-one\" style=\"--awb-margin-top-small:0px;--awb-margin-right-small:0px;--awb-margin-bottom-small:20px;--awb-margin-left-small:0px;\"><h1 class=\"fusion-title-heading title-heading-left\" style=\"margin:0;\"><h3>Frequently-Asked Questions about the AutoDock Suite<\/h3><\/h1><\/div><div class=\"fusion-clearfix\"><\/div><\/div><\/div><\/div><\/div><div class=\"fusion-fullwidth fullwidth-box fusion-builder-row-2 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-1 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-title title fusion-title-2 fusion-sep-none fusion-title-text fusion-title-size-one\" style=\"--awb-margin-top-small:0px;--awb-margin-right-small:0px;--awb-margin-bottom-small:20px;--awb-margin-left-small:0px;\"><h1 class=\"fusion-title-heading title-heading-left\" style=\"margin:0;\"><h2 style=\"text-align: center;\">FAQ<\/h2><\/h1><\/div><style type=\"text\/css\">#accordian-1 .fusion-panel:hover,#accordian-1 .fusion-panel.hover{ background-color: #f9f9f9 } #accordian-1 .fusion-panel { border-color:#cccccc; border-width:1px; background-color:#ffffff; }.fusion-accordian #accordian-1 .panel-title a .fa-fusion-box:before{ font-size: 13px;width: 13px;}.fusion-accordian #accordian-1 .panel-title a .fa-fusion-box{ color: #000000;}.fusion-accordian  #accordian-1 .panel-title a{font-family:\"Montserrat\";font-style:normal;font-weight:400;}.fusion-accordian  #accordian-1 .panel-title a:not(:hover){}.fusion-accordian  #accordian-1 .toggle-content{font-family:\"Hind\";font-style:normal;font-weight:400;}.fusion-accordian #accordian-1 .fa-fusion-box { background-color: #e91e63 !important;border-color: #e91e63 !important;}.fusion-accordian #accordian-1 .panel-title a:hover,.fusion-accordian #accordian-1 .panel-title a.hover { color: #337d93;}.fusion-faq-shortcode .fusion-accordian #accordian-1 .fusion-toggle-boxed-mode:hover .panel-title a { color: #337d93;}.fusion-accordian #accordian-1 .panel-title .active .fa-fusion-box,.fusion-accordian #accordian-1 .panel-title a:hover .fa-fusion-box,.fusion-accordian #accordian-1 .panel-title a.hover .fa-fusion-box { background-color: #337d93!important;border-color: #337d93!important;}<\/style><div class=\"fusion-faq-shortcode\" style=\"\"><ul role=\"menu\" class=\"fusion-filters clearfix\"><li role=\"presentation\" class=\"fusion-filter fusion-active\"><a role=\"menuitem\" data-filter=\".general\" href=\"#\">General Information<\/a><\/li><li role=\"presentation\" class=\"fusion-filter fusion-hidden\"><a role=\"menuitem\" data-filter=\".science\" href=\"#\">Scientific Questions<\/a><\/li><\/ul><div class=\"fusion-faqs-wrapper\"><div class=\"accordian fusion-accordian\"><div class=\"panel-group \" id=\"accordian-1\"><div class=\"fusion-panel fusion-toggle-no-divider fusion-toggle-boxed-mode panel-default fusion-faq-post fusion-faq-post-328 science \"><span class=\"entry-title rich-snippet-hidden\">Where do I set the AutoDock 4 force field parameters?<\/span><span class=\"vcard rich-snippet-hidden\"><span class=\"fn\"><a href=\"https:\/\/ccsb.scripps.edu\/autodocksuite\/author\/mgl-admin\/\" title=\"Posts by mgl-admin\" rel=\"author\">mgl-admin<\/a><\/span><\/span><span class=\"updated rich-snippet-hidden\">2019-03-18T21:11:48+00:00<\/span><div class=\"panel-heading\"><h4 id=\"faq_1-328\" class=\"panel-title toggle\"><a data-toggle=\"collapse\" class=\"collapsed\" data-parent=\"#accordian-1\" data-target=\"#collapse-1-328\" href=\"#collapse-1-328\" aria-expanded=\"false\"><div class=\"fusion-toggle-icon-wrapper\"><div class=\"fusion-toggle-icon-wrapper-main\"><div class=\"fusion-toggle-icon-wrapper-sub\"><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><\/div><\/div><\/div><div class=\"fusion-toggle-heading\">Where do I set the AutoDock 4 force field parameters?