{"id":313,"date":"2017-05-10T21:50:24","date_gmt":"2017-05-11T01:50:24","guid":{"rendered":"http:\/\/williamkennerly.com\/blog\/?p=313"},"modified":"2018-05-31T10:55:49","modified_gmt":"2018-05-31T14:55:49","slug":"helpful-cpptraj-commands-part-1-topology-commands","status":"publish","type":"post","link":"http:\/\/williamkennerly.com\/blog\/helpful-cpptraj-commands-part-1-topology-commands\/","title":{"rendered":"Helpful CPPTRAJ Commands Part 1: Topology Commands"},"content":{"rendered":"<p>CPPTRAJ has a variety of commands for analyzing MD Simulation outputs, but because there are so many commands it would be very difficult to describe them all in detail in a single blogpost. As such, this first post will consist of the descriptions of three Topology Commands that I found to be useful for my research of the Tryptophan residue in Melittin. These Topology Commands print out Molecular Topology related information in CPPTRAJ&#8217;s interactive mode. For all intents and purposes, the visuals used in this blogpost will strictly be regarding Melittin.<\/p>\n<p>Note:\u00a0<strong>[&lt;mask&gt;] <\/strong>indicates a single residue\/atom or range of residues\/atoms<\/p>\n<p>&nbsp;<\/p>\n<p><strong>atominfo [&lt;mask&gt;]<\/strong><\/p>\n<p>This command prints out general information on each atom specified by the given <strong>[&lt;mask&gt;]<\/strong> modifier. The information is outputted into 12 columns. The following visual is an example output of the command being called on the 19<sup>th<\/sup> residue of a Melittin .mdcrd file.<\/p>\n<p><a href=\"http:\/\/williamkennerly.com\/blog\/wp-content\/uploads\/2017\/05\/Screen-Shot-2017-04-25-at-11.37.22-PM.png\"><img loading=\"lazy\" decoding=\"async\" class=\"aligncenter wp-image-314 size-large\" src=\"http:\/\/williamkennerly.com\/blog\/wp-content\/uploads\/2017\/05\/Screen-Shot-2017-04-25-at-11.37.22-PM-1024x651.png\" width=\"500\" height=\"318\" srcset=\"http:\/\/williamkennerly.com\/blog\/wp-content\/uploads\/2017\/05\/Screen-Shot-2017-04-25-at-11.37.22-PM-1024x651.png 1024w, http:\/\/williamkennerly.com\/blog\/wp-content\/uploads\/2017\/05\/Screen-Shot-2017-04-25-at-11.37.22-PM-300x191.png 300w, http:\/\/williamkennerly.com\/blog\/wp-content\/uploads\/2017\/05\/Screen-Shot-2017-04-25-at-11.37.22-PM-768x488.png 768w, http:\/\/williamkennerly.com\/blog\/wp-content\/uploads\/2017\/05\/Screen-Shot-2017-04-25-at-11.37.22-PM.png 1152w\" sizes=\"auto, (max-width: 500px) 100vw, 500px\" \/><\/a><\/p>\n<ul>\n<li><strong>#Atom<\/strong> refers to the atom\u2019s index as given by Amber16<\/li>\n<li><strong>Name<\/strong> refers to the atom\u2019s name identifier as given by Amber16<\/li>\n<li><strong>#Res<\/strong> refers to the residue number in which the atom is located<\/li>\n<li>2<sup>nd<\/sup> <strong>Name <\/strong>refers to the shorthand name of the residue in which the atom is located<\/li>\n<li><strong>#Mol<\/strong> refers to the atom\u2019s molecule number<\/li>\n<li><strong>Type<\/strong> refers to the type of atom in the residue (i.e. alpha, beta, etc)<\/li>\n<li><strong>Charge<\/strong> refers to the electron charge of the atom<\/li>\n<li><strong>Mass<\/strong> refers to the mass of the atom<\/li>\n<li><strong>GBradius<\/strong> refers to the