{"id":466,"date":"2016-10-19T18:29:14","date_gmt":"2016-10-19T09:29:14","guid":{"rendered":"https:\/\/www.ag.kagawa-u.ac.jp\/charlesy\/?page_id=466"},"modified":"2017-01-11T18:16:43","modified_gmt":"2017-01-11T09:16:43","slug":"protein-ligand-complex","status":"publish","type":"page","link":"https:\/\/www.ag.kagawa-u.ac.jp\/charlesy\/memo\/md-simulation\/protein-ligand-complex\/","title":{"rendered":"Protein-ligand complex"},"content":{"rendered":"<h1>PKC C1\u30c9\u30e1\u30a4\u30f3\u3068phorbol-13-acetate\u8907\u5408\u4f53\u306eMD\u30b7\u30df\u30e5\u30ec\u30fc\u30b7\u30e7\u30f3<\/h1>\n<p>Gromacs\u3067PKC C1\u30c9\u30e1\u30a4\u30f3\u3068\u30ea\u30ac\u30f3\u30c9\u306e\u8907\u5408\u4f53\u306eMD\u30b7\u30df\u30e5\u30ec\u30fc\u30b7\u30e7\u30f3\u3092\u884c\u3046\u305f\u3081\u306e\u30e1\u30e2\u3067\u3059\uff0e<\/p>\n<h2><span style=\"font-weight: bold;\">\u529b\u5834<\/span><\/h2>\n<ul>\n<li>\u30bf\u30f3\u30d1\u30af\u8cea: AMBER ff14SB + ZAFF<\/li>\n<li>\u30ea\u30ac\u30f3\u30c9: GAFF2<\/li>\n<li>\u6c34: TIP3P<\/li>\n<\/ul>\n<p>\u53c2\u8003\u30b5\u30a4\u30c8: <a href=\"http:\/\/blog.livedoor.jp\/ag_plusplus\/archives\/68324049.html\">Ag++: antechamber\u3092\u4f7f\u3063\u3066Gaussian 09\u304b\u3089AMBER\u7528\u306e\u529b\u5834\u30fb\u96fb\u8377\u30d1\u30e9\u30e1\u30fc\u30bf\u3092\u4f5c\u6210\u3059\u308b<\/a><\/p>\n<h2><span style=\"font-weight: bold;\">\u30c8\u30dd\u30ed\u30b8\u30fc\u30d5\u30a1\u30a4\u30eb\u306e\u4f5c\u6210<\/span><\/h2>\n<p>\u30bf\u30f3\u30d1\u30af\u8cea\u30d5\u30a1\u30a4\u30eb\u306e\u5074\u9396\u88dc\u5b8c\uff0c\u6b8b\u57fa\u4ed8\u52a0\uff0c\u4fee\u6b63\u306b\u3064\u3044\u3066\u306f\uff0c<a href=\"https:\/\/www.ag.kagawa-u.ac.jp\/charlesy\/memo\/md-simulation\/\">\u5225\u30da\u30fc\u30b8<\/a>\u3068\u540c\u3058\uff0emodeller.pdb\u304b\u3089\u30ea\u30ac\u30f3\u30c9\u5ea7\u6a19\u3092PRB.pdb\u3068\u3057\u3066\u4e00\u65e6\u5206\u96e2\uff0eAvogadro\u3067\u30ea\u30ac\u30f3\u30c9\u5ea7\u6a19\u30d5\u30a1\u30a4\u30eb (PRB.pdb) \u3092\u958b\u304d\uff0c\u7d50\u5408\u306e\u4e0d\u98fd\u548c\u5ea6\u3092\u4fee\u6b63\u3057\u305f\u5f8c\uff0c\u6c34\u7d20\u3092\u4ed8\u52a0\uff0cMMFF94s\u529b\u5834\u3067\u6700\u9069\u5316\uff0cpdb\u5f62\u5f0f\u3067\u4fdd\u5b58\u3059\u308b\uff0e\u91cd\u539f\u5b50\u3068\u6c34\u7d20\u539f\u5b50\u3067<span style=\"color: #ff0000;\">\u6b8b\u57fa\u540d\u3068\u6b8b\u57fa\u756a\u53f7\u304c\u7570\u306a\u308b\u5834\u5408\u306f\u7d71\u4e00\u3059\u308b<\/span>\uff08\u91cd\u8981\uff0eAvogadro\u3067\u4ed8\u52a0\u3057\u305f\u6c34\u7d20\u539f\u5b50\u306e\u898b\u51fa\u3057\u306fHETATM\uff0c\u6b8b\u57fa\u540d\u306fLIG\uff0c\u6b8b\u57fa\u756a\u53f7\u306f1\u306b\u306a\u3063\u3066\u3044\u308b\uff09\uff0e<\/p>\n<pre class=\"command-line\"><code class=\"language-bash\" data-line=\"\">$ antechamber -fi pdb -fo prepi -i PRB.pdb -o PRB.prep -c bcc -at gaff2\n$ parmchk2 -i PRB.prep -o PRB.frcmod -f prepi -s gaff2\n$ tleap\n&gt; source leaprc.gaff2\n&gt; loadamberprep PRB.prep\n&gt; loadamberparams PRB.frcmod\n&gt; mol = loadpdb NEWPDB.PDB\n&gt; saveamberparm mol PRB.prmtop PRB.inpcrd\n&gt; quit<\/code><\/pre>\n<p>Antechamber\u306e\u5b9f\u884c\u306b\u306f1\u5206\u534a\u7a0b\u304b\u304b\u308b\uff0eAmber16\u4ed8\u5c5e\u306eParmEd\u3092\u4f7f\u3063\u3066\uff0cAMBER\u5f62\u5f0f\u306e\u30d5\u30a1\u30a4\u30eb\u3092GROMACS\u5f62\u5f0f\u3078\u5909\u63db\u3059\u308b\uff0e<\/p>\n<pre