<\/div><\/a><\/h4><\/div><div id=\"collapse-1-328\" aria-labelledby=\"faq_1-328\" class=\"panel-collapse collapse\"><div class=\"panel-body toggle-content post-content\"><div class=\"fusion-fullwidth fullwidth-box fusion-builder-row-2-1 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-2 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\"><div class=\"documentDescription\">The &#8220;parameter_file&#8221; command allows you to specify a new parameter library file that contains the various force field parameters.\u00a0 In most cases, you will not need to modify these values, but you can make changes if you have special needs for your application.<\/div>\n<div>\n<p>The standard AutoDock 4 parameters are in the file &#8220;AD4_parameters.dat&#8221; which can be found in the &#8220;autodocksuite-4.<em>n<\/em>.<em>m<\/em>\/src\/autodock-4.<em>x<\/em>.<em>y<\/em>&#8221; directory of the AutoDock 4 distribution, where <em>n<\/em> and <em>m<\/em> are the major and minor version numbers of the AutoDock Suite, and <em>x<\/em> and <em>y<\/em> are the major and minor version numbers of AutoDock.\u00a0These are the default values that are &#8220;baked in&#8221; to AutoGrid 4 and AutoDock 4, and are the values that will be used if you do not specify your own parameter file explicitly in your GPF or DPF with the &#8220;parameter_file&#8221; command.<\/p>\n<p>You <a href=\"http:\/\/autodock.scripps.edu\/faqs-help\/faq\/how-do-i-add-new-atom-types-to-autodock-4\">can add new atom types and parameters to this file<\/a>, or modify the existing ones. \u00a0Please refer to the <a href=\"https:\/\/ccsb.scripps.edu\/autodocksuite\/wp-content\/uploads\/sites\/31\/2019\/03\/AutoDock4.2.6_UserGuide.pdf\">AutoDock4.2.6_UserGuide<\/a>\u00a0for information on the parameters and format of the file.\u00a0If you come up with new or modified parameters, we would like to know about them, so we can incorporate them in future releases.\u00a0 Thanks!<\/p>\n<\/div>\n<\/div><div class=\"fusion-clearfix\"><\/div><\/div><\/div><\/div><\/div>\n<\/div><\/div><\/div><div class=\"fusion-panel fusion-toggle-no-divider fusion-toggle-boxed-mode panel-default fusion-faq-post fusion-faq-post-326 science \"><span class=\"entry-title rich-snippet-hidden\">Can AutoDock be used for &#8220;Blind Docking&#8221;?<\/span><span class=\"vcard rich-snippet-hidden\"><span class=\"fn\"><a href=\"https:\/\/ccsb.scripps.edu\/autodocksuite\/author\/mgl-admin\/\" title=\"Posts by mgl-admin\" rel=\"author\">mgl-admin<\/a><\/span><\/span><span class=\"updated rich-snippet-hidden\">2019-03-18T21:15:21+00:00<\/span><div class=\"panel-heading\"><h4 id=\"faq_1-326\" class=\"panel-title toggle\"><a data-toggle=\"collapse\" class=\"collapsed\" data-parent=\"#accordian-1\" data-target=\"#collapse-1-326\" href=\"#collapse-1-326\" aria-expanded=\"false\"><div class=\"fusion-toggle-icon-wrapper\"><div class=\"fusion-toggle-icon-wrapper-main\"><div class=\"fusion-toggle-icon-wrapper-sub\"><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><\/div><\/div><\/div><div class=\"fusion-toggle-heading\">Can AutoDock be used for &#8220;Blind Docking&#8221;?<\/div><\/a><\/h4><\/div><div id=\"collapse-1-326\" aria-labelledby=\"faq_1-326\" class=\"panel-collapse collapse\"><div class=\"panel-body toggle-content post-content\"><div class=\"documentDescription\">AutoDock can be used when the structure of the ligand and the protein are both known, but the location of the binding site is unknown. \u00a0This is often referred to as &#8220;blind docking.