generalized Born radius of the atom<\/li>\n<li><strong>E1<\/strong> refers to the element symbol<\/li>\n<li><strong>rVDW<\/strong> refers to the Van der Waal\u2019s force radius of the atom<\/li>\n<li><strong>eVDW<\/strong> refers to the epsilon Van der Waal\u2019s force of the atom<\/li>\n<\/ul>\n<p>Example Usage:\u00a0<strong>atominfo :19<\/strong><\/p>\n<p>&nbsp;<\/p>\n<p><strong>bondinfo [&lt;mask&gt;]<\/strong><\/p>\n<p>This command prints out general information in the form of 6 columns about each bond between each atom as specified by the <strong>[&lt;mask&gt;]<\/strong> modifier. The following visual is an example output of the command being called on a specific carbon atom in the 19<sup>th<\/sup> residue of a Melittin .mdcrd file.<\/p>\n<p><a href=\"http:\/\/williamkennerly.com\/blog\/wp-content\/uploads\/2017\/05\/Screen-Shot-2017-04-25-at-11.58.07-PM.png\"><img loading=\"lazy\" decoding=\"async\" class=\"alignnone size-full wp-image-315\" src=\"http:\/\/williamkennerly.com\/blog\/wp-content\/uploads\/2017\/05\/Screen-Shot-2017-04-25-at-11.58.07-PM.png\" alt=\"\" width=\"956\" height=\"250\" srcset=\"http:\/\/williamkennerly.com\/blog\/wp-content\/uploads\/2017\/05\/Screen-Shot-2017-04-25-at-11.58.07-PM.png 956w, http:\/\/williamkennerly.com\/blog\/wp-content\/uploads\/2017\/05\/Screen-Shot-2017-04-25-at-11.58.07-PM-300x78.png 300w, http:\/\/williamkennerly.com\/blog\/wp-content\/uploads\/2017\/05\/Screen-Shot-2017-04-25-at-11.58.07-PM-768x201.png 768w, http:\/\/williamkennerly.com\/blog\/wp-content\/uploads\/2017\/05\/Screen-Shot-2017-04-25-at-11.58.07-PM-770x200.png 770w\" sizes=\"auto, (max-width: 956px) 100vw, 956px\" \/><\/a><\/p>\n<ul>\n<li><strong>Bond<\/strong> refers to the bond index as specified by Amber16<\/li>\n<li><strong>Kb<\/strong> refers to the bond force constant<\/li>\n<li><strong>Req<\/strong> refers to the bond equilibrium value in Angstroms<\/li>\n<li><strong>atom names<\/strong> refers to the names of the bonded atoms as specified by Amber16<\/li>\n<li><strong>(numbers)<\/strong> refers to the atom indexes as specified by Amber16 as well as the types of atoms that are bonded together<\/li>\n<\/ul>\n<p>Example Usage:\u00a0<strong>bondinfo :19@CA<\/strong><\/p>\n<p>&nbsp;<\/p>\n<p><strong>resinfo [&lt;mask&gt;]<\/strong><\/p>\n<p>This command prints out general information in 7 columns about a single residue or range of residues as specified by the given <strong>[&lt;mask&gt;]<\/strong> modifier. The following visual is an example output of this command being called on the range of residues that make up Melittin. The reason I had to indicate all the residues was because the .mdcrd file that I used had Melittin simulated in a water box. If the command was called without specifying the <strong>[&lt;mask&gt;]<\/strong> modifier, the output will include the residue info for all the water molecules in the water box as well. This goes for the <strong>atominfo<\/strong> and <strong>bondinfo<\/strong> commands too.