{"id":462,"date":"2016-10-19T18:09:05","date_gmt":"2016-10-19T09:09:05","guid":{"rendered":"https:\/\/www.ag.kagawa-u.ac.jp\/charlesy\/?page_id=462"},"modified":"2021-08-02T12:53:29","modified_gmt":"2021-08-02T03:53:29","slug":"md-simulation","status":"publish","type":"page","link":"https:\/\/www.ag.kagawa-u.ac.jp\/charlesy\/memo\/md-simulation\/","title":{"rendered":"MD simulation"},"content":{"rendered":"<h1>PKC C1\u30c9\u30e1\u30a4\u30f3\u306eMD\u30b7\u30df\u30e5\u30ec\u30fc\u30b7\u30e7\u30f3 (Gromacs, AmberTools, ZAFF)<\/h1>\n<p>\u30bf\u30f3\u30d1\u30af\u8cea\u5358\u72ec\u306e\u30c8\u30dd\u30ed\u30b8\u30fc\u4f5c\u6210\u65b9\u6cd5\u3092\u4ee5\u4e0b\u306b\u793a\u3059\uff0e<a href=\"https:\/\/www.ag.kagawa-u.ac.jp\/charlesy\/protein-ligand-complex\/\">\u30bf\u30f3\u30d1\u30af\u8cea-\u30ea\u30ac\u30f3\u30c9\u8907\u5408\u4f53\u306e\u5834\u5408\u306f\u3053\u3061\u3089<\/a>\uff0e<\/p>\n<h2>Step 1.&nbsp;Generating Zinc-finger domain topology files using AmberTools and ZAFF<\/h2>\n<p>\u53c2\u8003\u30b5\u30a4\u30c8: <a href=\"http:\/\/ambermd.org\/tutorials\/advanced\/tutorial20\/ZAFF.htm\">http:\/\/ambermd.org\/tutorials\/advanced\/tutorial20\/ZAFF.htm<\/a><br \/>\n<a href=\"http:\/\/www.rcsb.org\/pdb\/explore.do?structureId=1PTR\">1PTR.pdb<\/a> (PKC\u03b4 C1B\u30c9\u30e1\u30a4\u30f3) \u3092Protein Data Bank\u304b\u3089\u30c0\u30a6\u30f3\u30ed\u30fc\u30c9\u3059\u308b\uff0e<br \/>\n\u6b20\u3051\u305f\u5074\u9396\u3092\u88dc\u5b8c\u3057\uff0cN\u672b\u3068C\u672b\u306bGly\u6b8b\u57fa\u3092\u8ffd\u52a0\u3059\u308b (\u4e9c\u925b\u306b\u914d\u4f4d\u3059\u308bHIS\u3068CYS\u304c\u672b\u7aef\u306b\u4f4d\u7f6e\u3057\u306a\u3044\u3088\u3046\u306b)\uff0ePymol\u3068Modeller\u3092\u4f7f\u7528\u3057\u305f\u65b9\u6cd5\u306b\u3064\u3044\u3066\u306f<a href=\"https:\/\/www.ag.kagawa-u.ac.jp\/charlesy\/2016\/10\/20\/modeller%e3%81%ab%e3%82%88%e3%82%8bmissing-side-chain%e3%81%ae%e4%bb%98%e5%8a%a0\/\">\u5225\u8a18\u4e8b<\/a>\u3092\u53c2\u7167\u306e\u3053\u3068\uff0emodeller.pdb\u3068\u3057\u3066\u30b3\u30d4\u30fc\uff0e<br \/>\n1PTR\u30d5\u30a1\u30a4\u30eb\u4e2d\u306ePRB\u6b8b\u57fa (phorbol 13-acetate) \u306e\u884c\u3092\u5206\u96e2\u3057\u3066\u5225\u30d5\u30a1\u30a4\u30eb\u306b\u3059\u308b (PRB.pdb)\uff0e<\/p>\n<pre class=\"command-line language-bash\"><code class=\"\" data-line=\"\">$ pdb4amber -i modeller.pdb &gt; 1PTR_pdb4amber.pdb<\/code><\/pre>\n<p>1PTR\u4e2d\u306eZinc finger\u306fCCCH\u578b\u3067\u914d\u4f4d\u3057\u3066\u3044\u308b\u30d2\u30b9\u30c1\u30b8\u30f3\u306f\u3069\u3061\u3089\u3082HIE (\u03b5-nitrogen\u306b\u6c34\u7d20\u304c\u4ed8\u3044\u3066\u3044\u308b: \u03b4-nitrogen\u3067\u4e9c\u925b\u306b\u914d\u4f4d\u3057\u3066\u3044\u308b) \u306a\u306e\u3067\uff0c<a href=\"http:\/\/ambermd.org\/tutorials\/advanced\/tutorial20\/ZAFF.htm\">\u4e0a\u8a18\u53c2\u8003\u30b5\u30a4\u30c8<\/a>\u4e2d\u306e\u8868\u306eCenter ID 2\u3068\u306a\u308b\uff0e\u305d\u3053\u3067\uff0c1PTR_pdb4amber.pdb\u4e2d\u306e6\u3064\u306eCYS\u306e\u6b8b\u57fa\u540d\u3092CY2, HIS2\u3068HIS40\u3092HE1\u306b\uff0c2\u3064\u306e\u4e9c\u925bZN\u3092ZN2\u306b\u4fee\u6b63\u3059\u308b\uff0e\u30bf\u30f3\u30d1\u30af\u8cea\u3068\u4e9c\u925b\u306e\u9593\u3068\uff0c2\u3064\u306e\u4e9c\u925b\u306e\u9593\u306bTER\u884c\u3092\u631f\u3093\u3067\u304a\u304f (tleap\u3092\u5b9f\u884c\u3057\u305f\u969b\uff0c\u4e9c\u925b\u9593\u306b\u7d50\u5408\u304c\u3067\u304d\u3066\u3057\u307e\u3046)\uff0e<\/p>\n<pre class=\"prettyprint\">ATOM    408  C   GLY    52      28.447  17.465  44.064  1.00 47.64           C  \nATOM    409  O   GLY    52      27.783  18.409  43.643  1.00 47.64           O\nTER  \nHETATM  410  ZN  ZN2    53      21.740  18.670  42.875  1.00 40.35          ZN  \nTER\nHETATM  411  ZN  ZN2    54      11.959  13.171  32.940  1.00 47.44          ZN  \nEND<\/pre>\n<p>1PTR_ZAFF.pdb\u3068\u3057\u3066\u4fdd\u5b58\uff0e<\/p>\n<p><del>$AMBERHOME\/dat\/mtkpp\/ZAFF\/201108\/ZAFF.prep\u3068$AMBERHOME\/dat\/mtkpp\/ZAFF\/201108\/ZAFF.frcmod\u306e2\u30d5\u30a1\u30a4\u30eb\u3092\u4f5c\u696d\u30c7\u30a3\u30ec\u30af\u30c8\u30ea\u306b\u30b3\u30d4\u30fc\u3059\u308b\uff0e<\/del><\/p>\n<p>\u203b\u6700\u65b0\u306eAmberTools 2019\u306b\u306f\u542b\u307e\u308c\u306a\u3044\u306e\u3067<a href=\"https:\/\/ambermd.org\/tutorials\/advanced\/tutorial20\/ZAFF.htm\">ZAFF Modeling Tutorial<\/a>\u304b\u3089\u30c0\u30a6\u30f3\u30ed\u30fc\u30c9\u3057\u3066\u304f\u3060\u3055\u3044\u3002<\/p>\n<p>AmberTools\u306b\u542b\u307e\u308c\u308btleap\u7528\u306einput\u30d5\u30a1\u30a4\u30eb\u3092\u4f5c\u6210 (1PTR_ZAFF_tleap.in)\uff0eAmber16\u304b\u3089\u306f\u30bf\u30f3\u30d1\u30af\u8cea\u306e\u305f\u3081\u306e\u529b\u5834AMBER ff15ipq\u304c\u5c0e\u5165\u3055\u308c\u307e\u3057\u305f\uff0e\u3053\u306e\u529b\u5834\u306fSPC\/E<sub>b<\/sub>\u6c34\u30e2\u30c7\u30eb\u306b\u5bfe\u3057\u3066\u6700\u9069\u5316\u3055\u308c\u3066\u3044\u307e\u3059 (\u3053\u308c\u307e\u3067\u306eff14SB\u306fTIP3P\u6c34\u30e2\u30c7\u30eb\u3092\u4f7f\u7528\u3059\u308b)\uff0e\u4eca\u56de\u306fZAFF\u3068GAFF2\u3092\u4f7f\u3046\u305f\u3081\u306b\uff0c\u5f93\u6765\u306eff14SB\u3092\u4f7f\u3044\u307e\u3057\u305f\uff0e<\/p>\n<pre