&#8221; This is a challenge because you need to set up the dockings to search the entire surface of the protein (or other macromolecule) of interest. This can be achieved using AutoGrid to create very large grid maps, with the maximum number of points in each dimension, and if necessary, creating sets of adjacent grid map volumes that cover the macromolecule. The third-party tool <span class=\"link-external\"><a href=\"http:\/\/www.quimica.urv.cat\/~pujadas\/BDT\/index.html\">BDT<\/a><\/span> can be used to set up such sets of grid maps.<\/div>\n<div>\n<p>You can also use <a href=\"https:\/\/ccsb.scripps.edu\/autodocksuite\/autoligand\/\">AutoLigand<\/a> to predict the probable binding sites on a protein surface, and limit docking simulations to those locations.<\/p>\n<p>Several laboratories have used AutoDock to perform blind docking, for example:<\/p>\n<ol>\n<li>Hetenyi, C. and van der Spoel, D. (2002) Efficient docking of peptides to proteins without prior knowledge of the binding site. <em>Protein Science<\/em>, <u>11<\/u>(7): 1729-1737.<\/li>\n<li>Kovacs, M., Toth, J., Hetenyi, C., Malnasi-Csizmadia, A., and Sellers, J.R. (2004) Mechanism of blebbistatin inhibition of myosin II. <em>Journal of Biological Chemistry<\/em>, <u>279<\/u>(34): 35557-35563.<\/li>\n<li>Bikadi, Z., Hazai, E., Zsila, F., and Lockwood, S.F. (2006) Molecular modeling of non-covalent binding of homochiral (3S,3 &#8216; S)-astaxanthin to matrix metalloproteinase-13 (MMP-13). <em>Bioorganic &amp; Medicinal Chemistry<\/em>, <u>14<\/u>(16): 5451-5458.<\/li>\n<li>Hazai, E., Bikadi, Z., Zsila, F., and Lockwood, S.F. (2006) Molecular modeling of the non-covalent binding of the dietary tomato carotenoids lycopene and lycophyll, and selected oxidative metabolites with 5-lipoxygenase. <em>Bioorganic &amp; Medicinal Chemistry<\/em>, <u>14<\/u>(20): 6859-6867.<\/li>\n<li>Hetenyi, C. and van der Spoel, D. (2006) Blind docking of drug-sized compounds to proteins with up to a thousand residues. <em>FEBS Letters<\/em>, <u>580<\/u>(5): 1447-1450.<\/li>\n<li>Iorga, B., Herlem, D., Barre, E., and Guillou, C. (2006) Acetylcholine nicotinic receptors: finding the putative binding site of allosteric modulators using the &#8220;blind docking&#8221; approach. <em>Journal of Molecular Modeling<\/em>, <u>12<\/u>(3): 366-372.<\/li>\n<\/ol>\n<\/div>\n<\/div><\/div><\/div><div class=\"fusion-panel fusion-toggle-no-divider fusion-toggle-boxed-mode panel-default fusion-faq-post fusion-faq-post-321 general \"><span class=\"entry-title rich-snippet-hidden\">Is there a graphical user interface to AutoGrid and AutoDock?<\/span><span class=\"vcard rich-snippet-hidden\"><span class=\"fn\"><a href=\"https:\/\/ccsb.scripps.edu\/autodocksuite\/author\/mgl-admin\/\" title=\"Posts by mgl-admin\" rel=\"author\">mgl-admin<\/a><\/span><\/span><span class=\"updated rich-snippet-hidden\">2019-03-18T21:18:47+00:00<\/span><div class=\"panel-heading\"><h4 id=\"faq_1-321\" class=\"panel-title toggle\"><a data-toggle=\"collapse\" class=\"collapsed\" data-parent=\"#accordian-1\" data-target=\"#collapse-1-321\" href=\"#collapse-1-321\" aria-expanded=\"false\"><div class=\"fusion-toggle-icon-wrapper\"><div class=\"fusion-toggle-icon-wrapper-main\"><div class=\"fusion-toggle-icon-wrapper-sub\"><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><\/div><\/div><\/div><div class=\"fusion-toggle-heading\">Is there a graphical user interface to AutoGrid and AutoDock?<\/div><\/a><\/h4><\/div><div id=\"collapse-1-321\" aria-labelledby=\"faq_1-321\" class=\"panel-collapse collapse\"><div class=\"panel-body toggle-content post-content\"><div class=\"documentDescription\"><a href=\"http:\/\/autodock.scripps.edu\/faqs-help\/faq\/resources\/adt\">ADT (also known as AutoDockTools) <\/a>is a graphical user interface to help you set up AutoGrid map calculations, AutoDock dockings, and analysis of results.