{"id":544,"date":"2016-10-27T10:55:57","date_gmt":"2016-10-27T01:55:57","guid":{"rendered":"https:\/\/www.ag.kagawa-u.ac.jp\/charlesy\/?p=544"},"modified":"2017-01-11T18:11:56","modified_gmt":"2017-01-11T09:11:56","slug":"%e8%86%9c%e3%82%bf%e3%83%b3%e3%83%91%e3%82%af%e8%b3%aa%e3%81%ae%e3%83%a2%e3%83%87%e3%83%aa%e3%83%b3%e3%82%b0-charmm-gui-amber-lipid14-force-field","status":"publish","type":"post","link":"https:\/\/www.ag.kagawa-u.ac.jp\/charlesy\/2016\/10\/27\/%e8%86%9c%e3%82%bf%e3%83%b3%e3%83%91%e3%82%af%e8%b3%aa%e3%81%ae%e3%83%a2%e3%83%87%e3%83%aa%e3%83%b3%e3%82%b0-charmm-gui-amber-lipid14-force-field\/","title":{"rendered":"\u819c\u30bf\u30f3\u30d1\u30af\u8cea\u306e\u30e2\u30c7\u30ea\u30f3\u30b0 (CHARMM-GUI, Amber Lipid14 force field)"},"content":{"rendered":"<p>\u74b0\u5883: macOS Sierra 10.12.1, 3.3 GHz Intel Core i5, \u30e1\u30e2\u30ea8 GB\uff0eAmberTools 16, Gromacs 5.1.4.<br \/>\n\u53c2\u8003: <a href=\"http:\/\/ambermd.org\/tutorials\/advanced\/tutorial16\/\">An Amber Lipid Force Field Tutorial: Lipid14 Edition<\/a><br \/>\n\u3053\u306e\u8a18\u4e8b\u306f\u4e3b\u306b\u81ea\u5206\u3068\u7814\u7a76\u5ba4\u306e\u5b66\u751f\u5411\u3051\u306e\u30e1\u30e2\u3067\u3059\uff0eC1\u30c9\u30e1\u30a4\u30f3\u306f\u30ea\u30ac\u30f3\u30c9\u304c\u7d50\u5408\u3059\u308b\u3053\u3068\u3067\uff0c\u819c\u3078\u30c8\u30e9\u30f3\u30b9\u30ed\u30b1\u30fc\u30b7\u30e7\u30f3\u3057\uff0c\u819c\u3068\u30ea\u30ac\u30f3\u30c9\uff0c\u30bf\u30f3\u30d1\u30af\u8cea\u306e\u8907\u5408\u4f53\u3092\u4f5c\u308a\u307e\u3059 (peripheral membrane protein)\uff0eC1\u30c9\u30e1\u30a4\u30f3\u306fphosphatidylserine (PS) \u306b\u5bfe\u3057\u3066\u7279\u7570\u6027\u3092\u6301\u3061\u307e\u3059\u304c\uff0cAmber\u306eLipid14\u529b\u5834\u306f\uff0cNP\u03b3T\uff08\u6e29\u5ea6\u30fb\u5727\u529b\u30fb\u8868\u9762\u5f35\u529b\u4e00\u5b9a\uff09\u3084NPAT\uff08\u6e29\u5ea6\u30fb\u5727\u529b\u30fb\u819c\u9762\u7a4d\u4e00\u5b9a\uff09\u6761\u4ef6\u304c\u5fc5\u8981\u3060\u3063\u305fLipid11\u529b\u5834\u3068\u306f\u7570\u306a\u308a\uff0cNPT\uff08\u6e29\u5ea6\u30fb\u5727\u529b\u4e00\u5b9a\uff09\u6761\u4ef6\u3067\u819c\u306e\u9762\u7a4d\u304c\u7dad\u6301\u3055\u308c\u308b\u3088\u3046\u306b\u306a\u308a\u307e\u3057\u305f\uff0e\u3057\u304b\u3057\uff0cLipid14\u306f\u73fe\u5728phosphatidylcholine (PC) \u3068phosphatidylethanolamine (PE) \u306e\u30d1\u30e9\u30e1\u30fc\u30bf\u3057\u304b\u6301\u305f\u306a\u3044\u305f\u3081\uff0c\u30ea\u30f3\u8102\u8cea\u306b\u306fPOPC\u3092\u9078\u629e\u3057\u307e\u3057\u305f\uff0eAmber Lipid11\u529b\u5834\u3084charmm\u529b\u5834\u306b\u306fPS\u306e\u30d1\u30e9\u30e1\u30fc\u30bf\u304c\u542b\u307e\u308c\u3066\u3044\u307e\u3059\uff0e<\/p>\n<p>\u30bf\u30f3\u30d1\u30af\u8cea\u69cb\u9020\u306b\u306fPKC\u03b4 C1B\u30c9\u30e1\u30a4\u30f3\u3068phorbol 13-acetate\u306e\u8907\u5408\u4f53\u7d50\u6676\u69cb\u9020 (<a href=\"http:\/\/www.rcsb.org\/pdb\/explore.do?structureId=1PTR\">1PTR.pdb<\/a>) \u3092\u4f7f\u7528\u3057\u307e\u3059\uff0e<\/p>\n<h2>CHARMM-GUI\u306b\u5165\u529b\u3059\u308b\u30d5\u30a1\u30a4\u30eb\u306e\u6e96\u5099<\/h2>\n<p>\u30bf\u30f3\u30d1\u30af\u8cea\u69cb\u9020\u306e\u4fee\u6b63\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\u8003\u306b\u3057\u3066\u304f\u3060\u3055\u3044 (modeller.pdb\u3068\u3059\u308b)\uff0e<\/p>\n<p><a href=\"http:\/\/opm.phar.umich.edu\/server.php\">PPM Server<\/a>\u3067\u306f\u819c\u30bf\u30f3\u30d1\u30af\u8cea\u3084\u819c\u8fd1\u508d\u30bf\u30f3\u30d1\u30af\u8cea\u306e\u819c\u4e2d\u306e\u914d\u5411\u3084\u4f4d\u7f6e\u3092\u8a08\u7b97\u3057\u3066\u304f\u308c\u307e\u3059\uff0e<a href=\"https:\/\/www.ag.kagawa-u.ac.jp\/charlesy\/2016\/10\/27\/%e8%86%9c%e3%82%bf%e3%83%b3%e3%83%91%e3%82%af%e8%b3%aa%e3%81%ae%e3%83%a2%e3%83%87%e3%83%aa%e3%83%b3%e3%82%b0-charmm-gui-amber-lipid14-force-field\/ppm\/\" rel=\"attachment wp-att-546\"><img loading=\"lazy\" decoding=\"async\" class=\"size-medium wp-image-546 alignright\" src=\"https:\/\/www.ag.kagawa-u.ac.jp\/charlesy\/wp\/wp-content\/uploads\/2016\/10\/ppm-250x300.png\" alt=\"ppm\" width=\"250\" height=\"300\" srcset=\"https:\/\/www.ag.kagawa-u.ac.jp\/charlesy\/wp\/wp-content\/uploads\/2016\/10\/ppm-250x300.png 