{"id":2623,"date":"2023-09-23T20:24:56","date_gmt":"2023-09-24T00:24:56","guid":{"rendered":"https:\/\/www.med.unc.edu\/pharm\/miaolab\/?page_id=2623"},"modified":"2023-10-11T18:59:00","modified_gmt":"2023-10-11T22:59:00","slug":"vmd-tcl-scripts","status":"publish","type":"page","link":"https:\/\/www.med.unc.edu\/pharm\/miaolab\/resources\/vmd-tcl-scripts\/","title":{"rendered":"VMD TCL scripts"},"content":{"rendered":"<p class=\"body\">Following is a list of TCL scripts that can be <a href=\"http:\/\/www.ks.uiuc.edu\/Research\/vmd\/\">executed with VMD<\/a> using \u201cvmd -dispdev text -e *.tcl\u201d. They can be used to prepare systems for NAMD simulations and analyze simulation output trajectories, notably on viral capsids.<\/p>\n<p class=\"body\"><a href=\"https:\/\/www.med.unc.edu\/pharm\/miaolab\/wp-content\/uploads\/sites\/1385\/2023\/09\/AddTime2VMDmovie.tcl_-1.txt\" rel=\"noopener\">AddTime2VMDmovie.tcl<\/a><br \/>\nA TCL script used to take a set of .ppm images renderred with VMD (\u201cExtensions\u201d -&gt; \u201cVisualization\u201d -&gt; \u201cMovie Maker\u201d), resize\/crop the images, add time, and then generate a .gif animation.<\/p>\n<p class=\"body\"><a href=\"https:\/\/www.med.unc.edu\/pharm\/miaolab\/wp-content\/uploads\/sites\/1385\/2023\/09\/para.dat_-1.txt\">para.dat:<\/a><\/p>\n<p class=\"body\">Sample input file for running AddTime2VMDmovie.tcl<\/p>\n<p class=\"body\"><a href=\"https:\/\/www.med.unc.edu\/pharm\/miaolab\/wp-content\/uploads\/sites\/1385\/2023\/09\/AddTime2VMDmovie-examples.zip\">AddTime2VMDmovie-examples.zip<\/a><\/p>\n<p class=\"body\">A test example for running AddTime2VMDmovie.<\/p>\n<p class=\"body\"><a href=\"https:\/\/www.med.unc.edu\/pharm\/miaolab\/wp-content\/uploads\/sites\/1385\/2023\/09\/solvate.tcl_.txt\">solvate.tcl<\/a><br \/>\nGenerate the .psf and .pdb files from input PDB structure, solvate the structure in water and ionize the system with VMD to prepare the system for simulation.<\/p>\n<p class=\"body\"><a href=\"https:\/\/www.med.unc.edu\/pharm\/miaolab\/wp-content\/uploads\/sites\/1385\/2023\/09\/analysis-capsid-cRadius-rmsd.tcl_.txt\">analysis-capsid-cRadius-rmsd.tcl<\/a><\/p>\n<p class=\"body\">1) Analyize the changes in the radii of viral capsid backbone, i.e., the average, maximum and minimum distances between atoms in the capsid backbone and the capsid center of mass, in a simulation trajectory.<\/p>\n<p>2) Calculate the RMSD between viral capsid snapthots along simulation trajectory and a reference structure.<\/p>\n<p class=\"body\"><a href=\"https:\/\/www.med.unc.edu\/pharm\/miaolab\/wp-content\/uploads\/sites\/1385\/2023\/09\/analysis-sasa.tcl_.txt\">analysis-sasa.tcl<\/a><br \/>\nCalculate the interior, exerior and total SASA of viral capsids from a simulation trajectory.<\/p>\n<p class=\"body\"><a href=\"https:\/\/www.med.unc.edu\/pharm\/miaolab\/wp-content\/uploads\/sites\/1385\/2023\/09\/analysis-capsid-volume.tcl_.txt\">analysis-capsid-volume.tcl<\/a><br \/>\nCalculate the volume of a viral capsid and that inside the capsid cavity. In case the capsid is solvated in a water box, the volume of the host medium outside of the capsid is also calculated.<\/p>\n<p class=\"body\"><a href=\"https:\/\/www.med.unc.edu\/pharm\/miaolab\/wp-content\/uploads\/sites\/1385\/2023\/09\/analysis-capsid-waterdensity.tcl_.txt\">analysis-capsid-waterdensity.tcl<\/a><br \/>\nCalculate the density of water inside viral capsid cavity and that outside of the capsid by using the volume data obtained from executing script \u201canalysis-capsidvolume.tcl\u201d.<\/p>\n<p class=\"body\"><a href=\"https:\/\/www.med.unc.edu\/pharm\/miaolab\/wp-content\/uploads\/sites\/1385\/2023\/09\/analysis-56mers-TR.tcl_.txt\">analysis-56mers-TR.tcl<\/a><br \/>\nAnalyize the rigid-body translation and rotation of capsomeres (i.e., pentamers and hexamers) in CCMV capsid.<\/p>\n","protected":false},"excerpt":{"rendered":"<p>Following is a list of TCL scripts that can be executed with VMD using \u201cvmd -dispdev text -e *.tcl\u201d. They can be used to prepare systems for NAMD simulations and analyze simulation output trajectories, notably on viral capsids. AddTime2VMDmovie.tcl A TCL script used to take a set of .ppm images renderred with VMD (\u201cExtensions\u201d -&gt; &hellip; <a href=\"https:\/\/www.med.unc.edu\/pharm\/miaolab\/resources\/vmd-tcl-scripts\/\" aria-label=\"Read more about VMD TCL scripts\">Read more<\/a><\/p>\n","protected":false},"author":115433,"featured_media":0,"parent":2507,"menu_order":6,"comment_status":"closed","ping_status":"closed","template":"","meta":{"_acf_changed":false,"layout":"","cellInformation":"","apiCallInformation":"","footnotes":"","_links_to":"","_links_to_target":""},"class_list":["post-2623","page","type-page","status-publish","hentry","odd"],"acf":[],"_links_to":[],"_links_to_target":[],"_links":{"self":[{"href":"https:\/\/www.med.unc.edu\/pharm\/miaolab\/wp-json\/wp\/v2\/pages\/2623","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/www.med.unc.edu\/pharm\/miaolab\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/www.med.unc.edu\/pharm\/miaolab\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/www.med.unc.edu\/pharm\/miaolab\/wp-json\/wp\/v2\/users\/115433"}],"replies":[{"embeddable":true,"href":"https:\/\/www.med.unc.edu\/pharm\/miaolab\/wp-json\/wp\/v2\/comments?post=2623"}],"version-history":[{"count":0,"href":"https:\/\/www.med.unc.edu\/pharm\/miaolab\/wp-json\/wp\/v2\/pages\/2623\/revisions"}],"up":[{"embeddable":true,"href":"https:\/\/www.med.unc.edu\/pharm\/miaolab\/wp-json\/wp\/v2\/pages\/2507"}],"wp:attachment":[{"href":"https:\/\/www.med.unc.edu\/pharm\/miaolab\/wp-json\/wp\/v2\/media?parent=2623"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}