class=\"command-line\"><code class=\"language-bash\" data-line=\"\">$ python\n&gt;&gt;&gt; import parmed as pmd\n&gt;&gt;&gt; amber = pmd.load_file(&#039;PRB.prmtop&#039;,xyz=&#039;PRB.inpcrd&#039;)\n&gt;&gt;&gt; amber.save(&#039;gromacs.top&#039;)\n&gt;&gt;&gt; amber.save(&#039;gromacs.gro&#039;)\n&gt;&gt;&gt; quit()<\/code><\/pre>\n<p>\u3053\u3053\u3067\u4f5c\u6210\u3057\u305f\u30c8\u30dd\u30ed\u30b8\u30fc\u304c\u6b63\u5e38\u304b\u3069\u3046\u304b\uff0cGromacs\u3067\u30a8\u30cd\u30eb\u30ae\u30fc\u6700\u5c0f\u5316\u8a08\u7b97\u3092\u5b9f\u884c\u3057\u3066\u307f\u308b\uff0e<\/p>\n<pre class=\"command-line\"><code class=\"language-bash\" data-line=\"\">$ gmx grompp -f em.mdp -c gromacs.gro -p gromacs.top -o em.tpr\n$ gmx mdrun -v -deffnm em<\/code><\/pre>\n<p>em.gro\u3092pymol\u3067\u958b\u3044\u3066\u307f\u308b\u3068\uff0c13\u4f4d\u5468\u8fba\u304c\u6b6a\u3093\u3060\u69cb\u9020\u306b\u306a\u3063\u3066\u3057\u307e\u3063\u3066\u3044\u308b\uff0ePRB_GMX.top\u3092\u30c6\u30ad\u30b9\u30c8\u30a8\u30c7\u30a3\u30bf\u3067\u958b\u3044\u3066\uff0c13\u4f4d\u9178\u7d20\u539f\u5b50 (\u4eca\u56de\u306fOA1) \u306b\u95a2\u3059\u308b\u30d1\u30e9\u30e1\u30fc\u30bf\u3092\u898b\u3066\u307f\u308b\u3068\uff0c<\/p>\n<pre class=\"prettyprint\">&#91; bonds &#93;\r\n     52     53     1   0.14370 233885.600000\r\n&#91; angles &#93;\r\n     48     52     53     1   115.68005 693.590048\r\n&nbsp; &nbsp; &nbsp;27 &nbsp; &nbsp; 52 &nbsp; &nbsp; 53 &nbsp; &nbsp; 1 &nbsp; 59.09003 975.641856\r\n&nbsp; &nbsp; &nbsp;28 &nbsp; &nbsp; 52 &nbsp; &nbsp; 53 &nbsp; &nbsp; 1 &nbsp; 59.09003 975.641856<\/pre>\n<p>2\u7b87\u6240\u306eangle\u304c59.09\u00b0\u3068\u306a\u3063\u3066\u3044\u3066\uff0c\u3069\u3046\u3084\u3089\u30b7\u30af\u30ed\u30d7\u30ed\u30d1\u30f3\u74b0\u306e\u70ad\u7d20\u539f\u5b50 (atom type: cx) \u306b\u7d50\u5408\u3057\u305f13\u4f4d\u9178\u7d20\u539f\u5b50 (atom type: os) \u306fepoxide\u306e\u9178\u7d20\u539f\u5b50\u3068\u5224\u5b9a\u3057\u3066\u3044\u308b\u3089\u3057\u3044 (\u30a8\u30b9\u30c6\u30eb\u3068\u30a8\u30fc\u30c6\u30eb\u306esp3\u9178\u7d20\u539f\u5b50\u306eatom type\u306f\u540c\u3058)\uff0e\u307e\u305f\uff0c<\/p>\n<pre class=\"prettyprint\">1-4: angle 28 52 duplicates bond (&#39;triangular&#39; bond) or angle (&#39;square&#39; bond)\r\n\r\n1-4: angle 27 52 duplicates bond (&#39;triangular&#39; bond) or angle (&#39;square&#39; bond)\r\n\r\n1-4: angle 27 28 duplicates bond (&#39;triangular&#39; bond) or angle (&#39;square&#39; bond)<\/pre>\n<p>\u3068\u3044\u3046Warning\u304c\u51fa\u308b\uff0e\u30b7\u30af\u30ed\u30d7\u30ed\u30d1\u30f3\u74b0\u304c\u3042\u308b\u3068\u51fa\u308bWarning\u3068\u306e\u3053\u3068 (2\u3064\u306e\u30a2\u30f3\u30b0\u30eb\u3092\u6307\u5b9a\u3059\u308c\u3070\uff0c\u5f8c1\u3064\u306f\u5fc5\u8981\u306a\u3044\u305f\u3081)\uff0e<\/p>\n<p>\u30b7\u30af\u30ed\u30d7\u30ed\u30d1\u30f3\u74b0\u306b\u7d50\u5408\u3057\u305f\u30a8\u30b9\u30c6\u30eb\u57fa\u306e\u30d1\u30e9\u30e1\u30fc\u30bf\u304c\u306a\u3044\u306e\u3067\uff0c\u3053\u306e\u90e8\u5206\u306e\u89d2\u5ea6\u306b\u3064\u3044\u3066\u306f\u8a08\u7b97\u5024\u3092\u5165\u308c\u308b\u3053\u3068\u306b\u3057\u305f\uff0e<br \/>\nBabel\u3067Gaussian\u306einput\u30d5\u30a1\u30a4\u30eb\u306b\u5909\u63db\u3057\u305f\u5f8c\uff0cheader\u3092\u4fee\u6b63\u3057\u3066\u69cb\u9020\u6700\u9069\u5316\u3092\u5b9f\u884c\uff0e<\/p>\n<pre class=\"command-line\"><code