250w, https:\/\/www.ag.kagawa-u.ac.jp\/charlesy\/wp\/wp-content\/uploads\/2016\/10\/ppm-225x270.png 225w, https:\/\/www.ag.kagawa-u.ac.jp\/charlesy\/wp\/wp-content\/uploads\/2016\/10\/ppm.png 400w\" sizes=\"auto, (max-width: 250px) 100vw, 250px\" \/><\/a>Include heteroatoms, excluding water and detergents, for positioning in membrane: yes\u306b\u30c1\u30a7\u30c3\u30af\u3092\u5165\u308c\u3066\uff0cupload your PDB file\u304b\u3089\u30d5\u30a1\u30a4\u30eb\u3092\u9078\u629e\u3057\uff0csubmit\u30dc\u30bf\u30f3\u3092\u62bc\u3057\u307e\u3059\uff0e\u6570\u79d2\u3067\u7d50\u679c\u304c\u51fa\u307e\u3059\uff0e\u819c\u3078\u633f\u5165\u3055\u308c\u308b\u9577\u3055\uff0c\u89d2\u5ea6\uff0c\u819c\u633f\u5165\u306e\u81ea\u7531\u30a8\u30cd\u30eb\u30ae\u30fc\u5909\u5316\u306a\u3069\u304c\u66f8\u304b\u308c\u3066\u3044\u307e\u3059\uff0eDownload Output File\u304b\u3089\u51fa\u529b\u3055\u308c\u305fPDB\u30d5\u30a1\u30a4\u30eb\u3092\u30c0\u30a6\u30f3\u30ed\u30fc\u30c9\u3057\u307e\u3059 (modellerout.pdb)\uff0e\u9752\u3044\u30c0\u30df\u30fc\u539f\u5b50\u306f\u30ea\u30f3\u8102\u8cea\u306e\u30ab\u30eb\u30dc\u30cb\u30eb\u57fa\u306e\u4f4d\u7f6e\u306b\u76f8\u5f53\u3057\u307e\u3059\uff0e<\/p>\n<p>\u51fa\u529b\u30d5\u30a1\u30a4\u30eb\u306b\u306f\u6c34\u7d20\u539f\u5b50\u304c\u542b\u307e\u308c\u3066\u3044\u306a\u3044\u306e\u3067\uff0c\u30ea\u30ac\u30f3\u30c9\u306e\u5ea7\u6a19\u3092\u62bd\u51fa\u3057\u3066PRB.pdb\u3068\u3057\u3066\uff0cAvogadro\u3067\u6c34\u7d20\u539f\u5b50\u3092\u4ed8\u52a0\u3057\u307e\u3059\uff0eAvogadro\u3067\u4ed8\u52a0\u3057\u305f\u6c34\u7d20\u539f\u5b50\u306e\u5148\u982d\u306fATOM\uff0c\u6b8b\u57fa\u756a\u53f7\u306f1\uff0c\u6b8b\u57fa\u540d\u306fLIG\u306b\u306a\u3063\u3066\u3044\u308b\u306e\u3067\uff0c\u305d\u308c\u305e\u308c\uff0cHETATM\uff0c55\uff0cPRB\u306b\u7d71\u4e00\u3057\u307e\u3057\u305f\uff0eAntechamber\u3092\u4f7f\u3063\u3066\u305d\u308c\u305e\u308c\u306e\u539f\u5b50\u306b\u56fa\u6709\u306eID\u3092\u632f\u308a\uff0cbabel\u3067mol2\u5f62\u5f0f\u306e\u30d5\u30a1\u30a4\u30eb\u3092\u4f5c\u308a\u307e\u3059 (CHARMM-GUI\u3078\u306e\u5165\u529b\u306b\u5fc5\u8981)\uff0e<\/p>\n<pre class=\"command-line\"><code class=\"language-bash\" data-line=\"\">$ antechamber -fi pdb -fo pdb -i PRB.pdb -o PRB_AC.pdb\n$ babel PRB_AC.pdb PRB_AC.mol2<\/code><\/pre>\n<p>PRB_ante.pdb\u306e\u5148\u982d\u3092ATOM\u304b\u3089HETATM\u3078\u5909\u66f4\u3057\uff0cmodellerout.pdb\u306e\u30ea\u30ac\u30f3\u30c9\u5ea7\u6a19\u306b\u4e0a\u66f8\u304d\u3057\u3066\u4fdd\u5b58\u3057\u307e\u3059\uff0e\u307e\u305f\uff0c\u4e9c\u925b\u306b\u914d\u4f4d\u3059\u308bCYS\u6b8b\u57fa\u306e\u6b8b\u57fa\u540d\u3092CYM\u306b (\u96fb\u8377\u3092\u5408\u308f\u305b\u308b\u305f\u3081)\uff0cHIS\u6b8b\u57fa (HIS2, HIS40) \u306e\u6b8b\u57fa\u540d\u3092HSE\u306b (\u6c34\u7d20\u539f\u5b50\u306e\u4f4d\u7f6e\u3092\u6307\u5b9a\u3059\u308b\u305f\u3081) \u5909\u66f4\u3057\u307e\u3059\uff0e\u4fee\u6b63\u3057\u305fPDB\u30d5\u30a1\u30a4\u30eb\u306e\u540d\u79f0\u306fmodellerout_mod.pdb\u3068\u3057\u307e\u3059\uff0e<\/p>\n<h2>CHARMM-GUI\u306b\u3088\u308b\u819c-\u30ea\u30ac\u30f3\u30c9-\u30bf\u30f3\u30d1\u30af\u8cea\u8907\u5408\u4f53\u69cb\u9020\u306e\u69cb\u7bc9<\/h2>\n<p><a href=\"http:\/\/www.charmm-gui.org\/?doc=input\/membrane\">CHARMM-GUI<\/a>\u306eMembrane Builder\u304b\u3089\u4fee\u6b63\u3057\u305fPDB\u30d5\u30a1\u30a4\u30eb (modellerout_mod.pdb) \u3092\u30a2\u30c3\u30d7\u30ed\u30fc\u30c9\u3057\u307e\u3059\uff0e<a href=\"https:\/\/www.ag.kagawa-u.ac.jp\/charlesy\/2016\/10\/27\/%e8%86%9c%e3%82%bf%e3%83%b3%e3%83%91%e3%82%af%e8%b3%aa%e3%81%ae%e3%83%a2%e3%83%87%e3%83%aa%e3%83%b3%e3%82%b0-charmm-gui-amber-lipid14-force-field\/%e3%82%b9%e3%82%af%e3%83%aa%e3%83%bc%e3%83%b3%e3%82%b7%e3%83%a7%e3%83%83%e3%83%88-2016-10-27-11-12-42\/\" rel=\"attachment wp-att-556\"><img loading=\"lazy\" decoding=\"async\" class=\"size-medium wp-image-556 alignright\" src=\"https:\/\/www.ag.kagawa-u.ac.jp\/charlesy\/wp\/wp-content\/uploads\/2016\/10\/a28f06356b3739a07b478e1cb6280de0-187x300.png\" alt=\"%e3%82%b9%e3%82%af%e3%83%aa%e3%83%bc%e3%83%b3%e3%82%b7%e3%83%a7%e3%83%83%e3%83%88-2016-10-27-11-12-42\" width=\"187\" height=\"300\" srcset=\"https:\/\/www.ag.kagawa-u.ac.jp\/charlesy\/wp\/wp-content\/uploads\/2016\/10\/a28f06356b3739a07b478e1cb6280de0-187x300.png 