{"id":93,"date":"2013-09-19T16:18:17","date_gmt":"2013-09-19T20:18:17","guid":{"rendered":"http:\/\/research.chemistry.ohio-state.edu\/bruschweiler\/?page_id=93"},"modified":"2025-02-02T07:52:14","modified_gmt":"2025-02-02T12:52:14","slug":"protein-force-field","status":"publish","type":"page","link":"https:\/\/research.cbc.osu.edu\/bruschweiler.1\/protein-force-field\/","title":{"rendered":"Protein force fields"},"content":{"rendered":"<p><strong>Amber99SBNMR1<\/strong><\/p>\n<ul>\n<li>Force filed is included in Amber12.<\/li>\n<li>For other version of Amber:\n<ol>\n<li>Download <a href=\"https:\/\/research.cbc.osu.edu\/bruschweiler.1\/wp-content\/uploads\/2017\/02\/nmr1-amber.tar\">frcmod.ff99SBnmr<\/a>\u00a0and put it into your amberhome\/dat\/leap\/parm folder<\/li>\n<li>Run command &#8220;loadamberparams frcmod.ff99SBnmr&#8221; after load in ff99SB and\u00a0before build your topology in tleap.<\/li>\n<\/ol>\n<\/li>\n<li>For Gromacs 4.5 and higher, <a href=\"https:\/\/research.cbc.osu.edu\/bruschweiler.1\/wp-content\/uploads\/2013\/09\/nmr1.tar\">download<\/a> the package to Gromacs\/top then untar<\/li>\n<\/ul>\n<p><strong>Amber99SBNMR1-ILDN<\/strong><\/p>\n<ul>\n<li>For Gromacs 4.5 and higher, <a href=\"https:\/\/research.cbc.osu.edu\/bruschweiler.1\/wp-content\/uploads\/2013\/09\/nmr1-ildn.tar\">download<\/a> the package to Gromacs\/top then untar<\/li>\n<li>For Amber:\n<ol>\n<li>Download <a href=\"https:\/\/research.cbc.osu.edu\/bruschweiler.1\/wp-content\/uploads\/2017\/02\/nmr1-amber.tar\">frcmod.ff99SBnmr<\/a>\u00a0and put it into your amberhome\/dat\/leap\/parm folder<\/li>\n<li>Run command &#8220;loadamberparams frcmod.ff99SBnmr&#8221;after load in ff99SBildn and before build your topology in tleap.<\/li>\n<\/ol>\n<\/li>\n<\/ul>\n<p><strong>Amber99SBNMR2 (with ILDN)<\/strong><\/p>\n<ul>\n<li>For Gromacs 5 and higher, download the <a href=\"https:\/\/research.cbc.osu.edu\/bruschweiler.1\/wp-content\/uploads\/2023\/02\/nmr2.tar\">package<\/a> then follow instructions.<\/li>\n<\/ul>\n<p><strong>Amber99SBNMR2chi (with ILDN)<\/strong><\/p>\n<ul>\n<li>For Gromacs 5 and higher, download the <a href=\"https:\/\/research.cbc.osu.edu\/bruschweiler.1\/wp-content\/uploads\/2025\/02\/nmr2Chi1.zip\">nmr2Chi1<\/a>\u00a0then follow instructions.<\/li>\n<\/ul>\n<p><strong>Amber99SB_\u03a6\u03a8(G24,CS)<\/strong><\/p>\n<p style=\"padding-left: 30px;\">Instructions: Download the <a href=\"https:\/\/research.cbc.osu.edu\/bruschweiler.1\/wp-content\/uploads\/2013\/09\/cmap.itp_.tar\">cmap.itp<\/a> file to you working directory then modify your top file generated by pdb2gmx program of gromacs in two steps.<\/p>\n<p style=\"padding-left: 30px;\">1 add #include &#8220;.\/cmap.itp&#8221; after the line that include the forcefield paramters (A line that read #include &#8220;amber99sb-ildn.ff\/forcefield.itp&#8221;).<br \/>\n2 add a new section after the dihedral section like this:<\/p>\n<p style=\"padding-left: 30px;\">[ cmap ]<br \/>\n18\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0 20\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0 22\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0 30\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0 32<br \/>\n30\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0 32\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0 34\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0 41\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0 43<br \/>\n&#8230;&#8230;&#8230;&#8230;.