class=\"language-bash\" data-line=\"\">$ babel PRB.pdb PRB.com<\/code><\/pre>\n<pre class=\"prettyprint\"># opt wb97xd&#47;6-31g(d) geom=connectivity<\/pre>\n<p><a href=\"https:\/\/www.ag.kagawa-u.ac.jp\/charlesy\/memo\/md-simulation\/protein-ligand-complex\/angle1\/\" rel=\"attachment wp-att-562\"><img loading=\"lazy\" decoding=\"async\" class=\"size-medium wp-image-562 alignright\" src=\"https:\/\/www.ag.kagawa-u.ac.jp\/charlesy\/wp\/wp-content\/uploads\/2016\/10\/angle1-300x225.png\" alt=\"angle1\" width=\"300\" height=\"225\" srcset=\"https:\/\/www.ag.kagawa-u.ac.jp\/charlesy\/wp\/wp-content\/uploads\/2016\/10\/angle1-300x225.png 300w, https:\/\/www.ag.kagawa-u.ac.jp\/charlesy\/wp\/wp-content\/uploads\/2016\/10\/angle1-360x270.png 360w, https:\/\/www.ag.kagawa-u.ac.jp\/charlesy\/wp\/wp-content\/uploads\/2016\/10\/angle1.png 640w\" sizes=\"auto, (max-width: 300px) 100vw, 300px\" \/><\/a>DFT\u8a08\u7b97\u3067\u306e\u6700\u9069\u5316\u69cb\u9020\u306e13\u4f4d\u5468\u308a\u306e\u89d2\u5ea6\u3068\u8ddd\u96e2\u306f\u53f3\u56f3\u306e\u3088\u3046\u306b\u306a\u3063\u305f\uff0e\u3053\u306e\u5024\u3092\u30c8\u30dd\u30ed\u30b8\u30fc\u30d5\u30a1\u30a4\u30eb\u306b\u5165\u308c\u305f\uff0e<\/p>\n<p>\u4fee\u6b63\u5f8c:<\/p>\n<pre class=\"prettyprint\">     48     52     53     1   111.0 693.590048\r\n     27     52     53     1   118.7 693.590048\r\n     28     52     53     1   112.3 693.590048<\/pre>\n<p>\u3082\u3046\u4e00\u5ea6Gromacs\u3067\u6700\u9069\u5316\u8a08\u7b97\u3092\u884c\u3063\u305f\u3068\u3053\u308d\uff0c\u6b63\u5e38\u306a\u69cb\u9020\u306b\u306a\u3063\u3066\u3044\u305f\uff0e<br \/>\n<!-- --><\/p>\n<p>\u6c34\u7d20\u304c\u4ed8\u52a0\u3055\u308c\u305f\u30ea\u30ac\u30f3\u30c9\u306e\u5ea7\u6a19\u304c\u542b\u307e\u308c\u308bPDB\u30d5\u30a1\u30a4\u30eb\u30921PTR_ZAFF_PRB.pdb\u3068\u3057\u307e\u3059\uff0e<\/p>\n<pre class=\"prettyprint\">ATOM    408  C   GLY    52      28.447  17.465  44.064  1.00 47.64           C  \r\nATOM    409  O   GLY    52      27.783  18.409  43.643  1.00 47.64           O\r\nTER  \r\nHETATM  410  ZN  ZN2    53      21.740  18.670  42.875  1.00 40.35          ZN  \r\nTER\r\nHETATM  411  ZN  ZN2    54      11.959  13.171  32.940  1.00 47.44          ZN\r\nTER\r\nATOM      1  O3  PRB     1       7.931  22.364  24.610 -0.519100\r\nATOM      2  C3  PRB     1       8.750  23.087  24.056  0.544300\r\nATOM      3  C2  PRB     1       9.135  22.950  22.639 -0.222400\r\nATOM      4  C19 PRB     1       8.565  21.929  21.737 -0.039900\r\nATOM      5  H24 PRB     1       8.997  21.999  20.733  0.050367<\/pre>\n<p>AmberTools\u306b\u542b\u307e\u308c\u308btleap\u7528\u306einput\u30d5\u30a1\u30a4\u30eb\u3092\u4f5c\u6210 (1PTR_ZAFF_PRB_tleap.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.gaff2 #Source the GAFF force field\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 .&#47;PRB.prep\r\nloadamberparams .