{"id":403,"date":"2016-10-18T16:12:50","date_gmt":"2016-10-18T07:12:50","guid":{"rendered":"https:\/\/www.ag.kagawa-u.ac.jp\/charlesy\/wp\/?page_id=403"},"modified":"2017-01-11T18:15:28","modified_gmt":"2017-01-11T09:15:28","slug":"docking-simulation","status":"publish","type":"page","link":"https:\/\/www.ag.kagawa-u.ac.jp\/charlesy\/memo\/docking-simulation\/","title":{"rendered":"Docking simulation"},"content":{"rendered":"<p>Updated on October 19, 2016.<\/p>\n<p>AutoDock4\u306b\u3088\u308a\u4f4e\u5206\u5b50\u5316\u5408\u7269\u3068\u30bf\u30f3\u30d1\u30af\u8cea\u3068\u306e\u30c9\u30c3\u30ad\u30f3\u30b0\u30b7\u30df\u30e5\u30ec\u30fc\u30b7\u30e7\u30f3\u3092\u884c\u3046\uff0eAutoDock\u306f\u6a19\u7684\u30bf\u30f3\u30d1\u30af\u8cea\u306e\u30ea\u30ac\u30f3\u30c9\u7d50\u5408\u90e8\u4f4d\u3092\u30b0\u30ea\u30c3\u30c9\u3068\u3057\u3066\u8868\u73fe\u3057\uff0c\u3053\u306e\u30b0\u30ea\u30c3\u30c9\u306b\u5bfe\u3059\u308b\u30ea\u30ac\u30f3\u30c9\u306e\u7d50\u5408\u69d8\u5f0f\u3092\u907a\u4f1d\u7684\u30a2\u30eb\u30b4\u30ea\u30ba\u30e0\u3084Monte Carlo Simulated Annealing\u6cd5\u306a\u3069\u306b\u3088\u308a\u6700\u9069\u5316\u3059\u308b\uff0e<br \/>\n\u307e\u305a\u30bf\u30f3\u30d1\u30af\u8cea\u5074\u9396\u3092\u52d5\u304b\u3055\u306a\u3044rigid docking\u306e\u65b9\u6cd5\u3092\u89e3\u8aac\u3059\u308b\uff0e<br \/>\nAutoDock4\u304a\u3088\u3073MGL Tools\u3092\u30a4\u30f3\u30b9\u30c8\u30fc\u30eb\u3057\u3066\uff0cPATH\u3092\u901a\u3057\u3066\u304a\u304f\uff0e<\/p>\n<h2>Step 1: Building a small molecule<\/h2>\n<p>\u4f4e\u5206\u5b50\u306e\u7acb\u4f53\u69cb\u9020\u306e\u4f5c\u6210\u306b\u306fAvogadro\u304c\u4f7f\u7528\u3067\u304d\u308b.&nbsp; \u30c9\u30c3\u30ad\u30f3\u30b0\u3067\u306f\u74b0\u69cb\u9020\u306f\u5909\u5316\u3057\u306a\u3044\u305f\u3081\uff0c\u30d5\u30ec\u30ad\u30b7\u30d6\u30eb\u306a\u74b0\u69cb\u9020\u3092\u6301\u3064\u5316\u5408\u7269\u306b\u3064\u3044\u3066\u306f<a href=\"https:\/\/www.ag.kagawa-u.ac.jp\/charlesy\/wp\/index.php\/memo\/conformational-search\/\">conformation search<\/a>\u3092\u884c\u3046\u5fc5\u8981\u304c\u3042\u308b\uff0e<br \/>\n\u4eca\u56de\u306f\uff0c1PTR.pdb\u30d5\u30a1\u30a4\u30eb\u304b\u3089\u62bd\u51fa\u3057\u305fphorbol-13-acetate (PRBH.pdb\uff0c\u6c34\u7d20\u4ed8\u52a0\u6e08\u307f) \u3092\u5143\u306e\u30bf\u30f3\u30d1\u30af\u8cea\u7d50\u6676\u69cb\u9020 (1PTR_apo.pdb) \u306b\u5bfe\u3057\u3066\u30c9\u30c3\u30ad\u30f3\u30b0\u3057\uff0c\u30b7\u30df\u30e5\u30ec\u30fc\u30b7\u30e7\u30f3\u306e\u59a5\u5f53\u6027\u3092\u691c\u8a3c\u3059\u308b\uff0e1PTR\u306f\u30a2\u30df\u30ce\u9178\u5074\u9396\u30923\u6b8b\u57fa\u6b20\u3044\u3066\u3044\u308b\u304c\uff0c\u5316\u5408\u7269\u306e\u7d50\u5408\u90e8\u4f4d\u304b\u3089\u306f\u96e2\u308c\u3066\u3044\u308b\u305f\u3081\uff0c\u4fee\u6b63\u305b\u305a\u306b\u30c9\u30c3\u30ad\u30f3\u30b0\u306b\u4f7f\u7528\u3059\u308b\uff0e<\/p>\n<h2>Step 2: Preparing Protein<\/h2>\n<p>\u4f5c\u696d\u30c7\u30a3\u30ec\u30af\u30c8\u30ea (\u65e5\u672c\u8a9e\u304cPATH\u306b\u542b\u307e\u308c\u3066\u3044\u308b\u3068\u5f8c\u3067\u30a8\u30e9\u30fc\u304c\u51fa\u308b\u306e\u3067\uff0c\u4e0a\u4f4d\u30d5\u30a9\u30eb\u30c0\u306b\u3082\u65e5\u672c\u8a9e\u3092\u542b\u307e\u306a\u3044\u3053\u3068) \u3067PMV\u3092\u8d77\u52d5\uff0e<\/p>\n<pre class=\"command-line\"><code class=\"language-bash\" data-line=\"\">$ pmv &amp;\n[Menu] File &gt; Read Molecule &gt; Open...&nbsp; 1PTR_apo.pdb\n[Menu] Edit &gt; Hydrogens &gt; Add &gt; OK (All Hydrogens, noBondOrder, Yes)\n[Menu] File &gt; Save as &gt; Write PDB &gt; Filename\u30921PTR_H.pdb\u3068\u3057\u3066 &gt; OK<\/code><\/pre>\n<h2>Step 3: Preparing Ligand<\/h2>\n<p>\u4e0a\u90e8\u30a2\u30a4\u30b3\u30f3\u53f3\u304b\u30893\u756a\u76ee\u306eAutoDock Tools\u30dc\u30bf\u30f3\u3092\u30af\u30ea\u30c3\u30af\u3059\u308b\u3068ADT4.2\u30e1\u30cb\u30e5\u30fc\u304c\u3042\u3089\u308f\u308c\u308b\uff0e<\/p>\n<pre class=\"command-line\"><code class=\"language-bash\" data-line=\"\">[ADT Menu] Ligand &gt; Input &gt; Open...&nbsp; &gt; PRBH.pdb &gt; OK<\/code><\/pre>\n<p>non-polar\u306a\u6c34\u7d20\u539f\u5b50\u306f\u524a\u9664\u3055\u308c\uff0cPDB\u30d5\u30a1\u30a4\u30eb\u3092\u958b\u3044\u305f\u5834\u5408\u306fgasteiger charge\u304c\u4ed8\u52a0\u3055\u308c\u308b\uff0e\u90e8\u5206\u96fb\u8377\u60c5\u5831\u3092\u6301\u3064mol2\u30d5\u30a1\u30a4\u30eb\u3092\u4f7f\u7528\u3057\u305f\u5834\u5408\u306f\uff0c\u305d\u306e\u96fb\u8377\u60c5\u5831\u304c\u4f7f\u7528\u3055\u308c\u308b\u305f\u3081\uff0c\u4e88\u3081MOPAC\u3084GAMESS\u7b49\u3067\u69cb\u9020\u6700\u9069\u5316\u7b49\u3092\u884c\u3044\uff0c\u7d50\u679c\u30d5\u30a1\u30a4\u30eb\u3092openbabel\u3067\u96fb\u8377\u60c5\u5831\u3092\u542b\u3080mol2\u5f62\u5f0f\u306b\u5909\u63db\u3057\u3066\u3082\u3088\u3044\uff0e<br \/>\nMOPAC\u3092\u5229\u7528\u3057\u305f\u4f8b\uff08\u69cb\u9020\u6700\u9069\u5316\uff09:<\/p>\n<pre class=\"command-line\"><code class=\"language-bash\" data-line=\"\">$ babel PRBH.pdb PRBH.mop<\/code><\/pre>\n<p>PRBH.mop\u306e1\u884c\u76ee\u3092 \u201cPM7 BONDS CHARGE=0 SINGLET XYZ PRNT=2 PRECISE GNORM=0.0\u201d\u306b \u66f8\u304d\u63db\u3048\u308b\uff0e<\/p>\n<pre class=\"command-line\"><code class=\"language-bash\" data-line=\"\">$ mopac PRBH.mop<\/code><\/pre>\n<p>30\u79d2\u7a0b\u5ea6\u3067\u7d42\u4e86\uff0e\u51fa\u529b\u30d5\u30a1\u30a4\u30eb\u3092mol2\u306b\u5909\u63db\u3059\u308b\uff0e<\/p>\n<pre class=\"command-line\"><code class=\"language-bash\" data-line=\"\">$ babel -imopout PRBH.out PRBH.mol2<\/code><\/pre>\n<p>AutoDock Tools\u3067\u30ea\u30ac\u30f3\u30c9\u3092\u8aad\u307f\u8fbc\u3093\u3060\u969b\u306b\uff0c\u30b7\u30af\u30ed\u30d7\u30ed\u30d1\u30f3\u74b0\u306e\u70ad\u7d20\u539f\u5b50\u304c\u82b3\u9999\u65cf\u70ad\u7d20\u3067\u3042\u308b\u3068\u8aa4\u5224\u5b9a\u3055\u308c\u308b\u306e\u3067\uff0c\u4fdd\u5b58\u3057\u305f\u5f8c\u306b\u624b\u52d5\u3067\u4fee\u6b63\u3059\u308b\uff0e<\/p>\n<pre class=\"command-line\"><code class=\"language-bash\" data-line=\"\">[ADT Menu] Ligand &gt; Torsion Tree &gt; Detect root...\n[ADT Menu] Ligand &gt; Output &gt; Save as PDBQT...<\/code><\/pre>\n<p>\u30c6\u30ad\u30b9\u30c8\u30a8\u30c7\u30a3\u30bf\u3067PRBH.pdbqt\u3092\u958b\u304f\uff0e<\/p>\n<pre class=\"prettyprint\">ATOM     14  C   LIG d   1      11.019  29.040  23.863  0.00  0.00     0.072 A \r\nATOM     15  C   LIG d   1      11.408  28.203  25.066  0.00  0.00    -0.050 A \r\nATOM     16  C   LIG d   1      10.439  29.377  25.237  0.00  0.00     0.038 A<\/pre>\n<p>A (\u82b3\u9999\u65cf)\u3068\u5224\u5b9a\u3055\u308c\u3066\u3044\u308b\u70ad\u7d20\u539f\u5b50\u3092C\u306b\u66f8\u304d\u63db\u3048\u3066\u4fdd\u5b58\uff0e<\/p>\n<pre class=\"prettyprint\">ATOM     14  C   LIG d   1      11.019  29.040  23.863  0.00  0.00     0.072 C \r\nATOM     15  C   LIG d   1      11.408  28.203  25.066  0.00  0.00    -0.050 C \r\nATOM     16  C   LIG d   1      10.439  29.377  25.237  0.00  0.00     0.038 C<\/pre>\n<p>PMV\u4e0a\u306e\u30ea\u30ac\u30f3\u30c9\u306f\u4e00\u65e6\u524a\u9664\u3057\u3066\uff0c\u4fee\u6b63\u3057\u305fPDBQT\u30d5\u30a1\u30a4\u30eb\u3092\u518d\u5ea6\u8aad\u307f\u8fbc\u3080\uff0e<\/p>\n<pre class=\"command-line\"><code class=\"language-bash\" data-line=\"\">[Menu] File &gt; Read Molecule &gt; Open... &gt; PRBH.pdbqt<\/code><\/pre>\n<h2>Step 4: Creating grid parameter file (gpf)<\/h2>\n<pre class=\"command-line\"><code class=\"language-bash\" data-line=\"\">[ADT Menu] Grid &gt; Macromolecule &gt; Choose... &gt; 1PTR_apo &gt; Select Molecule &gt; OK &gt; Save &gt; OK<\/code><\/pre>\n<p>Non-polar\u306a\u6c34\u7d20\u539f\u5b50\u304c\u524a\u9664\u3055\u308c\uff0cPDBQT\u30d5\u30a1\u30a4\u30eb\u304c\u4fdd\u5b58\u3055\u308c\u308b\uff0eZn\u30a4\u30aa\u30f3\u306e\u96fb\u8377\u304c0\u3068\u8b66\u544a\u304c\u51fa\u308b\uff0ePDBQT\u30d5\u30a1\u30a4\u30eb\u3092\u30c6\u30ad\u30b9\u30c8\u30a8\u30c7\u30a3\u30bf\u3067\u958b\u304f\u3068\uff0cZn\u30a4\u30aa\u30f3\u306e\u96fb\u8377\u306f0\u3067\uff0c\u30b7\u30b9\u30c6\u30a4\u30f3\u306e\u786b\u9ec4\u539f\u5b50\u306e\u96fb\u8377\u3082\u304a\u304b\u3057\u3044\u304c\uff0c \u5316\u5408\u7269\u306e\u7d50\u5408\u90e8\u4f4d\u304b\u3089\u306f\u96e2\u308c\u3066\u3044\u308b\u305f\u3081\u4fee\u6b63\u3057\u306a\u3044\uff0e<\/p>\n<pre class=\"command-line\"><code class=\"language-bash\" data-line=\"\">[ADT Menu] Grid &gt; Set Map Types &gt; Choose Ligand... &gt; PDBH &gt; Select Ligand\n[ADT Menu] Grid &gt; Grid Box...<\/code><\/pre>\n<p>\u30ea\u30ac\u30f3\u30c9\u7d50\u5408cleft\u304c\u5168\u3066\u542b\u307e\u308c\u308b\u3088\u3046\u306bBox\u306e\u30b5\u30a4\u30ba\u3068\u4f4d\u7f6e\u3092\u8abf\u6574\u3059\u308b\uff0e<\/p>\n<pre class=\"command-line\"><code class=\"language-bash\" data-line=\"\">[Grid Options Menu] File &gt; &lt;span style=&quot;font-weight: bold;&quot;&gt;Close saving current&lt;\/span&gt;\n[ADT Menu] Grid &gt; Output &gt; Save GPF.. &gt; File name \u201cR.gpf\u201d &gt; Save<\/code><\/pre>\n<h2>Step 5: Creating docking parameter file (dpf)<\/h2>\n<pre class=\"command-line\"><code class=\"language-bash\" data-line=\"\">[ADT Menu] Docking &gt; Macromolecule &gt; Set Rigid Filename... &gt; 1PTR_apo.pdbqt &gt; Open\n[ADT Menu] Docking &gt; Ligand &gt; Choose... &gt; PRBH &gt; Select Ligand &gt; Accept\n[ADT Menu] Docking &gt; Search Parameters &gt; Genetic Algorithm... &gt; Number of GA Runs\u3084Maximum Number of generations\u306a\u3069\u306e\u5024\u3092\u8a2d\u5b9a\uff08\u4eca\u56de\u306f100, Small\uff09 &gt; Accept\n[ADT Menu] Docking &gt; Output &gt; Lamarckian GA(4.2)... &gt; File name \u201cR.dpf\u201d &gt; Save<\/code><\/pre>\n<h2>Step 6: Running AutoGrid<\/h2>\n<pre class=\"command-line\"><code class=\"language-bash\" data-line=\"\">[ADT Menu] Run &gt; Run AutoGrid... &gt;<\/code><\/pre>\n<p>\u30ed\u30b0\u306e\u30d5\u30a1\u30a4\u30eb\u540d\u304c\u8a2d\u5b9a\u3055\u308c\u3066\u3044\u306a\u3044\u306e\u3067\uff0c<\/p>\n<pre class=\"command-line\"><code class=\"language-bash\" data-line=\"\">autogrid4 -p .\/R.gpf -l&nbsp; &amp;<\/code><\/pre>\n<p>\u3092<\/p>\n<pre class=\"command-line\"><code class=\"language-bash\" data-line=\"\">autogrid4 -p .\/R.gpf -l .