<\/p>\n<p style=\"padding-left: 30px;\">Each line in this section have 5 numbers, which are the atom index\u00a0 of C_i-1,<br \/>\nN_i, Ca_i, C_i, N_i+1 that define one particular phi-psi plane. You need to add<br \/>\nall phi-psi plane. Atom indexs can be obtained from the [ atoms ] section of<br \/>\nthe top file.<\/p>\n<p style=\"padding-left: 30px;\">The dihedral section looks like this<\/p>\n<p style=\"padding-left: 30px;\">[ dihedrals ]<br \/>\n;\u00a0 ai\u00a0\u00a0\u00a0 aj\u00a0\u00a0\u00a0 ak\u00a0\u00a0\u00a0 al funct\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0 c0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0 c1\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0 c2\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0 c3<br \/>\n5\u00a0\u00a0\u00a0 20\u00a0\u00a0\u00a0 18\u00a0\u00a0\u00a0 19\u00a0\u00a0\u00a0\u00a0 4<br \/>\n18\u00a0\u00a0\u00a0 22\u00a0\u00a0\u00a0 20\u00a0\u00a0\u00a0 21\u00a0\u00a0\u00a0\u00a0 4<br \/>\n22\u00a0\u00a0\u00a0 32\u00a0\u00a0\u00a0 30\u00a0\u00a0\u00a0 31\u00a0\u00a0\u00a0\u00a0 4<br \/>\n24\u00a0\u00a0\u00a0 28\u00a0\u00a0\u00a0 27\u00a0\u00a0\u00a0 29\u00a0\u00a0\u00a0\u00a0 4<br \/>\n30\u00a0\u00a0\u00a0 34\u00a0\u00a0\u00a0 32\u00a0\u00a0\u00a0 33\u00a0\u00a0\u00a0\u00a0 4<\/p>\n<p style=\"padding-left: 30px;\">the atoms section looks like this<\/p>\n<p style=\"padding-left: 30px;\">[ atoms ]<br \/>\n;\u00a0\u00a0 nr\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0 type\u00a0 resnr residue\u00a0 atom\u00a0\u00a0 cgnr\u00a0\u00a0\u00a0\u00a0 charge\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0 mass\u00a0 typeB\u00a0\u00a0\u00a0 chargeB\u00a0\u00a0\u00a0\u00a0\u00a0 massB<br \/>\n; residue\u00a0\u00a0 1 MET rtp NMET q +1.0<br \/>\n1\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0 N3\u00a0\u00a0\u00a0\u00a0\u00a0 1\u00a0\u00a0\u00a0 MET\u00a0\u00a0\u00a0\u00a0\u00a0 N\u00a0\u00a0\u00a0\u00a0\u00a0 1\u00a0\u00a0\u00a0\u00a0 0.1592\u00a0\u00a0\u00a0\u00a0\u00a0 14.01\u00a0\u00a0 ; qtot 0.1592<br \/>\n2\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0 H\u00a0\u00a0\u00a0\u00a0\u00a0 1\u00a0\u00a0\u00a0 MET\u00a0\u00a0\u00a0\u00a0 H1\u00a0\u00a0\u00a0\u00a0\u00a0 2\u00a0\u00a0\u00a0\u00a0 0.1984\u00a0\u00a0\u00a0\u00a0\u00a0 1.008\u00a0\u00a0 ; qtot 0.3576<br \/>\n3\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0 H\u00a0\u00a0\u00a0\u00a0\u00a0 1\u00a0\u00a0\u00a0 MET\u00a0\u00a0\u00a0\u00a0 H2\u00a0\u00a0\u00a0\u00a0\u00a0 3\u00a0\u00a0\u00a0\u00a0 0.1984\u00a0\u00a0\u00a0\u00a0\u00a0 1.008\u00a0\u00a0 ; qtot 0.556<br \/>\n4\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0 H\u00a0\u00a0\u00a0\u00a0\u00a0 1\u00a0\u00a0\u00a0 MET\u00a0\u00a0\u00a0\u00a0 H3\u00a0\u00a0\u00a0\u00a0\u00a0 4\u00a0\u00a0\u00a0\u00a0 0.1984\u00a0\u00a0\u00a0\u00a0\u00a0 1.008\u00a0\u00a0 ; qtot 0.7544<br \/>\n5\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0 CT\u00a0\u00a0\u00a0\u00a0\u00a0 1\u00a0\u00a0\u00a0 MET\u00a0\u00a0\u00a0\u00a0 CA\u00a0\u00a0\u00a0\u00a0\u00a0 5\u00a0\u00a0\u00a0\u00a0 0.0221\u00a0\u00a0\u00a0\u00a0\u00a0 12.01\u00a0\u00a0 ; qtot 0.7765<br \/>\n6\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0 HP\u00a0\u00a0\u00a0\u00a0\u00a0 1\u00a0\u00a0\u00a0 MET\u00a0\u00a0\u00a0\u00a0 HA\u00a0\u00a0\u00a0\u00a0\u00a0 6\u00a0\u00a0\u00a0\u00a0 0.1116\u00a0\u00a0\u00a0\u00a0\u00a0 1.008\u00a0\u00a0 ; qtot 0.8881<br \/>\n7\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0 CT\u00a0\u00a0\u00a0\u00a0\u00a0 1\u00a0\u00a0\u00a0 MET\u00a0\u00a0\u00a0\u00a0 CB\u00a0\u00a0\u00a0\u00a0\u00a0 7\u00a0\u00a0\u00a0\u00a0 0.0865\u00a0\u00a0\u00a0\u00a0\u00a0 12.01\u00a0\u00a0 ; qtot 0.9746<br \/>\n8\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0 