&#47;PRB.frcmod\r\nmol = loadpdb 1PTR_ZAFF_PRB.pdb #Load the PDB file\r\nbond mol.53.ZN mol.32.SG #Bond zinc ion with SG atom of residue CYM31\r\nbond mol.53.ZN mol.35.SG #Bond zinc ion with SG atom of residue CYM34\r\nbond mol.53.ZN mol.51.SG #Bond zinc ion with SG atom of residue CYM50\r\nbond mol.53.ZN mol.2.ND1 #Bond zinc ion with SG atom of residue HIE1\r\nbond mol.54.ZN mol.15.SG #Bond zinc ion with SG atom of residue CYM14\r\nbond mol.54.ZN mol.18.SG #Bond zinc ion with SG atom of residue CYM17\r\nbond mol.54.ZN mol.43.SG #Bond zinc ion with SG atom of residue CYM42\r\nbond mol.54.ZN mol.40.ND1 #Bond zinc ion with SG atom of residue HIE39\r\nsavepdb mol 1PTR_ZAFF_PRB_dry.pdb #Save the pdb file\r\nsaveamberparm mol 1PTR_ZAFF_PRB_dry.prmtop 1PTR_ZAFF_PRB_dry.inpcrd #Save the topology and coordiante files\r\nsolvatebox mol TIP3PBOX 10.0 #Solvate the system using TIP3P water box\r\naddions mol CL 0 #Neutralize the system using Cl- ions\r\nsavepdb mol 1PTR_ZAFF_PRB_solv.pdb #Save the pdb file\r\nsaveamberparm mol 1PTR_ZAFF_PRB_solv.prmtop 1PTR_ZAFF_PRB_solv.inpcrd #Save the topology and coordiante files\r\nquit #Quit tleap<\/pre>\n<p>tleap\u3092\u5b9f\u884c\uff0e<\/p>\n<pre class=\"command-line\"><code class=\"language-bash\" data-line=\"\">$ tleap -s -f 1PTR_ZAFF_PRB_tleap.in &gt; 1PTR_ZAFF_PRB_tleap.out<\/code><\/pre>\n<p>\u3059\u3050\u7d42\u4e86\uff0e<\/p>\n<pre class=\"command-line\"><code class=\"language-bash\" data-line=\"\">$ python\n&gt;&gt;&gt; import parmed as pmd\n&gt;&gt;&gt; amber = pmd.load_file(&#039;1PTR_ZAFF_PRB_solv.prmtop&#039;,xyz=&#039;1PTR_ZAFF_PRB_solv.inpcrd&#039;)\n&gt;&gt;&gt; amber.save(&#039;1PTR_ZAFF_PRB_solv.gro&#039;)\n&gt;&gt;&gt; amber.save(&#039;1PTR_ZAFF_PRB_solv.top&#039;)\n&gt;&gt;&gt; quit()<\/code><\/pre>\n<p>GROMACS\u7528\u5ea7\u6a19\u30d5\u30a1\u30a4\u30eb (1PTR_ZAFF_PRB_solv_GMX.gro) \u3068GROMACS\u7528\u30c8\u30dd\u30ed\u30b8\u30fc\u30d5\u30a1\u30a4\u30eb (1PTR_ZAFF_PRB_solv_GMX.top) \u304c\u751f\u6210\u3059\u308b\uff0e<\/p>\n<p>\u4e0a\u3067\u8aac\u660e\u3057\u305f\u3088\u3046\u306b\uff0c\u30ea\u30ac\u30f3\u30c9\u90e8\u5206\u306etopology\u3092\u66f8\u304d\u63db\u3048\u308b\uff0e<\/p>\n<h2><span style=\"font-weight: bold;\">\u30a8\u30cd\u30eb\u30ae\u30fc\u6700\u5c0f\u5316<\/span><\/h2>\n<p>minim.mdp (\u4ee5\u4e0b\u306einput files\u306f<a href=\"http:\/\/www.bevanlab.biochem.vt.edu\/Pages\/Personal\/justin\/gmx-tutorials\/complex\/index.html\">GROMACS Tutorial: Protein-Ligand<\/a>\u3088\u308a)<\/p>\n<pre class=\"prettyprint\">integrator\t= steep\t\t; Algorithm (steep = steepest descent minimization)\r\nemtol\t\t= 1000.0  \t; Stop minimization when the maximum force &lt; 1000.0 kJ&#47;mol&#47;nm\r\nemstep          = 0.01          ; Energy step size\r\nnsteps\t\t= 50000\t  \t; Maximum number of (minimization) steps to perform\r\nnstlist\t\t= 1\t\t; Frequency to update the neighbor list and long range forces\r\nns_type\t\t= grid\t\t; Method to determine neighbor list (simple, grid)\r\nrlist\t\t= 1.0\t\t; Cut-off for making neighbor list (short range forces)\r\ncoulombtype\t= PME\t\t; Treatment of long range electrostatic interactions\r\nrcoulomb\t= 1.0\t\t; Short-range electrostatic cut-off\r\nrvdw\t\t= 1.0\t\t; Short-range Van der Waals cut-off\r\npbc\t\t= xyz \t\t; Periodic Boundary Conditions (yes&#47;no)<\/pre>\n<pre class=\"command-line\"><code class=\"language-bash\" data-line=\"\">$ gmx grompp -minim.mdp -c 1PTR_ZAFF_PRB_solv_GMX.gro -p 1PTR_ZAFF_PRB_solv_GMX.top -o em.tpr\n$ gmx mdrun -v -deffnm em<\/code><\/pre>\n<p>Index\u30d5\u30a1\u30a4\u30eb\u306e\u4f5c\u6210<\/p>\n<pre class=\"command-line\"><code class=\"language-bash\" data-line=\"\">$ gmx make_ndx -f em.gro\n  0 System              : 11677 atoms\n  1 Protein             :   709 atoms\n  2 Protein-H           :   354 atoms\n  