187w, https:\/\/www.ag.kagawa-u.ac.jp\/charlesy\/wp\/wp-content\/uploads\/2016\/10\/a28f06356b3739a07b478e1cb6280de0-168x270.png 168w, https:\/\/www.ag.kagawa-u.ac.jp\/charlesy\/wp\/wp-content\/uploads\/2016\/10\/a28f06356b3739a07b478e1cb6280de0.png 612w\" sizes=\"auto, (max-width: 187px) 100vw, 187px\" \/><\/a><\/p>\n<ul>\n<li>\u30d5\u30a1\u30a4\u30eb\u3092\u9078\u629e &gt; modellerout_mod.pdb (\u4fee\u6b63\u6e08) &gt; PDB\u306b\u30c1\u30a7\u30c3\u30af &gt; Next Step<\/li>\n<li>Model\/Chain Selection Option &gt; ZN\u3068PRB\u306b\u30c1\u30a7\u30c3\u30af &gt; Next Step<\/li>\n<li>Renaming Engineered Residues: Rename CYM to CYM<\/li>\n<li>PRB &gt; Use CHARMM General Force Field to generate CHARMM top &amp; par files &gt; the MOL2 file uploaded from \u306b\u30c1\u30a7\u30c3\u30af\u3057\u3066PRB_AC.mol2\u3092\u9078\u629e\uff0e\u4e0b\u306e\u65b9\u306e<span style=\"color: #ff0000;\">Has three membered ring\u306b\u30c1\u30a7\u30c3\u30af<\/span> &gt; Next Step<\/li>\n<li>Orientations Options: Use PDB Orientation &gt; Next Step<\/li>\n<li>System Size Determination Options: Homogeneous Lipid &gt; Use Geometry &gt; Length of X: 66 (Upper leaflet\u306b\u542b\u307e\u308c\u308b\u30ea\u30f3\u8102\u8cea\u304c64\u5206\u5b50\u306b\u306a\u308b\u9577\u3055), Lipid Type: POPC &gt; Next Step &gt; \u5168\u3066\u30c7\u30d5\u30a9\u30eb\u30c8\u306e\u307e\u307e\u3067Next Step &gt; Next Step (\u5c11\u3005\u6642\u9593\u304c\u304b\u304b\u308b) &gt; Next Step<\/li>\n<li>System Size\u306eA, B, C\u306e\u5024\u3092\u30e1\u30e2\u3057\u3066\u304a\u304f &gt; Next Step (\u5c11\u3005\u6642\u9593\u304c\u304b\u304b\u308b)<\/li>\n<li>download .tgz\u3092\u30af\u30ea\u30c3\u30af\u3057\u3066\u30d5\u30a1\u30a4\u30eb\u3092\u30c0\u30a6\u30f3\u30ed\u30fc\u30c9<\/li>\n<\/ul>\n<p>\u89e3\u51cd\u3057\u305f\u30d5\u30a1\u30a4\u30eb\u306b\u542b\u307e\u308c\u308bstep5_assembly.pdb\u3092\u4ee5\u5f8c\u4f7f\u7528\u3057\u307e\u3059\uff0e<\/p>\n<h2>AmberTools\u306b\u3088\u308b\u30c8\u30dd\u30ed\u30b8\u30fc\u306e\u751f\u6210<\/h2>\n<p>CHARMM\u306e\u8102\u8cea\u306f1\u3064\u306e\u6b8b\u57fa\u306b\u306a\u3063\u3066\u3044\u307e\u3059\u304c\uff0cAmber Lipid14\u529b\u5834\u3067\u306f\u30e2\u30b8\u30e5\u30fc\u30eb\u69cb\u9020\u306b\u306a\u3063\u3066\u3044\u307e\u3059\uff0eAmber\u304c\u8aad\u307f\u8fbc\u3081\u308b\u5f62\u5f0f\u306b\u3059\u308b\u305f\u3081\uff0cAmberTools16\u4ed8\u5c5e\u306e\u30b9\u30af\u30ea\u30d7\u30c8\u3092\u4f7f\u3044\u307e\u3059\uff0e<\/p>\n<pre class=\"command-line\"><code class=\"language-bash\" data-line=\"\">$ charmmlipid2amber.py -i step5_assembly.pdb -c $AMBERHOME\/dat\/charmmlipid2amber\/charmmlipid2amber.csv -o 1PTR_POPC.pdb<\/code><\/pre>\n<p>tleap\u3067\u306e\u51e6\u7406\u306e\u305f\u3081\u306b\uff0c<\/p>\n<ol>\n<li>\u30bf\u30f3\u30d1\u30af\u8cea\u306e\u6c34\u7d20\u539f\u5b50\u3092\u9664\u53bb ($ babel -d protein.pdb protein_noh.pdb\u3068\u30bf\u30f3\u30d1\u30af\u8cea\u90e8\u5206\u306e\u307f\u51e6\u7406\u3057\u3066\u304b\u3089\u5143\u30d5\u30a1\u30a4\u30eb\u306b\u4e0a\u66f8\u304d\u3059\u308b)\uff0eGLY52\u306eOT2\u539f\u5b50\u306e\u884c\u3092\u524a\u9664\uff0eGLY52\u306eOT1\u539f\u5b50\u3092O\u306b\u4fee\u6b63\uff0e<\/li>\n<li>\u6b8b\u57fa\u540d\u3092CYM\u2192CY2\uff0cHSE2\u3068HSE40\u2192HE1\uff0cHSD\u2192HID\u306b\u4fee\u6b63\uff0e<span style=\"color: #ff0000;\">\u30bf\u30f3\u30d1\u30af\u8cea\u3068ZN\u306e\u9593\uff0cZN\u3068ZN\u306e\u9593\uff0cZN\u3068\u30ea\u30ac\u30f3\u30c9\u306e\u9593\uff0c\u30ea\u30ac\u30f3\u30c9 (PRB) \u3068\u8102\u8cea (PA) \u306e\u9593\u306bTER\u884c\u3092\u631f\u307f\u307e\u3059<\/span>\uff0e<\/li>\n<li>1PTR_POPC_ZAFF.pdb\u3068\u3057\u3066\u4fdd\u5b58\uff0e<\/li>\n<\/ol>\n<p>\u4fee\u6b63\u5f8c\u306e\u30d5\u30a1\u30a4\u30eb (1PTR_POPC_ZAFF.pdb) \u306e\u4e00\u90e8\u5206:<\/p>\n<pre class=\"prettyprint\">ATOM    408  C   GLY    52      -0.993  -8.981 -39.022  1.00  0.00           C  \r\nATOM    409  O   GLY    52      -1.727  -8.677 -38.044  1.00  0.00           O\r\nTER\r\nATOM    804  ZN  ZN2    53      -1.831  -3.757 -34.565  1.00  0.00      HETA\r\nTER\r\nATOM    805  ZN  ZN2    54       7.207   2.614 -24.450  1.00  0.00      HETA\r\nTER\r\nATOM    806  C8  PRB    55      -1.115  -2.860 -12.178  1.00  0.00      HETB\r\nATOM    807  C9  PRB    55       0.100  -3.129 -11.198  1.00  0.00      HETB\r\nATOM    808  H8  PRB    55      -1.358  -1.776 -12.164  1.00  0.00      HETB<\/pre>\n<p>\u4e9c\u925b\u30d5\u30a1\u30a4\u30f3\u30ac\u30fc\u306e\u305f\u3081\u306ePREP\u30d5\u30a1\u30a4\u30eb\u3068frcmod\u30d5\u30a1\u30a4\u30eb\u3092\u4f5c\u696d\u30c7\u30a3\u30ec\u30af\u30c8\u30ea\u306b\u30b3\u30d4\u30fc\u3057\u307e\u3059\uff0e<\/p>\n<pre class=\"command-line\"><code class=\"language-bash\" data-line=\"\">$ cp $AMBERHOME\/dat\/mtkpp\/ZAFF\/201108\/ZAFF.prep $AMBERHOME\/dat\/mtkpp\/ZAFF\/201108\/ZAFF.frcmod .<\/code><\/pre>\n<p>\u30ea\u30ac\u30f3\u30c9\u30d5\u30a1\u30a4\u30eb\u306eAmber\u7528\u30c8\u30dd\u30ed\u30b8\u30fc\u3092\u4f5c\u6210\u3057\u307e\u3059\uff0eAM1-BCC\u96fb\u8377 (-c bcc) \u306f\uff0c\u975e\u7d4c\u9a13\u7684\u5206\u5b50\u8ecc\u9053\u8a08\u7b97\u306b\u3088\u308bRESP (Restrained ElectroStatic Potential) \u96fb\u8377\u306b\u8fd1\u3044\u5024\u3092\u534a\u7d4c\u9a13\u7684\u624b\u6cd5\u306b\u3088\u308a\u8a08\u7b97\u3057\u305f\u96fb\u8377\u3067\u3059\uff0eMM\u6cd5\u3067\u306f\u539f\u5b50\u6838\u306e\u4f4d\u7f6e\u306b\u90e8\u5206\u96fb\u8377\u3092\u7f6e\u304d\u307e\u3059\u304c\uff0c\u672c\u6765\u306e\u96fb\u5b50\u96f2\u306e\u5206\u5e03\u306b\u3088\u308b\u5206\u5b50\u306e\u9759\u96fb\u30dd\u30c6\u30f3\u30b7\u30e3\u30eb\u3092\u3053\u306e\u90e8\u5206\u96fb\u8377\u304c\u518d\u73fe\u3067\u304d\u308b\u3088\u3046\u306b\u5024\u3092\u6c7a\u3081\u308b\u5fc5\u8981\u304c\u3042\u308a\u307e\u3059\uff0e<\/p>\n<pre class=\"command-line\"><code class=\"language-bash\" data-line=\"\">$ antechamber -fi pdb -i PRB_AC.pdb -fo prepi -o PRB.prep -c bcc -at gaff2\n$ parmchk2 -i PRB.prep -o PRB.frcmod -f prepi -s gaff2<\/code><\/pre>\n<p>\u4ee5\u4e0b\u306e\u30b9\u30af\u30ea\u30d7\u30c8\u3092tleap\u3067\u5b9f\u884c\u3057\u307e\u3059\uff0e<br \/>\ntleap.in<\/p>\n<pre class=\"prettyprint\">source leaprc.protein.ff14SB #Source the ff14SB force field\r\nsource leaprc.water.tip3p #Source water parameters\r\nsource leaprc.lipid14 #Source the Lipid14 force field\r\nsource leaprc.gaff2 #Source the GAFF2 force filed for small molecules\r\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\r\nloadamberprep ZAFF.prep #Load ZAFF prep file\r\nloadamberparams ZAFF.frcmod #Load ZAFF frcmod file\r\nloadamberprep PRB.prep\r\nloadamberparams PRB.frcmod\r\nmol = loadpdb 1PTR_POPC_ZAFF.pdb #Load the PDB file #this residue is split into PA and PC.\u3068\u3044\u3046\u8b66\u544a\u306f\u7121\u8996\r\nset mol box {66.2645315, 66.2645315, 100.353} #\u30e1\u30e2\u3057\u305f\u5024\r\nbond mol.53.ZN mol.32.SG #Bond zinc ion with SG atom of residue CY2_32\r\nbond mol.53.ZN mol.35.SG #Bond zinc ion with SG atom of residue CY2_35\r\nbond mol.53.ZN mol.51.SG #Bond zinc ion with SG atom of residue CY2_51\r\nbond mol.53.ZN mol.2.ND1 #Bond zinc ion with SG atom of residue HE1_2\r\nbond mol.54.ZN mol.15.SG #Bond zinc ion with SG atom of residue CY2_15\r\nbond mol.54.ZN mol.18.SG #Bond zinc ion with SG atom of residue CY2_18\r\nbond mol.54.ZN mol.43.SG #Bond zinc ion with SG atom of residue CY2_43\r\nbond mol.54.ZN mol.40.ND1 #Bond zinc ion with SG atom of residue HE1_40\r\nsavepdb mol 1PTR_POPC_ZAFF_leap.pdb #Save the pdb file\r\nsaveamberparm mol 1PTR_POPC_ZAFF_leap.prmtop 1PTR_POPC_ZAFF_leap.inpcrd #Save the topology and coordiante files\r\nquit #Quit tleap<\/pre>\n<pre class=\"command-line\"><code class=\"language-bash\" data-line=\"\">$ tleap -s -f tleap.in &gt; tleap.out<\/code><\/pre>\n<p>tleap.out\u3092\u958b\u3044\u3066\uff0c\u554f\u984c\u306a\u304f\u5b9f\u884c\u3055\u308c\u3066\u3044\u308b\u3053\u3068\u3092\u78ba\u8a8d\u3057\u307e\u3059\uff0e<\/p>\n<h2>Amber\u5f62\u5f0f\u304b\u3089GROMACS\u5f62\u5f0f\u3078\u306e\u5909\u63db\u3068\u30c8\u30dd\u30ed\u30b8\u30fc\u30d5\u30a1\u30a4\u30eb\u306e\u4fee\u6b63<\/h2>\n<p>AMBER\u5f62\u5f0f\u306e\u30d5\u30a1\u30a4\u30eb\u3092AmberTools16\u4ed8\u5c5e\u306eParmEd\u3092\u4f7f\u7528\u3057\u3066GROMACS\u5f62\u5f0f\u306b\u5909\u63db\u3057\u307e\u3059\uff0e<br \/>\n\u4ee5\u4e0b\u306epython\u30b9\u30af\u30ea\u30d7\u30c8\u3092\u5b9f\u884c\u3057\u3066\u304f\u3060\u3055\u3044\uff0e<br \/>\n<code class=\"\" data-line=\"\">ambertogromacs.py<\/code><\/p>\n<pre class=\"prettyprint\">import parmed as pmd\r\namber = pmd.load_file(&#39;1PTR_POPC_ZAFF_leap.prmtop&#39;,xyz=&#39;1PTR_POPC_ZAFF_leap.inpcrd&#39;)\r\namber.save(&#39;1PTR_POPC.top&#39;)\r\namber.save(&#39;1PTR_POPC.gro&#39;)<\/pre>\n<pre class=\"command-line\"><code class=\"language-bash\" data-line=\"\">$ python .\/ambertogromacs.py<\/code><\/pre>\n<p>\u51fa\u529b\u3055\u308c\u305f1PTR_POPC.top\u3092\u958b\u304d\uff0c\u30ea\u30ac\u30f3\u30c9\u306e13\u4f4d\u9178\u7d20\u539f\u5b50\u306b\u95a2\u3059\u308bangle\u306e\u30d1\u30e9\u30e1\u30fc\u30bf\u3092\u4fee\u6b63\u3057\u307e\u3059 (<a href=\"https:\/\/www.ag.kagawa-u.ac.jp\/charlesy\/memo\/md-simulation\/protein-ligand-complex\/\">\u5225\u8a18\u4e8b\u3092\u53c2\u7167<\/a>)\uff0e<br \/>\n\u4fee\u6b63\u524d:<\/p>\n<pre class=\"prettyprint\">     28     52     53     1   59.09003 975.641856\r\n     27     52     53     1   59.09003 975.641856\r\n     48     52     53     1   115.68005 693.590048<\/pre>\n<p>\u4fee\u6b63\u5f8c:<\/p>\n<pre class=\"prettyprint\">     28     52     53     1   111.0 693.590048\r\n     27     52     53     1   118.7 693.590048\r\n     48     52     53     1   112.3 693.590048<\/pre>\n<p>\u307e\u305f\uff0cPRB\u6b8b\u57fa\u306e\u96fb\u8377\u306e\u7dcf\u548c\u304c-0.004\u30670\u304b\u3089\u305a\u308c\u3066\u3044\u308b\u306e\u3067\uff0c\u5168\u3066\u306e\u539f\u5b50\u306b\u5272\u308a\u632f\u3063\u3066\u7dcf\u548c\u30920\u306b\u3057\u307e\u3059\uff0e<br \/>\n\u4fee\u6b63\u524d (\u5148\u982d\u90e8\u5206):<\/p>\n<pre class=\"prettyprint\">&#91; atoms &#93;\r\n;   nr       type  resnr residue  atom   cgnr    charge       mass  typeB    chargeB      massB\r\n; residue    1 PRB rtp PRB q -0.0\r\n    1          o      1    PRB     O3      1  -0.520100    16.0000   ; qtot -0.5201\r\n    2          c      1    PRB     C3      2   0.549300    12.0100   ; qtot 0.0292\r\n    3         ce      1    PRB     C2      3  -0.221400    12.0100   ; qtot -0.1922\r\n    4         c3      1    PRB    C19      4  -0.038900    12.0100   ; qtot -0.2311<\/pre>\n<p>\u4fee\u6b63\u5f8c:<\/p>\n<pre class=\"prettyprint\">&#91; atoms &#93;\r\n;   nr       type  resnr residue  atom   cgnr    charge       mass  typeB    chargeB      massB\r\n; residue    1 PRB rtp PRB q -0.0\r\n    1          o      1    PRB     O3      1  -0.520032    16.0000   ; qtot -0.5201\r\n    2          c      1    PRB     C3      2   0.549368    12.0100   ; qtot 0.0292\r\n    3         ce      1    PRB     C2      3  -0.221332    12.0100   ; qtot -0.1922\r\n    4         c3      1    PRB    C19      4  -0.038832    12.0100   ; qtot -0.2311<\/pre>\n<p><a href=\"https:\/\/www.ag.kagawa-u.ac.jp\/charlesy\/2016\/10\/27\/%e8%86%9c%e3%82%bf%e3%83%b3%e3%83%91%e3%82%af%e8%b3%aa%e3%81%ae%e3%83%a2%e3%83%87%e3%83%aa%e3%83%b3%e3%82%b0-charmm-gui-amber-lipid14-force-field\/zentai\/\" rel=\"attachment wp-att-568\"><img loading=\"lazy\" decoding=\"async\" class=\"size-medium wp-image-568 alignright\" src=\"https:\/\/www.ag.kagawa-u.ac.jp\/charlesy\/wp\/wp-content\/uploads\/2016\/10\/zentai-225x300.png\" alt=\"zentai\" width=\"225\" height=\"300\" srcset=\"https:\/\/www.ag.kagawa-u.ac.jp\/charlesy\/wp\/wp-content\/uploads\/2016\/10\/zentai-225x300.png 225w, https:\/\/www.ag.kagawa-u.ac.jp\/charlesy\/wp\/wp-content\/uploads\/2016\/10\/zentai-203x270.png 203w, https:\/\/www.ag.kagawa-u.ac.jp\/charlesy\/wp\/wp-content\/uploads\/2016\/10\/zentai.png 480w\" sizes=\"auto, (max-width: 225px) 100vw, 225px\" \/><\/a>Pymol\u30671PTR_DOPC.gro\u3092\u958b\u3044\u3066\uff0c\u69cb\u9020\u3092\u78ba\u8a8d\u3057\u307e\u3059 (\u53f3\u56f3)\uff0e\u8d64\u8272\u306e\u7403\u306f\u30ea\u30f3\u8102\u8cea\u306e\u30ab\u30eb\u30dc\u30cb\u30eb\u9178\u7d20\u539f\u5b50\u3067\u3059\uff0e<\/p>\n<h2>GROMACS\u306b\u3088\u308bMD\u30b7\u30df\u30e5\u30ec\u30fc\u30b7\u30e7\u30f3<\/h2>\n<h3>Index\u30d5\u30a1\u30a4\u30eb\u3068restraint\u30d5\u30a1\u30a4\u30eb\u306e\u4f5c\u6210<\/h3>\n<p>charmm-gui.tgz\u3092\u89e3\u51cd\u3057\u305f\u30c7\u30a3\u30ec\u30af\u30c8\u30ea\u4e2d\u306echarmm-gui\/gromacs\u3092\u898b\u3066\u307f\u307e\u3059\uff0eGROMACS\u7528\u306emdp\u30d5\u30a1\u30a4\u30eb\u3068restraints\u30d5\u30a1\u30a4\u30eb\u304c\u5165\u3063\u3066\u3044\u307e\u3059\uff0eCHARMM-GUI\u63a8\u5968\u306e\u7cfb\u306e\u5e73\u8861\u5316\u624b\u9806\u306f\u4ee5\u4e0b\u306e\u901a\u308a\u3067\u3059\uff0e<\/p>\n<pre class=\"prettyprint\">!\r\n! Setup Restraints for Protein and Lipids (see @liptype_restraint.str)\r\n!\r\n! Suggested Equilibration Scheme &#91;Reducing Force Constants&#93;\r\n! (5 Cycles, 1 cycle = 50 - 100 ps )\r\n!------------------------------------------------------------------------\r\n!        1 cycle    2 cycle    3 cycle    4 cycle    5 cycle    6 cycle\r\n!------------------------------------------------------------------------\r\n! BB       10.0        5.0        2.5        1.0        0.5        0.1  \r\n! SC        5.0        2.5        1.0        0.5        0.1        0.0  \r\n! tforce    2.5        1.0        0.5        0.0        0.0        0.0  \r\n! mforce    2.5        0.0        0.0        0.0        0.0        0.0\r\n! ion      10.0        0.0        0.0        0.0        0.0        0.0\r\n!------------------------------------------------------------------------\r\n!<\/pre>\n<p>\u30bf\u30f3\u30d1\u30af\u8cea\u306e\u4e3b\u9396\u306e\u91cd\u539f\u5b50 (\u4e9c\u925b\u3092\u542b\u3080) \u304a\u3088\u3073\u30ea\u30ac\u30f3\u30c9\u306e\u91cd\u539f\u5b50\u306e\u4f4d\u7f6e\uff0c\u5074\u9396\u306e\u91cd\u539f\u5b50\u306e\u4f4d\u7f6e\uff0c\u30ea\u30f3\u8102\u8cea\u306e\u30ea\u30f3\u539f\u5b50\u306e<span style=\"font-style: italic;\">Z<\/span>\u65b9\u5411\u306e\u4f4d\u7f6e\uff0c\u30ea\u30f3\u8102\u8cea\u306e<span style=\"font-style: italic;\">sn<\/span>-1\u70ad\u7d20\u2013<span style=\"font-style: italic;\">sn<\/span>-3\u70ad\u7d20\u2013<span style=\"font-style: italic;\">sn<\/span>-2\u70ad\u7d20\u2013<span style=\"font-style: italic;\">sn<\/span>-2\u9178\u7d20\u306e2\u9762\u89d2\uff0c\u30aa\u30ec\u30aa\u30a4\u30eb\u57fa\u306e<span style=\"font-style: italic;\">cis<\/span>\u4e8c\u91cd\u7d50\u5408\u306e2\u9762\u89d2\u306b\u5236\u9650\u3092\u304b\u3051\u3066\uff0c\u30b9\u30c6\u30c3\u30d7\u6bce\u306b\u5c11\u3057\u305a\u3064\u5236\u9650\u3092\u7de9\u548c\u3057\u3066\u3044\u304d\u307e\u3059\uff0eCHARMM-GUI\u304c\u51fa\u529b\u3057\u305f\u30d5\u30a1\u30a4\u30eb\u3068tleap\u3067\u51e6\u7406\u3057\u305f\u30d5\u30a1\u30a4\u30eb\u3067\u306f\u539f\u5b50\u306e\u9806\u756a\u304c\u5909\u308f\u3063\u3066\u3044\u308b\u305f\u3081\uff0cindex\u30d5\u30a1\u30a4\u30eb\u3068restraint\u30d5\u30a1\u30a4\u30eb\u3092\u81ea\u5206\u3067\u4f5c\u6210\u3057\u307e\u3059\uff0e<br \/>\nGROMACS\u306bCY2\u6b8b\u57fa\u3068HE1\u6b8b\u57fa\u3092\u30bf\u30f3\u30d1\u30af\u8cea\u3068\u8a8d\u8b58\u3057\u3066\u3082\u3089\u3046\u305f\u3081\uff0c$GMXPREFIX\/share\/gromacs\/top\/residuetypes.dat\u306b\u3053\u308c\u3089\u306e\u6b8b\u57fa\u3092\u8ffd\u52a0\u3057\u307e\u3059\uff0e<\/p>\n<pre class=\"prettyprint\">CY2     Protein\r\nHE1     Protein\r\nABU\tProtein<\/pre>\n<pre class=\"command-line\"><code class=\"language-bash\" data-line=\"\">$ gmx make_ndx -f 1PTR_POPC.gro -o index.ndx\n&gt; 4 | 13  (\u4e3b\u9396\u3068ZN\u3092merge)\n&gt; 8 &amp; !9 (\u5074\u9396\u306e\u91cd\u539f\u5b50\u3092\u9078\u629e)\n&gt; 1 | 13 (\u30bf\u30f3\u30d1\u30af\u8cea\u3068\u4e9c\u925b\u3092merge)\n&gt; name 34 RECEPTOR\n&gt; 34 | 14 (\u30bf\u30f3\u30d1\u30af\u8cea-\u4e9c\u925b\u3068\u30ea\u30ac\u30f3\u30c9\u3092merge)\n&gt; name 35 PROT\n&gt; 15 | 16 | 17 (\u30ea\u30f3\u8102\u8cea\u540c\u58eb\u3092merge)\n&gt; name 36 MEMB\n&gt; 26 | 27 | 28 (\u30a4\u30aa\u30f3\u3068\u6c34\u3092merge)\n&gt; name 37 SOL_ION\n&gt; q<\/code><\/pre>\n<p>\u4e3b\u9396+\u4e9c\u925b\u7528restraint\u30d5\u30a1\u30a4\u30eb\u306e\u4f5c\u6210:<\/p>\n<pre