\u00a0 ADT is available as part of\u00a0<span class=\"link-external\"><a href=\"http:\/\/mgltools.scripps.edu\/\">MGLTools<\/a><\/span>.<\/div>\n<div><\/div>\n<div><\/div>\n<\/div><\/div><\/div><div class=\"fusion-panel fusion-toggle-no-divider fusion-toggle-boxed-mode panel-default fusion-faq-post fusion-faq-post-312 general \"><span class=\"entry-title rich-snippet-hidden\">How do I join the AutoDock Mailing List?<\/span><span class=\"vcard rich-snippet-hidden\"><span class=\"fn\"><a href=\"https:\/\/ccsb.scripps.edu\/autodocksuite\/author\/mgl-admin\/\" title=\"Posts by mgl-admin\" rel=\"author\">mgl-admin<\/a><\/span><\/span><span class=\"updated rich-snippet-hidden\">2019-03-18T21:21:16+00:00<\/span><div class=\"panel-heading\"><h4 id=\"faq_1-312\" class=\"panel-title toggle\"><a data-toggle=\"collapse\" class=\"collapsed\" data-parent=\"#accordian-1\" data-target=\"#collapse-1-312\" href=\"#collapse-1-312\" aria-expanded=\"false\"><div class=\"fusion-toggle-icon-wrapper\"><div class=\"fusion-toggle-icon-wrapper-main\"><div class=\"fusion-toggle-icon-wrapper-sub\"><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><\/div><\/div><\/div><div class=\"fusion-toggle-heading\">How do I join the AutoDock Mailing List?<\/div><\/a><\/h4><\/div><div id=\"collapse-1-312\" aria-labelledby=\"faq_1-312\" class=\"panel-collapse collapse\"><div class=\"panel-body toggle-content post-content\"><p>You can subscribe to the ADL by going to the <span class=\"link-external\"><a href=\"http:\/\/mgldev.scripps.edu\/mailman\/listinfo\/autodock\">ADL Info Page<\/a><\/span>; you will need to give a valid email address, create a password, and decide if you want your messages to be sent as a daily digest or not.<\/p>\n<h4>About the AutoDock mailing list<\/h4>\n<p>This list is intended for novice and expert users of the ligand-protein and protein-protein docking software AutoDock, AutoGrid and ADT (AutoDockTools). This list will provide a forum for users to share experience, to ask questions about things not covered in the documentation, and hopefully, to get answers to these questions. Questions may range from technical to scientific, but should be about docking molecules using AutoDock and its associated programs and utilities. Suggestions for new features are also welcome. Announcements of new software versions and functionalities will be made on this list. In general, bugs should not be reported here but entered into our Bugzilla database. Just go to <span class=\"link-external\"><a href=\"http:\/\/mgldev.scripps.edu\/bugs\">http:\/\/mgldev.scripps.edu\/bugs\/<\/a><\/span> and click on the &#8220;Open a new Bugzilla account&#8221; link.<\/p>\n<\/div><\/div><\/div><\/div><\/div><\/div><\/div><div class=\"fusion-clearfix\"><\/div><\/div><\/div><\/div><\/div><\/p>\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-223","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"https:\/\/ccsb.scripps.edu\/autodocksuite\/wp-json\/wp\/v2\/pages\/223","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/ccsb.scripps.edu\/autodocksuite\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/ccsb.scripps.edu\/autodocksuite\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/ccsb.scripps.edu\/autodocksuite\/wp-json\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/ccsb.scripps.edu\/autodocksuite\/wp-json\/wp\/v2\/comments?post=223"}],"version-history":[{"count":15,"href":"https:\/\/ccsb.scripps.edu\/autodocksuite\/wp-json\/wp\/v2\/pages\/223\/revisions"}],"predecessor-version":[{"id":394,"href":"https:\/\/ccsb.scripps.edu\/autodocksuite\/wp-json\/wp\/v2\/pages\/223\/revisions\/394"}],"wp:attachment":[{"href":"https:\/\/ccsb.scripps.edu\/autodocksuite\/wp-json\/wp\/v2\/media?parent=223"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}