{"id":4514,"date":"2025-11-07T12:59:23","date_gmt":"2025-11-07T03:59:23","guid":{"rendered":"https:\/\/bdsl.jbnu.ac.kr\/blog\/?p=4514"},"modified":"2025-11-07T12:59:24","modified_gmt":"2025-11-07T03:59:24","slug":"autodock-vina-simple-example","status":"publish","type":"post","link":"https:\/\/bdsl.jbnu.ac.kr\/blog\/autodock-vina-simple-example\/","title":{"rendered":"AutoDock Vina &#8211; simple example"},"content":{"rendered":"\n<h2 class=\"wp-block-heading\">Introduction <\/h2>\n\n\n\n<p class=\"wp-block-paragraph\"><\/p>\n\n\n\n<p class=\"wp-block-paragraph\"><\/p>\n\n\n\n<h3 class=\"wp-block-heading\">Files <\/h3>\n\n\n\n\n\n<div class=\"wp-block-file\"><a id=\"wp-block-file--media-983cb727-42a3-436d-bbc2-f5bc44239bcc\" href=\"https:\/\/bdsl.jbnu.ac.kr\/blog\/wp-content\/uploads\/2025\/11\/ligand.pdbqt\">ligand<\/a><a href=\"https:\/\/bdsl.jbnu.ac.kr\/blog\/wp-content\/uploads\/2025\/11\/ligand.pdbqt\" class=\"wp-block-file__button wp-element-button\" download aria-describedby=\"wp-block-file--media-983cb727-42a3-436d-bbc2-f5bc44239bcc\">Download<\/a><\/div>\n\n\n\n<div class=\"wp-block-file\"><a id=\"wp-block-file--media-124c6a0b-2d29-4938-9649-a3b2a89b2285\" href=\"https:\/\/bdsl.jbnu.ac.kr\/blog\/wp-content\/uploads\/2025\/11\/receptor.pdbqt\">receptor<\/a><a href=\"https:\/\/bdsl.jbnu.ac.kr\/blog\/wp-content\/uploads\/2025\/11\/receptor.pdbqt\" class=\"wp-block-file__button wp-element-button\" download aria-describedby=\"wp-block-file--media-124c6a0b-2d29-4938-9649-a3b2a89b2285\">Download<\/a><\/div>\n\n\n\n<ul class=\"wp-block-list\">\n<li>Files <\/li>\n\n\n\n<li><\/li>\n<\/ul>\n\n\n\n<pre class=\"wp-block-code\"><code lang=\"python\" class=\"language-python\">from vina import Vina\n# Load Vina object\nv = Vina(sf_name='vina')\n\n# Set the receptor and ligand\nv.set_receptor('receptor.pdbqt')\nv.set_ligand_from_file('ligand.pdbqt')\n\n# Define the docking box\nv.compute_vina_maps(center=[63.051, \u00a022.770, \u00a015.879], box_size=[20, 20, 20])\n\n# Perform docking\nv.dock(exhaustiveness=32, n_poses=50)\n\n# Save the results\nv.write_poses('docked_ligand.pdbqt', n_poses=50, overwrite=True)\n<\/code><\/pre>\n","protected":false},"excerpt":{"rendered":"<p>Introduction Files<\/p>\n","protected":false},"author":1,"featured_media":0,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"_uag_custom_page_level_css":"","site-sidebar-layout":"default","site-content-layout":"","ast-site-content-layout":"default","site-content-style":"default","site-sidebar-style":"default","ast-global-header-display":"","ast-banner-title-visibility":"","ast-main-header-display":"","ast-hfb-above-header-display":"","ast-hfb-below-header-display":"","ast-hfb-mobile-header-display":"","site-post-title":"","ast-breadcrumbs-content":"","ast-featured-img":"","footer-sml-layout":"","ast-disable-related-posts":"","theme-transparent-header-meta":"","adv-header-id-meta":"","stick-header-meta":"","header-above-stick-meta":"","header-main-stick-meta":"","header-below-stick-meta":"","astra-migrate-meta-layouts":"set","ast-page-background-enabled":"default","ast-page-background-meta":{"desktop":{"background-color":"var(--ast-global-color-4)","background-image":"","background-repeat":"repeat","background-position":"center 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center","background-size":"auto","background-attachment":"scroll","background-type":"","background-media":"","overlay-type":"","overlay-color":"","overlay-opacity":"","overlay-gradient":""}},"footnotes":"","_members_access_role":[],"_members_access_error":""},"categories":[1],"tags":[],"class_list":["post-4514","post","type-post","status-publish","format-standard","hentry","category-uncategorized"],"yoast_head":"<!-- This site is optimized with the Yoast SEO plugin v28.4 - https:\/\/yoast.com\/product\/yoast-seo-wordpress\/ -->\n<title>AutoDock Vina - simple example - Biomedical Data Science Laboratory<\/title>\n<meta name=\"robots\" content=\"index, follow, max-snippet:-1, max-image-preview:large, max-video-preview:-1\" \/>\n<link rel=\"canonical\" href=\"https:\/\/bdsl.jbnu.ac.kr\/blog\/autodock-vina-simple-example\/\" \/>\n<meta property=\"og:locale\" content=\"en_US\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"AutoDock Vina - 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