<\/div>\n
Details: the program asks for the name and location for the target file that will be generated. It will then compute the affinity maps and store them in the target file along with meta data.<\/p>\n
![\"\"](\"https:\/\/ccsb.scripps.edu\/agfr\/wp-content\/uploads\/sites\/33\/2019\/04\/Screen-Shot-2019-04-15-at-11.28.11-AM.png\")
<\/p>\n
The generated target file describes the binding pocket targeted for docking on the receptor. It stores the PDBQT file of the receptor used to compute the affinity maps, the grid parameter file used to run AutoGrid,<\/em> as well as files generated by the AutoGrid<\/em>\u00a0run (i.e.<\/em> affinity maps, AutoGrid<\/em> log file, etc.). In addition, it stores meta-data about the generation of the target file such as: the time and computer architecture on which the maps were computed, the docking-box parameters, the grid parameter file, the versions of AGFR<\/em> and\u00a0AutoSite<\/em>, the water map parameters, etc.<\/p>\nIt is recommended to use names that are descriptive. In this case we use CDK2BindingSite_rigid<\/em> as we defined the docking box using a known binding site and we did not specify any flexible receptor side chains.<\/p>\nPressing the \u201cSave\u201d button will start the calculation in a separate thread, leaving the graphical user interface responsive. The progress bar below the button will indicate the level of completion of the calculation.<\/p>\n
![\"\"](\"https:\/\/ccsb.scripps.edu\/agfr\/wp-content\/uploads\/sites\/33\/2019\/04\/Screen-Shot-2019-04-15-at-11.33.22-AM.png\")
<\/p>\n
NOTE: a target file can be inspected from the command line using the about<\/em> command (AutoDockSuite-1.0\/bin\/about<\/em>)<\/p>\n<\/div><\/div><\/div><\/div><\/div><\/div><\/div><\/div>\n","protected":false},"excerpt":{"rendered":"
This page was last updated on May 22nd, 2019 at […]<\/p>\n","protected":false},"author":1,"featured_media":0,"parent":0,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"footnotes":""},"class_list":["post-576","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"https:\/\/ccsb.scripps.edu\/agfr\/wp-json\/wp\/v2\/pages\/576","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/ccsb.scripps.edu\/agfr\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/ccsb.scripps.edu\/agfr\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/ccsb.scripps.edu\/agfr\/wp-json\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/ccsb.scripps.edu\/agfr\/wp-json\/wp\/v2\/comments?post=576"}],"version-history":[{"count":14,"href":"https:\/\/ccsb.scripps.edu\/agfr\/wp-json\/wp\/v2\/pages\/576\/revisions"}],"predecessor-version":[{"id":898,"href":"https:\/\/ccsb.scripps.edu\/agfr\/wp-json\/wp\/v2\/pages\/576\/revisions\/898"}],"wp:attachment":[{"href":"https:\/\/ccsb.scripps.edu\/agfr\/wp-json\/wp\/v2\/media?parent=576"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}
![\"\"](\"https:\/\/ccsb.scripps.edu\/agfr\/wp-content\/uploads\/sites\/33\/2019\/04\/Screen-Shot-2019-04-15-at-8.50.57-AM.png\")
and select 4EK3_rec.pdbqt<\/span><\/h4>\n![](\"https:\/\/ccsb.scripps.edu\/agfr\/wp-content\/uploads\/sites\/33\/2019\/04\/word-image-1.png\")
<\/p>\n![\"\"](\"https:\/\/ccsb.scripps.edu\/agfr\/wp-content\/uploads\/sites\/33\/2019\/04\/word-image-59.png\")
\u00a0and select select residues ILE10, PHE80, PHE82, and LYS89![\"\"](\"https:\/\/ccsb.scripps.edu\/agfr\/wp-content\/uploads\/sites\/33\/2019\/04\/word-image-25.png\")
<\/p>\n![\"\"](\"https:\/\/ccsb.scripps.edu\/agfr\/wp-content\/uploads\/sites\/33\/2019\/04\/word-image-38.png\")
\u00a0to focus the 3D scene on the box.<\/li>\n![\"\"](\"https:\/\/ccsb.scripps.edu\/agfr\/wp-content\/uploads\/sites\/33\/2019\/04\/Screen-Shot-2019-04-15-at-11.06.14-AM.png\")
![\"\"](\"https:\/\/ccsb.scripps.edu\/agfr\/wp-content\/uploads\/sites\/33\/2019\/05\/Screen-Shot-2019-05-22-at-3.14.22-PM.png\")
<\/p>\n![\"\"](\"https:\/\/ccsb.scripps.edu\/agfr\/wp-content\/uploads\/sites\/33\/2019\/04\/Screen-Shot-2019-04-15-at-11.18.49-AM.png\")
button<\/span><\/h4>\n![\"\"](\"https:\/\/ccsb.scripps.edu\/agfr\/wp-content\/uploads\/sites\/33\/2019\/04\/Screen-Shot-2019-04-15-at-11.16.55-AM.png\")
<\/p>\n![\"\"](\"https:\/\/ccsb.scripps.edu\/agfr\/wp-content\/uploads\/sites\/33\/2019\/04\/Screen-Shot-2019-04-15-at-11.17.06-AM.png\")
<\/p>\n