class=\"command-line\"><code class=\"language-bash\" data-line=\"\">$ gmx genrestr -f 1PTR_POPC.gro -n index.ndx -o PROT_rest.itp\nSelect a group: 34<\/code><\/pre>\n<p>PROT_rest.itp\u3092\u7de8\u96c6\u3057\u307e\u3059\uff0e<br \/>\n\u4fee\u6b63\u524d:<\/p>\n<pre class=\"prettyprint\">; position restraints for Backbone of GROningen MAchine for Chemical Simulation\r\n\r\n&#91; position_restraints &#93;\r\n;  i funct       fcx        fcy        fcz\r\n   1    1       1000       1000       1000<\/pre>\n<p>\u4fee\u6b63\u5f8c:<\/p>\n<pre class=\"prettyprint\">#ifdef STEP6_0\r\n#ifdef STEP6_0\r\n#define fc_bb 4000.0\r\n#define fc_sc 2000.0\r\n#endif\r\n#ifdef STEP6_1\r\n#define fc_bb 4000.0\r\n#define fc_sc 2000.0\r\n#endif\r\n#ifdef STEP6_2\r\n#define fc_bb 2000.0\r\n#define fc_sc 1000.0\r\n#endif\r\n#ifdef STEP6_3\r\n#define fc_bb 1000.0\r\n#define fc_sc 500.0\r\n#endif\r\n#ifdef STEP6_4\r\n#define fc_bb 500.0\r\n#define fc_sc 200.0\r\n#endif\r\n#ifdef STEP6_5\r\n#define fc_bb 200.0\r\n#define fc_sc 50.0\r\n#endif\r\n#ifdef STEP6_6\r\n#define fc_bb 50.0\r\n#define fc_sc 0.0\r\n#endif\r\n#ifdef STEP7\r\n#define fc_bb 0.0\r\n#define fc_sc 0.0\r\n#endif\r\n\r\n&#91; position_restraints &#93;\r\n;  i funct       fcx        fcy        fcz\r\n   1    1       fc_bb       fc_bb       fc_bb<\/pre>\n<p>\u5074\u9396\u7528restraint\u30d5\u30a1\u30a4\u30eb\u306e\u4f5c\u6210:<\/p>\n<pre class=\"command-line\"><code class=\"language-bash\" data-line=\"\">$ gmx genrestr -f 1PTR_POPC.gro -n index.ndx -o SC_rest.itp\nSelect a group: 33<\/code><\/pre>\n<p>SC_rest.itp\u4e2d\u306eforce constants\u30921000\u304b\u3089fc_sc\u306b\u5168\u3066\u7f6e\u63db\u3057\uff0c[position_restraints] \u3088\u308a\u5f8c\u5074\u3092PROT_rest.itp\u306e\u304a\u3057\u308a\u306b\u30b3\u30d4\u30fc&amp;\u30da\u30fc\u30b9\u30c8\u3057\u307e\u3059\uff0e<br \/>\n\u3055\u3089\u306b\u4fee\u6b63\u5f8c\u306ePROT_rest.itp\u306e\u9014\u4e2d\u304b\u3089:<\/p>\n<pre class=\"prettyprint\">  801     1    fc_bb    fc_bb    fc_bb\r\n  802     1    fc_sc    fc_sc    fc_sc\r\n  803     1    fc_sc    fc_sc    fc_sc\r\n   6    1       fc_sc       fc_sc       fc_sc\r\n   7    1       fc_sc       fc_sc       fc_sc\r\n  13    1       fc_sc       fc_sc       fc_sc<\/pre>\n<p>\u30ea\u30ac\u30f3\u30c9\u7528restraint\u30d5\u30a1\u30a4\u30eb<span style=\"font-weight: bold;\">LIG_rest.itp<\/span>:<\/p>\n<pre class=\"prettyprint\">#ifdef STEP6_0\r\n#define fc_bb 4000.0\r\n#endif\r\n#ifdef STEP6_1\r\n#define fc_bb 4000.0\r\n#endif\r\n#ifdef STEP6_2\r\n#define fc_bb 2000.0\r\n#endif\r\n#ifdef STEP6_3\r\n#define fc_bb 1000.0\r\n#endif\r\n#ifdef STEP6_4\r\n#define fc_bb 500.0\r\n#endif\r\n#ifdef STEP6_5\r\n#define fc_bb 200.0\r\n#endif\r\n#ifdef STEP6_6\r\n#define fc_bb 50.0\r\n#endif\r\n#ifdef STEP7\r\n#define fc_bb 0.0\r\n#endif\r\n\r\n&#91; position_restraints &#93;\r\n;  i funct       fcx        fcy        fcz\r\n   1    1       fc_bb       fc_bb       fc_bb\r\n   2    1       fc_bb       fc_bb       fc_bb\r\n   3    1       fc_bb       fc_bb       fc_bb\r\n   4    1       fc_bb       fc_bb       fc_bb\r\n   8    1       fc_bb       fc_bb       fc_bb\r\n  10    1       fc_bb       fc_bb       fc_bb\r\n  12    1       fc_bb       fc_bb       fc_bb\r\n  13    1       fc_bb       fc_bb       fc_bb\r\n  15    1       fc_bb       fc_bb       fc_bb\r\n  18    1       fc_bb       fc_bb       fc_bb\r\n  19    1       fc_bb       fc_bb       fc_bb\r\n  20    1       fc_bb       fc_bb       fc_bb\r\n  24    1       fc_bb       fc_bb       fc_bb\r\n  26    1       fc_bb       fc_bb       fc_bb\r\n  27    1       fc_bb       fc_bb       fc_bb\r\n  28    1       fc_bb       fc_bb       fc_bb\r\n  29    1       fc_bb       fc_bb       fc_bb\r\n  33    1       fc_bb       fc_bb       fc_bb\r\n  39    1       fc_bb       fc_bb       fc_bb\r\n  40    1       fc_bb       fc_bb       fc_bb\r\n  42    1       fc_bb       fc_bb       fc_bb\r\n  43    1       fc_bb       fc_bb       fc_bb\r\n  48    1       fc_bb       fc_bb       fc_bb\r\n  49    1       fc_bb       fc_bb       fc_bb\r\n  52    1       fc_bb       