HC\u00a0\u00a0\u00a0\u00a0\u00a0 1\u00a0\u00a0\u00a0 MET\u00a0\u00a0\u00a0 HB1\u00a0\u00a0\u00a0\u00a0\u00a0 8\u00a0\u00a0\u00a0\u00a0 0.0125\u00a0\u00a0\u00a0\u00a0\u00a0 1.008\u00a0\u00a0 ; qtot 0.9871<br \/>\n9\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0 HC\u00a0\u00a0\u00a0\u00a0\u00a0 1\u00a0\u00a0\u00a0 MET\u00a0\u00a0\u00a0 HB2\u00a0\u00a0\u00a0\u00a0\u00a0 9\u00a0\u00a0\u00a0\u00a0 0.0125\u00a0\u00a0\u00a0\u00a0\u00a0 1.008\u00a0\u00a0 ; qtot 0.9996<br \/>\n10\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0 CT\u00a0\u00a0\u00a0\u00a0\u00a0 1\u00a0\u00a0\u00a0 MET\u00a0\u00a0\u00a0\u00a0 CG\u00a0\u00a0\u00a0\u00a0 10\u00a0\u00a0\u00a0\u00a0 0.0334\u00a0\u00a0\u00a0\u00a0\u00a0 12.01\u00a0\u00a0 ; qtot 1.033<br \/>\n11\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0 H1\u00a0\u00a0\u00a0\u00a0\u00a0 1\u00a0\u00a0\u00a0 MET\u00a0\u00a0\u00a0 HG1\u00a0\u00a0\u00a0\u00a0 11\u00a0\u00a0\u00a0\u00a0 0.0292\u00a0\u00a0\u00a0\u00a0\u00a0 1.008\u00a0\u00a0 ; qtot 1.062<br \/>\n12\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0 H1\u00a0\u00a0\u00a0\u00a0\u00a0 1\u00a0\u00a0\u00a0 MET\u00a0\u00a0\u00a0 HG2\u00a0\u00a0\u00a0\u00a0 12\u00a0\u00a0\u00a0\u00a0 0.0292\u00a0\u00a0\u00a0\u00a0\u00a0 1.008\u00a0\u00a0 ; qtot 1.091<br \/>\n13\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0 S\u00a0\u00a0\u00a0\u00a0\u00a0 1\u00a0\u00a0\u00a0 MET\u00a0\u00a0\u00a0\u00a0 SD\u00a0\u00a0\u00a0\u00a0 13\u00a0\u00a0\u00a0 -0.2774\u00a0\u00a0\u00a0\u00a0\u00a0 32.06\u00a0\u00a0 ; qtot 0.814<br \/>\n14\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0 CT\u00a0\u00a0\u00a0\u00a0\u00a0 1\u00a0\u00a0\u00a0 MET\u00a0\u00a0\u00a0\u00a0 CE\u00a0\u00a0\u00a0\u00a0 14\u00a0\u00a0\u00a0 -0.0341\u00a0\u00a0\u00a0\u00a0\u00a0 12.01\u00a0\u00a0 ; qtot 0.7799<\/p>\n<p style=\"padding-left: 30px;\">\n","protected":false},"excerpt":{"rendered":"<p>Amber99SBNMR1 Force filed is included in Amber12. For other version of Amber: Download frcmod.ff99SBnmr\u00a0and put it into your amberhome\/dat\/leap\/parm folder Run command &#8220;loadamberparams frcmod.ff99SBnmr&#8221; after load in ff99SB and\u00a0before build your topology in tleap. For Gromacs 4.5 and higher, download &hellip; <a href=\"https:\/\/research.cbc.osu.edu\/bruschweiler.1\/protein-force-field\/\">Continue reading <span class=\"meta-nav\">&rarr;<\/span><\/a><\/p>\n","protected":false},"author":1,"featured_media":0,"parent":0,"menu_order":4,"comment_status":"closed","ping_status":"closed","template":"","meta":{"_themeisle_gutenberg_block_has_review":false,"footnotes":""},"class_list":["post-93","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"https:\/\/research.cbc.osu.edu\/bruschweiler.1\/wp-json\/wp\/v2\/pages\/93","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/research.cbc.osu.edu\/bruschweiler.1\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/research.cbc.osu.edu\/bruschweiler.1\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/research.cbc.osu.edu\/bruschweiler.1\/wp-json\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/research.cbc.osu.edu\/bruschweiler.1\/wp-json\/wp\/v2\/comments?post=93"}],"version-history":[{"count":10,"href":"https:\/\/research.cbc.osu.edu\/bruschweiler.1\/wp-json\/wp\/v2\/pages\/93\/revisions"}],"predecessor-version":[{"id":869,"href":"https:\/\/research.cbc.osu.edu\/bruschweiler.1\/wp-json\/wp\/v2\/pages\/93\/revisions\/869"}],"wp:attachment":[{"href":"https:\/\/research.cbc.osu.edu\/bruschweiler.1\/wp-json\/wp\/v2\/media?parent=93"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}