class=\"prettyprint\">source leaprc.protein.ff14SB #Source the ff14SB force field\nsource leaprc.water.tip3p #Source water parameters\naddAtomTypes { { &#34;ZN&#34; &#34;Zn&#34; &#34;sp3&#34; } { &#34;S2&#34; &#34;S&#34; &#34;sp3&#34; } { &#34;N1&#34; &#34;N&#34; &#34;sp3&#34; } } #Add atom types for the ZAFF metal center with Center ID 2\nloadamberprep ZAFF.prep #Load ZAFF prep file\nloadamberparams ZAFF.frcmod #Load ZAFF frcmod file\nmol = loadpdb 1PTR_ZAFF.pdb #Load the PDB file\nbond mol.53.ZN mol.32.SG #Bond zinc ion with SG atom of residue CY232\nbond mol.53.ZN mol.35.SG #Bond zinc ion with SG atom of residue CY235\nbond mol.53.ZN mol.51.SG #Bond zinc ion with SG atom of residue CY251\nbond mol.53.ZN mol.2.ND1 #Bond zinc ion with SG atom of residue HIE2\nbond mol.54.ZN mol.15.SG #Bond zinc ion with SG atom of residue CY215\nbond mol.54.ZN mol.18.SG #Bond zinc ion with SG atom of residue CY218\nbond mol.54.ZN mol.43.SG #Bond zinc ion with SG atom of residue CY243\nbond mol.54.ZN mol.40.ND1 #Bond zinc ion with SG atom of residue HIE40\nsavepdb mol 1PTR_ZAFF_dry.pdb #Save the pdb file\nsaveamberparm mol 1PTR_ZAFF_dry.prmtop 1PTR_ZAFF_dry.inpcrd #Save the topology and coordiante files\nsolvatebox mol TIP3PBOX 10.0 #Solvate the system using TIP3P water box\naddions mol CL 0 #Neutralize the system using Cl- ions\nsavepdb mol 1PTR_ZAFF_solv.pdb #Save the pdb file\nsaveamberparm mol 1PTR_ZAFF_solv.prmtop 1PTR_ZAFF_solv.inpcrd #Save the topology and coordiante files\nquit #Quit tleap<\/pre>\n<p>tleap\u3092\u5b9f\u884c\uff0e<\/p>\n<pre class=\"command-line language-bash\"><code class=\"\" data-line=\"\">$ tleap -s -f 1PTR_ZAFF_tleap.in &gt; 1PTR_ZAFF_tleap.out<\/code><\/pre>\n<p>\u3059\u3050\u306b\u8a08\u7b97\u7d42\u4e86\uff0e<\/p>\n<h2>Step 2. Converting Amber topology and coordinate files to Gromacs files<\/h2>\n<p>\u53c2\u8003\u30b5\u30a4\u30c8: <a href=\"http:\/\/blog.livedoor.jp\/ag_plusplus\/archives\/68154284.html\">Ag++: ACPYPE.py\u3092\u4f7f\u3063\u305fAMBER\u2192Gromacs topology\u306e\u5909\u63db\u3068\u6ce8\u610f\u70b9\uff08\u30d0\u30b0\uff1f\uff09<\/a><\/p>\n<pre class=\"command-line language-bash\"><code class=\"\" data-line=\"\">$ acpype -p 1PTR_ZAFF_solv.prmtop -x 1PTR_ZAFF_solv.inpcrd<\/code><\/pre>\n<p>1\u79d2\u4ee5\u5185\u306b\u7d42\u4e86\u3057\uff0cGROMACS\u7528\u5ea7\u6a19\u30d5\u30a1\u30a4\u30eb (1PTR_ZAFF_solv_GMX.gro) \u3068GROMACS\u7528\u30c8\u30dd\u30ed\u30b8\u30fc\u30d5\u30a1\u30a4\u30eb (1PTR_ZAFF_solv_GMX.top) \u304c\u751f\u6210\u3059\u308b\uff0e<\/p>\n<p>\u30c6\u30b9\u30c8: gromacs\u3067\u30a8\u30cd\u30eb\u30ae\u30fc\u6700\u5c0f\u5316<\/p>\n<pre class=\"command-line language-bash\"><code class=\"\" data-line=\"\">$ gmx grompp -f em.mdp -c 1PTR_ZAFF_solv_GMX.gro -p 1PTR_ZAFF_solv_GMX.top -o em.tpr\n$ gmx mdrun -v -deffnm em\n<\/code><\/pre>\n<p>(\u4e86)<\/p>\n","protected":false},"excerpt":{"rendered":"<p>PKC C1\u30c9\u30e1\u30a4\u30f3\u306eMD\u30b7\u30df\u30e5\u30ec\u30fc\u30b7\u30e7\u30f3 (Gromacs &#8230;<\/p>\n","protected":false},"author":1,"featured_media":0,"parent":346,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"om_disable_all_campaigns":false,"_uag_custom_page_level_css":"","_monsterinsights_skip_tracking":false,"_monsterinsights_sitenote_active":false,"_monsterinsights_sitenote_note":"","_monsterinsights_sitenote_category":0,"_uf_show_specific_survey":0,"_uf_disable_surveys":false,"_locale":"","_original_post":"","footnotes":""},"class_list":["post-462","page","type-page","status-publish","hentry","ja"],"aioseo_notices":[],"uagb_featured_image_src":{"full":false,"thumbnail":false,"medium":false,"medium_large":false,"large":false,"1536x1536":false,"2048x2048":false,"onepress-blog-small":false,"onepress-small":false,"onepress-medium":false},"uagb_author_info":{"display_name":"RCY","author_link":"https:\/\/www.ag.kagawa-u.ac.jp\/charlesy\/author\/charlesy\/"},"uagb_comment_info":0,"uagb_excerpt":"PKC C1\u30c9\u30e1\u30a4\u30f3\u306eMD\u30b7\u30df\u30e5\u30ec\u30fc\u30b7\u30e7\u30f3 (Gromacs ...","_links":{"self":[{"href":"https:\/\/www.ag.kagawa-u.ac.jp\/charlesy\/wp-json\/wp\/v2\/pages\/462","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/www.ag.kagawa-u.ac.jp\/charlesy\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/www.ag.kagawa-u.ac.jp\/charlesy\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/www.ag.kagawa-u.ac.jp\/charlesy\/wp-json\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/www.ag.kagawa-u.ac.jp\/charlesy\/wp-json\/wp\/v2\/comments?post=462"}],"version-history":[{"count":14,"href":"https:\/\/www.ag.kagawa-u.ac.jp\/charlesy\/wp-json\/wp\/v2\/pages\/462\/revisions"}],"predecessor-version":[{"id":2804,"href":"https:\/\/www.ag.kagawa-u.ac.jp\/charlesy\/wp-json\/wp\/v2\/pages\/462\/revisions\/2804"}],"up":[{"embeddable":true,"href":"https:\/\/www.ag.kagawa-u.ac.jp\/charlesy\/wp-json\/wp\/v2\/pages\/346"}],"wp:attachment":[{"href":"https:\/\/www.ag.kagawa-u.ac.jp\/charlesy\/wp-json\/wp\/v2\/media?parent=462"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}