{"id":8522,"date":"2022-09-06T18:21:09","date_gmt":"2022-09-06T17:21:09","guid":{"rendered":"https:\/\/www.blopig.com\/blog\/?p=8522"},"modified":"2022-09-12T10:52:25","modified_gmt":"2022-09-12T09:52:25","slug":"do-you-have-cis-peptide-bonds-in-your-simulation-inputs","status":"publish","type":"post","link":"https:\/\/www.blopig.com\/blog\/2022\/09\/do-you-have-cis-peptide-bonds-in-your-simulation-inputs\/","title":{"rendered":"Do you have cis peptide bonds in your simulation inputs?"},"content":{"rendered":"\n

People who run molecular simulations quickly become familiar with all of the things about a PDB file – missing residues, missing heavy atoms in residues, missing hydrogens, non-standard amino acids, multiple conformations, crystallization ligands, etc. – that might need to be fixed before setting up a simulation. This blog post is a reminder to check, after you have “fixed” your PDB, if you have accidentally introduced<\/em> aberrant cis<\/em> peptide bonds into your structure during rebuilding. <\/p>\n\n\n\n\n\n\n\n

The vast majority of peptide bonds are trans<\/em>, with a small fraction (mostly involving proline) in the cis<\/em> conformation. However, programs like pdbfixer<\/code> and even the topology rebuilding function of CHARMM<\/code> (in my case, CHARMM35<\/code>) will sometimes introduce cis<\/em> peptide bonds into rebuilt systems. These programs are typically just dropping in a residue template, and sometimes it fails. You can read a detailed discussion of this in the context of pdbfixer<\/code> here<\/a>. <\/p>\n\n\n\n

Luckily, you can find and fix cis<\/em> peptides in your structures using the handy VMD<\/code> tool cispeptide<\/a>. Once you load a structure into VMD<\/code>, cispeptide<\/code> will first find the cis<\/em> peptide bond and then allow you to select a specific peptide bond atom to flip.<\/p>\n\n\n\n

In most cases, just flipping e.g. the “N” atom so that the peptide bond is now trans<\/em> but the rest of the protein’s configuration has not been altered will result in the “fixed” peptide bond rapidly flipping back to a cis<\/em> conformation due to the poor local geometry (which is why the rebuilding program had trouble in the first place!). The cispeptide<\/code> plugin can automatically generate restraints to maintain new trans<\/em> peptide bonds for NAMD<\/code>. If you are running in OpenMM<\/code> like me, you can use a CustomTorsionForce<\/code> to add a restraint to peptide bond during initial minimization and heating of your system. <\/p>\n","protected":false},"excerpt":{"rendered":"

People who run molecular simulations quickly become familiar with all of the things about a PDB file – missing residues, missing heavy atoms in residues, missing hydrogens, non-standard amino acids, multiple conformations, crystallization ligands, etc. – that might need to be fixed before setting up a simulation. This blog post is a reminder to check, […]<\/p>\n","protected":false},"author":69,"featured_media":0,"comment_status":"closed","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"nf_dc_page":"","wikipediapreview_detectlinks":true,"_monsterinsights_skip_tracking":false,"_monsterinsights_sitenote_active":false,"_monsterinsights_sitenote_note":"","_monsterinsights_sitenote_category":0,"ngg_post_thumbnail":0,"_jetpack_memberships_contains_paid_content":false,"footnotes":""},"categories":[296,647,228],"tags":[643,139,135,644],"ppma_author":[542],"class_list":["post-8522","post","type-post","status-publish","format-standard","hentry","category-hints-and-tips","category-molecular-dynamics","category-protein-structure","tag-cis-peptide-bonds","tag-molecular-dynamics","tag-proteins","tag-simulation"],"jetpack_featured_media_url":"","jetpack_sharing_enabled":true,"authors":[{"term_id":542,"user_id":69,"is_guest":0,"slug":"dan","display_name":"Daniel Nissley","avatar_url":"https:\/\/secure.gravatar.com\/avatar\/fd064a72579f11063ca36621317b744b6bc9df79116bc01af9b57f531bf10662?s=96&d=mm&r=g","0":null,"1":"","2":"","3":"","4":"","5":"","6":"","7":"","8":""}],"_links":{"self":[{"href":"https:\/\/www.blopig.com\/blog\/wp-json\/wp\/v2\/posts\/8522","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/www.blopig.com\/blog\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/www.blopig.com\/blog\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/www.blopig.com\/blog\/wp-json\/wp\/v2\/users\/69"}],"replies":[{"embeddable":true,"href":"https:\/\/www.blopig.com\/blog\/wp-json\/wp\/v2\/comments?post=8522"}],"version-history":[{"count":2,"href":"https:\/\/www.blopig.com\/blog\/wp-json\/wp\/v2\/posts\/8522\/revisions"}],"predecessor-version":[{"id":8557,"href":"https:\/\/www.blopig.com\/blog\/wp-json\/wp\/v2\/posts\/8522\/revisions\/8557"}],"wp:attachment":[{"href":"https:\/\/www.blopig.com\/blog\/wp-json\/wp\/v2\/media?parent=8522"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/www.blopig.com\/blog\/wp-json\/wp\/v2\/categories?post=8522"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/www.blopig.com\/blog\/wp-json\/wp\/v2\/tags?post=8522"},{"taxonomy":"author","embeddable":true,"href":"https:\/\/www.blopig.com\/blog\/wp-json\/wp\/v2\/ppma_author?post=8522"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}