fc_bb       fc_bb\r\n  53    1       fc_bb       fc_bb       fc_bb\r\n  54    1       fc_bb       fc_bb       fc_bb\r\n  55    1       fc_bb       fc_bb       fc_bb\r\n  56    1       fc_bb       fc_bb       fc_bb<\/pre>\n<p>\u30ea\u30f3\u8102\u8cea\u7528restraint\u30d5\u30a1\u30a4\u30eb<span style=\"font-weight: bold;\">POPC_rest.itp<\/span>:<\/p>\n<pre class=\"prettyprint\">#ifdef STEP6_0\r\n#define fc_lpos 1000.0\r\n#define fc_ldih 1000.0\r\n#endif\r\n#ifdef STEP6_1\r\n#define fc_lpos 1000.0\r\n#define fc_ldih 1000.0\r\n#endif\r\n#ifdef STEP6_2\r\n#define fc_lpos 1000.0\r\n#define fc_ldih 400.0\r\n#endif\r\n#ifdef STEP6_3\r\n#define fc_lpos 400.0\r\n#define fc_ldih 200.0\r\n#endif\r\n#ifdef STEP6_4\r\n#define fc_lpos 200.0\r\n#define fc_ldih 200.0\r\n#endif\r\n#ifdef STEP6_5\r\n#define fc_lpos 40.0\r\n#define fc_ldih 100.0\r\n#endif\r\n#ifdef STEP6_6\r\n#define fc_lpos 0.0\r\n#define fc_ldih 0.0\r\n#endif\r\n#ifdef STEP7\r\n#define fc_lpos 0.0\r\n#define fc_ldih 0.0\r\n#endif\r\n\r\n&#91; position_restraints &#93;\r\n   59     1      0.0      0.0  fc_lpos\r\n\r\n&#91; dihedral_restraints &#93;\r\n   50    55    53    82     1    120.0      2.5  fc_ldih\r\n  103   106   108   110     1      0.0      0.0  fc_ldih<\/pre>\n<p>\u5404restraint\u30d5\u30a1\u30a4\u30eb\u3092\u8aad\u307f\u8fbc\u307e\u305b\u308b\u305f\u3081\u306b\uff0c1PTR_POPC.top\u4e2d\u306e\u30bf\u30f3\u30d1\u30af\u8cea\uff0c\u30ea\u30ac\u30f3\u30c9\uff0c\u8102\u8cea\u305d\u308c\u305e\u308c\u306e\u8a18\u8ff0\u306e\u6700\u5f8c\u306b\u4ee5\u4e0b\u306e\u8a18\u8ff0\u3092\u8ffd\u52a0\u3057\u307e\u3059\uff0e<\/p>\n<pre class=\"prettyprint\">    794    798    796    797     4  180.00008  4.60240  2\r\n\r\n#ifdef REST_ON\r\n#include &#34;.&#47;PROT_rest.itp&#34;\r\n#endif\r\n\r\n\r\n&#91; moleculetype &#93;\r\n; Name            nrexcl\r\nPRB          3\r\n\r\n(\u7565)\r\n\r\n     10      3      8      9     4  180.00008  4.60240  2\r\n\r\n#ifdef REST_ON\r\n#include &#34;.&#47;LIG_rest.itp&#34;\r\n#endif\r\n\r\n&#91; moleculetype &#93;\r\n; Name            nrexcl\r\nsystem2          3\r\n\r\n(\u7565)\r\n\r\n    108    103    106    107     4  180.00008  4.60240  2\r\n\r\n#ifdef REST_ON\r\n#include &#34;.&#47;POPC_rest.itp&#34;\r\n#endif\r\n\r\n&#91; moleculetype &#93;\r\n; Name            nrexcl\r\nK+          3<\/pre>\n<h2>\u7cfb\u306e\u5e73\u8861\u5316<\/h2>\n<h3>Energy Minimization<\/h3>\n<pre class=\"command-line\"><code class=\"language-bash\" data-line=\"\">$ mkdir step6_0-6\n$ cd step6_0-6\n$ gmx grompp -f ..\/charmm-gui\/gromacs\/step6.0_minimization.mdp -c ..\/1PTR_POPC.gro -p ..\/1PTR_POPC.top -n ..\/index.ndx -o step6_0.tpr\n$ gmx mdrun -v -deffnm step6_0\n<\/code><\/pre>\n<p>Pymol\u3067step6_0.gro\u30681PTR_POPC.gro\u3092\u958b\u304d\uff0c\u30bf\u30f3\u30d1\u30af\u8cea\uff0c\u30ea\u30ac\u30f3\u30c9\uff0c\u30ea\u30f3\u539f\u5b50\u306e\u4f4d\u7f6e\u7b49\u304c\u5236\u9650\u3055\u308c\u3066\u3044\u308b\u3053\u3068\u3092\u78ba\u8a8d\u3057\u307e\u3059\uff0e<\/p>\n<h3>\u5e73\u8861\u5316step 1 (NVT, 25 ps, time step = 1 fs)<\/h3>\n<pre class=\"command-line\"><code class=\"language-bash\" data-line=\"\">$ gmx grompp -f ..\/charmm-gui\/gromacs\/step6.1_equilibration.mdp -c step6_0.gro -p ..\/1PTR_POPC.top -n ..\/index.ndx -o step6_1.tpr\n$ gmx mdrun -v -deffnm step6_1\n<\/code><\/pre>\n<p>\u3053\u306e25 ps\u306e\u8a08\u7b97\u306b10\u5206\u5f37\u304b\u304b\u308a\u307e\u3059\uff0e\u819c\u306e\u5e73\u8861\u5316\u306b\u304b\u304b\u308b\u6642\u9593\u3092\u8003\u3048\u308b\u3068\uff0c\u4ee5\u964d\u306e\u8a08\u7b97\u306f\u30b9\u30d1\u30b3\u30f3\u3067\u5b9f\u884c\u3057\u305f\u65b9\u304c\u3088\u3044\u3067\u3059\u306d\uff0e\u758e\u6c34\u6027\u306e\u74b0\u5883\u3067\u30bf\u30f3\u30d1\u30af\u8cea\u3068\u30ea\u30ac\u30f3\u30c9\u304c\u3069\u306e\u3088\u3046\u306b\u7d50\u5408\u3057\u3066\u3044\u308b\u304b\u306e\u30a4\u30e1\u30fc\u30b8\u306f\u3053\u308c\u3067\u51fa\u6765\u308b\u3068\u601d\u3044\u307e\u3059\uff0e<\/p>\n<p>(\u4e86)<\/p>\n","protected":false},"excerpt":{"rendered":"<p>\u74b0\u5883: macOS Sierra 10.12.1, 3.3  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