\/R.glg &amp;<\/code><\/pre>\n<p>\u306b\u66f8\u304d\u63db\u3048\u3066\u304b\u3089\uff0cLaunch\u3092\u30af\u30ea\u30c3\u30af\uff0e\u3059\u3050\u7d42\u4e86\u3057\uff0c\u30b0\u30ea\u30c3\u30c9\u30de\u30c3\u30d7\u30d5\u30a1\u30a4\u30eb\u304c\u751f\u6210\u3059\u308b\uff0e\u3042\u308b\u3044\u306f\uff0c\u4e0a\u8a18\u306e\u30b3\u30de\u30f3\u30c9\u3092Terminal\u304b\u3089\u5b9f\u884c\u3057\u3066\u3082\u3088\u3044\uff0e<\/p>\n<h2>Step 7: Running AutoDock<\/h2>\n<pre class=\"command-line\"><code class=\"language-bash\" data-line=\"\">[ADT Menu] Run &gt; Run AutoDock... &gt;<\/code><\/pre>\n<p>\u30ed\u30b0\u306e\u30d5\u30a1\u30a4\u30eb\u540d\u304c\u8a2d\u5b9a\u3055\u308c\u3066\u3044\u306a\u3044\u306e\u3067\uff0c<\/p>\n<pre class=\"command-line\"><code class=\"language-bash\" data-line=\"\">autodock4 -p R.dpf -l&nbsp; &amp;<\/code><\/pre>\n<p>\u3092<\/p>\n<pre class=\"command-line\"><code class=\"language-bash\" data-line=\"\">autodock4 -p R.dpf -l R.dlg &amp;<\/code><\/pre>\n<p>\u306b\u66f8\u304d\u63db\u3048\u3066\u304b\u3089\uff0cLaunch\u3092\u30af\u30ea\u30c3\u30af\uff0e\u3042\u308b\u3044\u306f\u4e0a\u8a18\u30b3\u30de\u30f3\u30c9\u3092Terminal\u304b\u3089\u5b9f\u884c\u3059\u308b\uff0e<br \/>\n\u3082\u3057AutoDock will say \u201cautodock4: FATAL ERROR: Sorry, I can&#8217;t find or open AD4.1_bound.dat\u201d.<br \/>\n\u3068\u3044\u3046\u30a8\u30e9\u30fc\u304c\u51fa\u305f\u5834\u5408\u306f\uff0cAD4.1_bound.dat\u3092\u63a2\u3057\u3066working directory\u306b\u30b3\u30d4\u30fc\u3059\u308b\uff0e<\/p>\n<pre class=\"command-line\"><code class=\"language-bash\" data-line=\"\">$ cp \/Library\/MGLTools\/1.5.7rc1\/MGLToolsPckgs\/AutoDockTools\/AD4.1_bound.dat .<\/code><\/pre>\n<p>\u518d\u5ea6Autodock4\u3092\u5b9f\u884c\u3059\u308b\uff0e<\/p>\n<pre class=\"command-line\"><code class=\"language-bash\" data-line=\"\">$ autodock4 -p R.dpf -l R.dlg &amp;<\/code><\/pre>\n<p>\u4eca\u56de\u306fMaximum Number of evaluations\u304cshort\uff0cNumber of GA Runs\u304c100\u306a\u306e\u30673\u5206\u7a0b\u5ea6\u3067\u7d42\u4e86\uff0eAutodock vina\u3068\u7570\u306a\u308aAutodock\u306f\u4e26\u5217\u3067\u5b9f\u884c\u3067\u304d\u306a\u3044\uff0e<\/p>\n<h2>Step 8: \u7d50\u679c\u306e\u89e3\u6790<\/h2>\n<p>R.dlg\u3092\u30c6\u30ad\u30b9\u30c8\u30a8\u30c7\u30a3\u30bf\u3067\u958b\u304d\uff0c\u201dHIST\u201d\u3068\u691c\u7d22\u3057\u3066\u30d5\u30a1\u30a4\u30eb\u306e\u6700\u5f8c\u90e8\u306e\u30d2\u30c8\u30b0\u30e9\u30e0\u306e\u7d50\u679c\u3092\u898b\u308b\uff0e<\/p>\n<pre class=\"prettyprint\">________________________________________________________________________________\r\n     |           |     |           |     |                                    \r\nClus | Lowest    | Run | Mean      | Num | Histogram                          \r\n-ter | Binding   |     | Binding   | in  |                                    \r\nRank | Energy    |     | Energy    | Clus|    5    10   15   20   25   30   35\r\n_____|___________|_____|___________|_____|____:____|____:____|____:____|____:___\r\n   1 |     -6.66 |  99 |     -6.14 |  78 |##############################################################################\r\n   2 |     -5.69 |  46 |     -5.38 |  15 |###############\r\n   3 |     -5.50 |  87 |     -5.30 |   7 |#######\r\n_____|___________|_____|___________|_____|______________________________________<\/pre>\n<p>Binding Energy\u3068\u5206\u5e03\u304c\u78ba\u8a8d\u3067\u304d\u308b\uff0eEnergy\u3088\u308a\u3082\u5206\u5e03\u306e\u65b9\u3092\u91cd\u8996\u3059\u308b\u4eba\u3082\u3044\u308b\u3068\u306e\u3053\u3068 (<a href=\"http:\/\/www.iam.u-tokyo.ac.jp\/chem\/IMCB-8ken-HP\/Lab_Manuals\/entori\/2011\/3\/11_Dockingmanyuaru_%28AutoDock%29_files\/Autodock%20manual.pdf\">\u30ea\u30f3\u30af\u5148PDF p.11<\/a>)\uff0e<br \/>\n<a href=\"http:\/\/autodock.scripps.edu\/faqs-help\/faq\/how-do-i-evaluate-autodock-s-clustering-results\">Autodock FAQ: How do I evaluate AutoDock\u2019s clustering results?<\/a> \u306e\u307e\u3068\u3081<\/p>\n<ul>\n<li>\u6709\u610f\u306a\u30b5\u30f3\u30d7\u30eb\u6570\u3092\u5f97\u308b\u305f\u3081\uff0c\u30c9\u30c3\u30ad\u30f3\u30b0\u306f\u5c11\u304f\u3068\u308250 runs\uff0c\u51fa\u6765\u308c\u3070100 runs\u3092\u884c\u3046\uff0e<\/li>\n<li>\u30ea\u30ac\u30f3\u30c9\u306e\u30b5\u30a4\u30ba\u306b\u5408\u3063\u305fRMSD tolerance (rmstol) \u3092\u8a2d\u5b9a\u3059\u308b (\u5927\u304d\u306a\u5206\u5b50\u306e\u5834\u5408\u5c11\u304f\u3068\u30822\u30aa\u30f3\u30b0\u30b9\u30c8\u30ed\u30fc\u30e0)\uff0e<\/li>\n<li>Docking search (ga_num_evals) \u304c\u5341\u5206\u9577\u3044\u304b\u3069\u3046\u304b\uff0e\u3053\u308c\u306f\u30ea\u30ac\u30f3\u30c9\u3084\u30bf\u30f3\u30d1\u30af\u8cea\u5074\u9396\u306e\u56de\u8ee2\u306e\u81ea\u7531\u5ea6\u306b\u4f9d\u5b58\u3059\u308b\uff0e\u7406\u60f3\u7684\u306b\u306fsearch\u304c\u5341\u5206\u9577\u3051\u308c\u3070\uff0c\u6700\u4f4e\u30a8\u30cd\u30eb\u30ae\u30fc\u306e1\u3064\u306e\u30af\u30e9\u30b9\u30bf\u30fc\u306e\u307f\u304c\u5f97\u3089\u308c\u308b\uff0e<\/li>\n<li>\u5224\u65ad\u304c\u4ed8\u304b\u306a\u3044\u5834\u5408\u306f\uff0c\u7d50\u5408\u69d8\u5f0f\u3092\u76ee\u3067\u898b\u3066\u3069\u3061\u3089\u304c\u5316\u5b66\u7684\u306b\u59a5\u5f53\u304b\u3092\u8003\u3048\u308b\uff0e<\/li>\n<li>\u30af\u30e9\u30b9\u30bf\u30fc\u306e\u5e73\u5747\u30a8\u30cd\u30eb\u30ae\u30fc\u306e\u5dee\u304c\u7d042.5 kcal\/mol\u4ee5\u4e0b\u306e\u5834\u5408\uff0cAutoDock force