<\/p>\n<p><a href=\"http:\/\/williamkennerly.com\/blog\/wp-content\/uploads\/2017\/05\/Screen-Shot-2017-04-26-at-12.05.40-AM.png\"><img loading=\"lazy\" decoding=\"async\" class=\"alignnone size-full wp-image-316\" src=\"http:\/\/williamkennerly.com\/blog\/wp-content\/uploads\/2017\/05\/Screen-Shot-2017-04-26-at-12.05.40-AM.png\" alt=\"\" width=\"596\" height=\"786\" srcset=\"http:\/\/williamkennerly.com\/blog\/wp-content\/uploads\/2017\/05\/Screen-Shot-2017-04-26-at-12.05.40-AM.png 596w, http:\/\/williamkennerly.com\/blog\/wp-content\/uploads\/2017\/05\/Screen-Shot-2017-04-26-at-12.05.40-AM-227x300.png 227w\" sizes=\"auto, (max-width: 596px) 100vw, 596px\" \/><\/a><\/p>\n<ul>\n<li><strong>#Res<\/strong> refers to the residue index as specified by Amber16<\/li>\n<li><strong>Name<\/strong> refers to the shorthand name for each residue<\/li>\n<li><strong>First<\/strong> refers to the atom index of the first atom in the residue<\/li>\n<li><strong>Last<\/strong> refers to the atom index of the last atom in the residue<\/li>\n<li><strong>Natom<\/strong> refers to the number of atoms in the residue<\/li>\n<li><strong>#Orig<\/strong> refers to the original residue number in the original PDB file of which the date comes from<\/li>\n<li><strong>#Mol<\/strong> refers to the molecule number<\/li>\n<\/ul>\n<p>One can also add the modifier, <strong>[short]<\/strong>, to display the residues in the FASTA code sequence form. For Melittin, the sequence would look like this: GIGAVLKVLTTGLPALISWIKRKRQQ.<\/p>\n<p>Example Usage: <strong>resinfo :1-26<\/strong><\/p>\n<p>&nbsp;<\/p>\n","protected":false},"excerpt":{"rendered":"<p>CPPTRAJ has a variety of commands for analyzing MD Simulation outputs, but because there are so many commands it would be very difficult to describe them all in detail in a single blogpost. As such, this first post will consist &hellip; <a href=\"http:\/\/williamkennerly.com\/blog\/helpful-cpptraj-commands-part-1-topology-commands\/\">Continue reading <span class=\"meta-nav\">&rarr;<\/span><\/a><\/p>\n","protected":false},"author":6,"featured_media":0,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"footnotes":""},"categories":[9,8],"tags":[17,29,15],"class_list":["post-313","post","type-post","status-publish","format-standard","hentry","category-chemistry","category-computing","tag-amber","tag-cpptraj","tag-molecular-dynamics"],"_links":{"self":[{"href":"http:\/\/williamkennerly.com\/blog\/wp-json\/wp\/v2\/posts\/313","targetHints":{"allow":["GET"]}}],"collection":[{"href":"http:\/\/williamkennerly.com\/blog\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"http:\/\/williamkennerly.com\/blog\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"http:\/\/williamkennerly.com\/blog\/wp-json\/wp\/v2\/users\/6"}],"replies":[{"embeddable":true,"href":"http:\/\/williamkennerly.com\/blog\/wp-json\/wp\/v2\/comments?post=313"}],"version-history":[{"count":1,"href":"http:\/\/williamkennerly.com\/blog\/wp-json\/wp\/v2\/posts\/313\/revisions"}],"predecessor-version":[{"id":317,"href":"http:\/\/williamkennerly.com\/blog\/wp-json\/wp\/v2\/posts\/313\/revisions\/317"}],"wp:attachment":[{"href":"http:\/\/williamkennerly.com\/blog\/wp-json\/wp\/v2\/media?parent=313"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"http:\/\/williamkennerly.com\/blog\/wp-json\/wp\/v2\/categories?post=313"},{"taxonomy":"post_tag","embeddable":true,"href":"http:\/\/williamkennerly.com\/blog\/wp-json\/wp\/v2\/tags?post=313"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}