3 C-alpha             :    44 atoms\n  4 Backbone            :   132 atoms\n  5 MainChain           :   177 atoms\n  6 MainChain+Cb        :   215 atoms\n  7 MainChain+H         :   222 atoms\n  8 SideChain           :   487 atoms\n  9 SideChain-H         :   177 atoms\n 10 Prot-Masses         :   709 atoms\n 11 non-Protein         : 10968 atoms\n 12 Other               :   155 atoms\n 13 HE1                 :    34 atoms\n 14 CY2                 :    60 atoms\n 15 ZN2                 :     2 atoms\n 16 PRB                 :    59 atoms\n 17 CL                  :     1 atoms\n 18 Ion                 :     1 atoms\n 19 HE1                 :    34 atoms\n 20 CY2                 :    60 atoms\n 21 ZN2                 :     2 atoms\n 22 PRB                 :    59 atoms\n 23 CL                  :     1 atoms\n 24 Water               : 10812 atoms\n 25 SOL                 : 10812 atoms\n 26 non-Water           :   865 atoms\n 27 Water_and_ions      : 10813 atoms\n\n&gt; 1 | 13 | 14 | 15  #\u30bf\u30f3\u30d1\u30af\u8cea\uff0c\u4e9c\u925b\u30a4\u30aa\u30f3\u3092merge\n&gt; 28 | 16 #\u30bf\u30f3\u30d1\u30af\u8cea\uff0c\u4e9c\u925b\u30a4\u30aa\u30f3\uff0c\u30ea\u30ac\u30f3\u30c9\u3092merge\n&gt; r 1-7 | r 15-21 | r 26-27 | r 29-54 #\u30ea\u30ac\u30f3\u30c9\u304b\u3089\u9060\u3044\u6b8b\u57fa\u3092\u30b0\u30eb\u30fc\u30d7\u5316\n&gt; q<\/code><\/pre>\n<p>\u30bf\u30f3\u30d1\u30af\u8cea-\u4e9c\u925b-\u30ea\u30ac\u30f3\u30c9\uff0c\u30ea\u30ac\u30f3\u30c9\u304b\u3089\u9060\u3044\u30bf\u30f3\u30d1\u30af\u8cea\uff0c\u30ea\u30ac\u30f3\u30c9\u305d\u308c\u305e\u308c\u306b\u5bfe\u3057\u3066restraint\u30d5\u30a1\u30a4\u30eb\u3092\u4f5c\u6210<\/p>\n<pre class=\"command-line\"><code class=\"language-bash\" data-line=\"\">$ gmx genrestr -f em.gro -n index.ndx -o posre.itp -fc 1000 1000 1000\n&gt; 29\n$ gmx genrestr -f em.gro -n index.ndx -o posre_far.itp -fc 1000 1000 1000\n&gt; 30<\/code><\/pre>\n<p>\u30c8\u30dd\u30ed\u30b8\u30fc\u30d5\u30a1\u30a4\u30eb (1PTR_ZAFF_PRB_solv_GMX.top) \u306bposition restraint\u30d5\u30a1\u30a4\u30eb\u306e\u60c5\u5831\u3092\u66f8\u304d\u8fbc\u3080\uff0e<\/p>\n<pre class=\"prettyprint\">   829    820    823    824      4   180.00   4.60240   2 ;     C7-    C5-    C6-   C20\r\n   861    860    859    858      4   180.00   4.60240   2 ;    CA2-   OA2-   CA1-   OA1\r\n\r\n#ifdef POSRES\r\n#include &#34;posre.itp&#34;\r\n#endif\r\n\r\n#ifdef POSRES_FAR\r\n#include &#34;posre_far.itp&#34;\r\n#endif\r\n\r\n&#91; moleculetype &#93;\r\n; molname       nrexcl ; TIP3P model\r\n  WAT             2<\/pre>\n<h2><span style=\"font-weight: bold;\">NVT equilibration<\/span><\/h2>\n<p>nvt.mdp<\/p>\n<pre class=\"prettyprint\">define      = -DPOSRES  ; position restrain the protein and ligand\r\n; Run parameters\r\nintegrator  = md        ; leap-frog integrator\r\nnsteps      = 50000     ; 2 * 50000 = 100 ps\r\ndt          = 0.002     ; 2 fs\r\n; Output control\r\nnstxout     = 500       ; save coordinates every 1.0 ps\r\nnstvout     = 500       ; save velocities every 1.0 ps\r\nnstenergy   = 500       ; save energies every 1.0 ps\r\nnstlog      = 500       ; update log file every 1.0 ps\r\nenergygrps  = Protein_HE1_CY2_ZN2 PRB\r\n; Bond parameters\r\ncontinuation    = no            ; first dynamics run\r\nconstraint_algorithm = lincs    ; holonomic constraints \r\nconstraints     = all-bonds     ; all bonds (even heavy atom-H bonds) constrained\r\nlincs_iter      = 1             ; accuracy of LINCS\r\nlincs_order     = 4             ; also related to accuracy\r\n; Neighborsearching\r\ncutoff-scheme   = Verlet\r\nns_type         = grid      ; search neighboring grid cells\r\nnstlist         = 10        ; 20 fs, largely irrelevant with Verlet\r\nrcoulomb        = 1.4       ; short-range electrostatic cutoff (in nm)\r\nrvdw            = 1.4       ; short-range van der Waals cutoff (in nm)\r\n; Electrostatics\r\ncoulombtype     = PME       ; Particle Mesh Ewald for long-range electrostatics\r\npme_order       = 4         ; cubic interpolation\r\nfourierspacing  = 0.16      ; grid spacing for FFT\r\n; Temperature coupling\r\ntcoupl      = V-rescale                     ; modified Berendsen thermostat\r\ntc-grps     = Protein_HE1_CY2_ZN2_PRB Water_and_ions    ; two coupling groups - more accurate\r\ntau_t       = 0.1   0.1                     ; time constant, in ps\r\nref_t       = 300   300                     ; reference temperature, one for each group, in K\r\n; Pressure coupling\r\npcoupl      = no        ; no pressure coupling in NVT\r\n; Periodic boundary conditions\r\npbc         = xyz       ; 3-D PBC\r\n; Dispersion correction\r\nDispCorr    = EnerPres  ; account for cut-off vdW scheme\r\n; Velocity generation\r\ngen_vel     = yes       ; assign velocities from Maxwell distribution\r\ngen_temp    = 300       ; temperature for Maxwell distribution\r\ngen_seed    = -1        ; generate a random seed<\/pre>\n<pre class=\"command-line\"><code class=\"language-bash\" data-line=\"\">$ gmx grompp -f nvt.mdp -c em.gro -p 1PTR_ZAFF_PRB_solv_GMX.top -n index.ndx -o nvt.tpr\n$ gmx mdrun -v -deffnm nvt\n$ gmx energy -f nvt.edr -o temperature.xvg<\/code><\/pre>\n<p>10\u5206\u7a0b\u3067\u8a08\u7b97\u7d42\u4e86\uff0e<\/p>\n<h2><span style=\"font-weight: bold;\">NPT equilibration<\/span><\/h2>\n<p>npt.mdp<\/p>\n<pre class=\"prettyprint\">define      = -DPOSRES  ; position restrain the protein and ligand\r\n; Run parameters\r\nintegrator  = md        ; leap-frog integrator\r\nnsteps      = 50000     ; 2 * 50000 = 100 ps\r\ndt          = 0.002     ; 2 fs\r\n; Output control\r\nnstxout     = 500       ; save coordinates every 1.0 ps\r\nnstvout     = 500       ; save velocities every 1.0 ps\r\nnstenergy   = 500       ; save energies every 1.0 ps\r\nnstlog      = 500       ; update log file every 1.0 ps\r\nenergygrps  = Protein_HE1_CY2_ZN2 PRB\r\n; Bond parameters\r\ncontinuation    = yes           ; first dynamics run\r\nconstraint_algorithm = lincs    ; holonomic constraints \r\nconstraints     = all-bonds     ; all bonds (even heavy atom-H bonds) constrained\r\nlincs_iter      = 1             ; accuracy of LINCS\r\nlincs_order     = 4             ; also related to accuracy\r\n; Neighborsearching\r\ncutoff-scheme   = Verlet\r\nns_type         = grid      ; search neighboring grid cells\r\nnstlist         = 10        ; 20 fs, largely irrelevant with Verlet\r\nrcoulomb        = 1.4       ; short-range electrostatic cutoff (in nm)\r\nrvdw            = 1.4       ; short-range van der Waals cutoff (in nm)\r\n; Electrostatics\r\ncoulombtype     = PME       ; Particle Mesh Ewald for long-range electrostatics\r\npme_order       = 4         ; cubic interpolation\r\nfourierspacing  = 0.16      ; grid spacing for FFT\r\n; Temperature coupling\r\ntcoupl      = V-rescale                     ; modified Berendsen thermostat\r\ntc-grps     = Protein_HE1_CY2_ZN2_PRB Water_and_ions    ; two coupling groups - more accurate\r\ntau_t       = 0.1   0.1                     ; time constant, in ps\r\nref_t       = 300   300                     ; reference temperature, one for each group, in K\r\n; Pressure coupling\r\npcoupl      = Parrinello-Rahman             ; pressure coupling is on for NPT\r\npcoupltype  = isotropic                     ; uniform scaling of box vectors\r\ntau_p       = 2.0                           ; time constant, in ps\r\nref_p       = 1.0                           ; reference pressure, in bar\r\ncompressibility = 4.5e-5                    ; isothermal compressibility of water, bar^-1\r\nrefcoord_scaling    = com\r\n; Periodic boundary conditions\r\npbc         = xyz       ; 3-D PBC\r\n; Dispersion correction\r\nDispCorr    = EnerPres  ; account for cut-off vdW scheme\r\n; Velocity generation\r\ngen_vel     = no        ; velocity generation off after NVT<\/pre>\n<pre class=\"command-line\"><code class=\"language-bash\" data-line=\"\">$ gmx grompp -f npt.mdp -c nvt.gro -t nvt.cpt -p 1PTR_ZAFF_PRB_solv_GMX.top -n index.ndx -o npt.tpr\n$ gmx mdrun -v -deffnm npt\n$ gmx energy -f npt.edr -o pressure.xvg<\/code><\/pre>\n<h2><span style=\"font-weight: bold;\">Production MD<\/span><\/h2>\n<p>md.mdp<\/p>\n<pre class=\"prettyprint\">; Run parameters\r\nintegrator  = md        ; leap-frog integrator\r\nnsteps      = 500000    ; 2 * 500000 = 1000 ps (1 ns)\r\ndt          = 0.002     ; 2 fs\r\n; Output control\r\nnstxout             = 0         ; suppress .trr output \r\nnstvout             = 0         ; suppress .trr output\r\nnstenergy           = 5000      ; save energies every 10.0 ps\r\nnstlog              = 5000      ; update log file every 10.0 ps\r\nnstxout-compressed  = 5000      ; write .xtc trajectory every 10.0 ps\r\ncompressed-x-grps   = System\r\nenergygrps          = Protein_HE1_CY2_ZN2 PRB\r\n; Bond parameters\r\ncontinuation    = yes           ; first dynamics run\r\nconstraint_algorithm = lincs    ; holonomic constraints \r\nconstraints     = all-bonds     ; all bonds (even heavy atom-H bonds) constrained\r\nlincs_iter      = 1             ; accuracy of LINCS\r\nlincs_order     = 4             ; also related to accuracy\r\n; Neighborsearching\r\ncutoff-scheme   = Verlet\r\nns_type         = grid      ; search neighboring grid cells\r\nnstlist         = 10        ; 20 fs, largely irrelevant with Verlet\r\nrcoulomb        = 1.4       ; short-range electrostatic cutoff (in nm)\r\nrvdw            = 1.4       ; short-range van der Waals cutoff (in nm)\r\n; Electrostatics\r\ncoulombtype     = PME       ; Particle Mesh Ewald for long-range electrostatics\r\npme_order       = 4         ; cubic interpolation\r\nfourierspacing  = 0.16      ; grid spacing for FFT\r\n; Temperature coupling\r\ntcoupl      = V-rescale                     ; modified Berendsen thermostat\r\ntc-grps     = Protein_HE1_CY2_ZN2_PRB Water_and_ions    ; two coupling groups - more accurate\r\ntau_t       = 0.1   0.1                     ; time constant, in ps\r\nref_t       = 300   300                     ; reference temperature, one for each group, in K\r\n; Pressure coupling \r\npcoupl      = Parrinello-Rahman             ; pressure coupling is on for NPT\r\npcoupltype  = isotropic                     ; uniform scaling of box vectors\r\ntau_p       = 2.0                           ; time constant, in ps\r\nref_p       = 1.0                           ; reference pressure, in bar\r\ncompressibility = 4.5e-5                    ; isothermal compressibility of water, bar^-1\r\n; Periodic boundary conditions\r\npbc         = xyz       ; 3-D PBC\r\n; Dispersion correction\r\nDispCorr    = EnerPres  ; account for cut-off vdW scheme\r\n; Velocity generation\r\ngen_vel     = no        ; assign velocities from Maxwell distribution<\/pre>\n<pre class=\"command-line\"><code class=\"language-bash\" data-line=\"\">$ gmx grompp -f md.mdp -c npt.gro -t npt.cpt -p 1PTR_ZAFF_PRB_solv_GMX.top -n index.ndx -o md_0_1.tpr\n$ gmx mdrun -v -deffnm md_0_1<\/code><\/pre>\n","protected":false},"excerpt":{"rendered":"<p>PKC C1\u30c9\u30e1\u30a4\u30f3\u3068phorbol-13-acetate\u8907 &#8230;<\/p>\n","protected":false},"author":1,"featured_media":562,"parent":462,"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-466","page","type-page","status-publish","has-post-thumbnail","hentry","ja"],"aioseo_notices":[],"uagb_featured_image_src":{"full":["https:\/\/www.ag.kagawa-u.ac.jp\/charlesy\/wp\/wp-content\/uploads\/2016\/10\/angle1.png",640,480,false],"thumbnail":["https:\/\/www.ag.kagawa-u.ac.jp\/charlesy\/wp\/wp-content\/uploads\/2016\/10\/angle1-150x150.png",150,150,true],"medium":["https:\/\/www.ag.kagawa-u.ac.jp\/charlesy\/wp\/wp-content\/uploads\/2016\/10\/angle1-300x225.png",300,225,true],"medium_large":["https:\/\/www.ag.kagawa-u.ac.jp\/charlesy\/wp\/wp-content\/uploads\/2016\/10\/angle1.png",640,480,false],"large":["https:\/\/www.ag.kagawa-u.ac.jp\/charlesy\/wp\/wp-content\/uploads\/2016\/10\/angle1.png",640,480,false],"1536x1536":["https:\/\/www.ag.kagawa-u.ac.jp\/charlesy\/wp\/wp-content\/uploads\/2016\/10\/angle1.png",640,480,false],"2048x2048":["https:\/\/www.ag.kagawa-u.ac.jp\/charlesy\/wp\/wp-content\/uploads\/2016\/10\/angle1.png",640,480,false],"onepress-blog-small":["https:\/\/www.ag.kagawa-u.ac.jp\/charlesy\/wp\/wp-content\/uploads\/2016\/10\/angle1.png",200,150,false],"onepress-small":["https:\/\/www.ag.kagawa-u.ac.jp\/charlesy\/wp\/wp-content\/uploads\/2016\/10\/angle1.png",400,300,false],"onepress-medium":["https:\/\/www.ag.kagawa-u.ac.jp\/charlesy\/wp\/wp-content\/uploads\/2016\/10\/angle1.png",533,400,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\u3068phorbol-13-acetate\u8907 ...","_links":{"self":[{"href":"https:\/\/www.ag.kagawa-u.ac.jp\/charlesy\/wp-json\/wp\/v2\/pages\/466","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=466"}],"version-history":[{"count":32,"href":"https:\/\/www.ag.kagawa-u.ac.jp\/charlesy\/wp-json\/wp\/v2\/pages\/466\/revisions"}],"predecessor-version":[{"id":977,"href":"https:\/\/www.ag.kagawa-u.ac.jp\/charlesy\/wp-json\/wp\/v2\/pages\/466\/revisions\/977"}],"up":[{"embeddable":true,"href":"https:\/\/www.ag.kagawa-u.ac.jp\/charlesy\/wp-json\/wp\/v2\/pages\/462"}],"wp:featuredmedia":[{"embeddable":true,"href":"https:\/\/www.ag.kagawa-u.ac.jp\/charlesy\/wp-json\/wp\/v2\/media\/562"}],"wp:attachment":[{"href":"https:\/\/www.ag.kagawa-u.ac.jp\/charlesy\/wp-json\/wp\/v2\/media?parent=466"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}