field\u306e\u6a19\u6e96\u504f\u5dee\u4ee5\u5185\u3067\u3042\u308a\uff0c\u30a8\u30cd\u30eb\u30ae\u30fc\u304b\u3089\u3069\u3061\u3089\u304c\u300c\u6b63\u3057\u3044\u300d\u304b\u3092\u3044\u3046\u3053\u3068\u306f\u51fa\u6765\u306a\u3044\uff0e<\/li>\n<\/ul>\n<h2>Step 5: \u7d50\u679c\u306e\u53ef\u8996\u5316\uff0c\u8907\u5408\u4f53\u69cb\u9020\u306e\u66f8\u304d\u51fa\u3057<\/h2>\n<pre class=\"command-line\"><code class=\"language-bash\" data-line=\"\">[ADT Menu] Analyze &gt; Dockings &gt; Open... &gt; R.dlg &gt; Open<\/code><\/pre>\n<p>\u5f8c\u306e\u8907\u5408\u4f53\u66f8\u304d\u51fa\u3057\u306e\u305f\u3081\u306bMacromolecule\u3092\u9078\u3093\u3067\u304a\u304f\uff0e<\/p>\n<pre class=\"command-line\"><code class=\"language-bash\" data-line=\"\">[ADT Menu] Analyze &gt; Macromolecule &gt; Choose... &gt; 1PTR_apo &gt; Select Macromolecule<\/code><\/pre>\n<p>\u30af\u30e9\u30b9\u30bf\u30fc\u306e\u30b0\u30e9\u30d5\u7b49\u3092\u898b\u308b\u3053\u3068\u3082\u3067\u304d\u308b\uff0e<\/p>\n<pre class=\"command-line\"><code class=\"language-bash\" data-line=\"\">[ADT Menu] Analyze &gt; Conformations &gt; Play, ranked by energy...<\/code><\/pre>\n<p>\u65b0\u305f\u306b\u958b\u304b\u308c\u305fwindow\u306e\u53f3\u304b\u30892\u756a\u76ee\u306e \u201d&amp;\u201d \u30dc\u30bf\u30f3\u3092\u30af\u30ea\u30c3\u30af\uff0e<\/p>\n<pre class=\"command-line\"><code class=\"language-bash\" data-line=\"\">[Set Play Options&nbsp; Window] Write Complex &gt; \u540d\u524d &gt; Save<\/code><\/pre>\n<p>\u4fdd\u5b58\u3057\u305fPDBQT\u30d5\u30a1\u30a4\u30eb\u306fpolar\u306a\u6c34\u7d20\u539f\u5b50\u3057\u304b\u542b\u3093\u3067\u3044\u306a\u3044\u306e\u3067\uff0c\u518d\u5ea6\u958b\u304d\uff0c\u6c34\u7d20\u539f\u5b50\u3092\u4ed8\u52a0\u3057\u305f\u5f8c\u306bPDB\u5f62\u5f0f\u3067\u4fdd\u5b58\u3059\u308b\uff0e<\/p>\n","protected":false},"excerpt":{"rendered":"<p>Updated on October 19, 2016. A &#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-403","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":"Updated on October 19, 2016. A ...","_links":{"self":[{"href":"https:\/\/www.ag.kagawa-u.ac.jp\/charlesy\/wp-json\/wp\/v2\/pages\/403","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=403"}],"version-history":[{"count":17,"href":"https:\/\/www.ag.kagawa-u.ac.jp\/charlesy\/wp-json\/wp\/v2\/pages\/403\/revisions"}],"predecessor-version":[{"id":975,"href":"https:\/\/www.ag.kagawa-u.ac.jp\/charlesy\/wp-json\/wp\/v2\/pages\/403\/revisions\/975"}],"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=403"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}