{"id":1115,"date":"2017-06-08T12:15:44","date_gmt":"2017-06-08T03:15:44","guid":{"rendered":"https:\/\/www.ag.kagawa-u.ac.jp\/charlesy\/?p=1115"},"modified":"2019-12-05T15:23:56","modified_gmt":"2019-12-05T06:23:56","slug":"building-topology-for-c1-domain-alone-or-in-complex-with-phorbol-13-acetate-with-the-charmm36-force-field-for-use-with-gromacs","status":"publish","type":"post","link":"https:\/\/www.ag.kagawa-u.ac.jp\/charlesy\/2017\/06\/08\/building-topology-for-c1-domain-alone-or-in-complex-with-phorbol-13-acetate-with-the-charmm36-force-field-for-use-with-gromacs\/","title":{"rendered":"Building topology for C1 domain alone or in complex with phorbol-13-acetate with the Charmm36 force field, for use with GROMACS"},"content":{"rendered":"<p>\u74b0\u5883: macOS Sierra 10.12.4, Gromacs 2016.3.<\/p>\n<p><a href=\"http:\/\/mackerell.umaryland.edu\/charmm_ff.shtml\">MacKerell Lab<\/a>\u3067\u914d\u5e03\u3055\u308c\u3066\u3044\u308bGROMACS\u7528\u306eCharmm\u529b\u5834\u30d5\u30a1\u30a4\u30eb\u306eNovember 2016\u7248\u306b\u4e9c\u925b\u306b\u914d\u4f4d\u3057\u305f\u30b7\u30b9\u30c6\u30a4\u30f3\u7528\u306e\u6b8b\u57fa\uff08CYN\uff09\u304c\u8ffd\u52a0\u3055\u308c\u3066\u3044\u305f\u3053\u3068\u306b\u6c17\u4ed8\u3044\u305f\u306e\u3067\uff08\u305f\u3060\u3057\u30d1\u30e9\u30e1\u30fc\u30bf\u306f\u5f93\u6765\u304b\u3089\u5b58\u5728\u3059\u308bCYM\u6b8b\u57fa\u3068\u5909\u66f4\u306f\u306a\u3044\uff09\uff0c\u3053\u308c\u3092\u4f7f\u3063\u3066\u4e9c\u925b\u30a4\u30aa\u30f3\u30922\u539f\u5b50\u914d\u4f4d\u3057\u305fC1\u30c9\u30e1\u30a4\u30f3\u306e\u30c8\u30dd\u30ed\u30b8\u30fc\u3092\u4f5c\u6210\u3057\u3066\u307f\u307e\u3057\u305f\uff0e<br \/>\nAMBER\u7528\u306e<a href=\"http:\/\/ambermd.org\/~cerutti\/amber_web\/tutorials\/advanced\/tutorial20\/ZAFF.htm\">ZAFF<\/a>\uff08Zinc AMBER Force Field\uff09\u306f\u914d\u4f4d\u30d1\u30bf\u30fc\u30f3\u305d\u308c\u305e\u308c\u306b\u7570\u306a\u308b\u30d1\u30e9\u30e1\u30fc\u30bf\u3092\u7528\u610f\u3057\u3066\uff0c\u4e9c\u925b\u30a4\u30aa\u30f3\u306e\u6b63\u96fb\u8377\u3068\u30b7\u30b9\u30c6\u30a4\u30f3\uff08thiolate form\uff09 \u306e\u8ca0\u96fb\u8377\u3092\u932f\u4f53\u5168\u4f53\u306b\u5206\u6563\u3055\u305b\u3066\u3044\u307e\u3059\uff0e\u305d\u308c\u306b\u5bfe\u3057\u3066\uff0cCharmm\u306b\u65b0\u305f\u306b\u6b8b\u57fa\u3068\u3057\u3066\u8ffd\u52a0\u3055\u308c\u3066\u3044\u308b\u306e\u306f\u4e9c\u925b\u306b\u914d\u4f4d\u3057\u305f\u30b7\u30b9\u30c6\u30a4\u30f3\uff08CYN\uff09 \u306e\u307f\u3067\uff0c \u4e9c\u925b\u3092\u542b\u3080\u7d50\u5408\uff0c\u7d50\u5408\u89d2\uff0c\u4e8c\u9762\u89d2\u306e\u30d1\u30e9\u30e1\u30fc\u30bf\u306f\u3042\u308a\u307e\u3059\u304c\uff0cZN\uff0cCYN\uff0cHIS\u6b8b\u57fa\u306f\u305d\u308c\u305e\u308c+2\uff0c\u22121\uff0c0\u306e\u96fb\u8377\u3092\u6301\u3064\u6b8b\u57fa\u3068\u3057\u3066\u8868\u73fe\u3055\u308c\u307e\u3059\uff0e\u30a2\u30d7\u30ed\u30fc\u30c1\u3068\u3057\u3066\u306f\uff0cZAFF\u306e\u65b9\u304c\u826f\u3055\u305d\u3046\u3067\u3059\uff0e<br \/>\n\u786b\u9ec4\u2013\u4e9c\u925b\u9593\u306e\u8ddd\u96e2\u306fZAFF\uff08CCCH\u578b\u3067H\u306fHIE\uff09\u304c0.2355\uff0cCharmm\u304c0.232\uff0c\u7a92\u7d20\u2013\u4e9c\u925b\u9593\u306fZAFF\u304c0.2176\uff0cCharmm\u304c0.207\u3067\u3057\u305f\uff0e<\/p>\n<h2>\u30bf\u30f3\u30d1\u30af\u8cea\u7528\u30c8\u30dd\u30ed\u30b8\u30fc<\/h2>\n<p><a href=\"http:\/\/mackerell.umaryland.edu\/charmm_ff.shtml\">MacKerell Lab<\/a>\u304b\u3089charmm36-nov2016.ff.tgz\u3092\u30c0\u30a6\u30f3\u30ed\u30fc\u30c9\u3057\u307e\u3059\uff0e<\/p>\n<pre class=\"command-line\"><code class=\"language-bash\" data-line=\"\">$ tar xvzf charmm36-nov2016.ff.tgz\n$ mv charmm36-nov2016.ff $GMXPREFIX\/share\/gromacs\/top\/\n<\/code><\/pre>\n<p><a href=\"http:\/\/www.rcsb.org\/pdb\/explore.do?structureId=1PTR\">1PTR.pdb<\/a> (PKC\u03b4 C1B\u30c9\u30e1\u30a4\u30f3) \u3092Protein Data Bank\u304b\u3089\u30c0\u30a6\u30f3\u30ed\u30fc\u30c9\u3059\u308b\uff0e<br \/>\n\u6b20\u3051\u305f\u5074\u9396\u3092\u88dc\u5b8c\u3057\uff0cN\u672b\u3068C\u672b\u306bGly\u6b8b\u57fa\u3092\u8ffd\u52a0\u3059\u308b (\u4e9c\u925b\u306b\u914d\u4f4d\u3059\u308bHIS\u3068CYS\u304c\u672b\u7aef\u306b\u4f4d\u7f6e\u3057\u306a\u3044\u3088\u3046\u306b)\uff0ePymol\u3068Modeller\u3092\u4f7f\u7528\u3057\u305f\u65b9\u6cd5\u306b\u3064\u3044\u3066\u306f<a href=\"https:\/\/www.ag.kagawa-u.ac.jp\/charlesy\/2016\/10\/20\/modeller%e3%81%ab%e3%82%88%e3%82%8bmissing-side-chain%e3%81%ae%e4%bb%98%e5%8a%a0\/\">\u5225\u8a18\u4e8b<\/a>\u3092\u53c2\u7167\u306e\u3053\u3068\uff0emodeller.pdb\u3068\u3057\u3066\u30b3\u30d4\u30fc\uff0e<br \/>\n1PTR\u30d5\u30a1\u30a4\u30eb\u4e2d\u306ePRB\u6b8b\u57fa (phorbol 13-acetate) \u306e\u884c\u3092\u5206\u96e2\u3057\u3066\u5225\u30d5\u30a1\u30a4\u30eb\u306b\u3059\u308b (PRB.pdb)\uff0e<\/p>\n<p>Gromacs\u306epdb2gmx\u3067PDB\u30d5\u30a1\u30a4\u30eb\u3092\u51e6\u7406\u3059\u308b\u969b\u306b\uff0c\u539f\u5b50\u9593\u3067\u8ffd\u52a0\u306e\u7d50\u5408\u3092\u5f62\u6210\u3055\u305b\u308b\u6761\u4ef6\u304c\u66f8\u304b\u308c\u305fspecbond.dat\u3092\u4f5c\u696d\u30c7\u30a3\u30ec\u30af\u30c8\u30ea\u306b\u30b3\u30d4\u30fc\u3057\u3066\u7de8\u96c6\u3057\u307e\u3059\uff0e<\/p>\n<pre class=\"command-line\"><code class=\"language-bash\" data-line=\"\">$ cp $GMXPREFIX\/share\/gromacs\/top\/specbond.dat .\n<\/code><\/pre>\n<p>specbond.dat\u3092\u4ee5\u4e0b\u306e\u3088\u3046\u306b\u7de8\u96c6\u3057\u307e\u3059\uff082\u884c\u8ffd\u52a0\u3057\u3066\uff0c1\u884c\u76ee\u306e\u6570\u5b57\u3092\u5909\u66f4\uff09\uff0e7\u5217\u76ee\u306e\u6570\u5024\uff08\u5358\u4f4d\u306fnm\uff09\u306e\u00b110%\u4ee5\u5185\u306b2\u3064\u306e\u539f\u5b50\u304c\u3042\u308b\u6642\u306b\u7d50\u5408\u304c\u5f62\u6210\u3055\u308c\u307e\u3059\uff0e<\/p>\n<pre class=\"prettyprint\">10\nCYS\tSG\t1\tZN\tZN\t1\t0.24\tCYN\tZN2\nHIS\tND1\t1\tZN \tZN\t1\t0.20\tHSE\tZN2\nCYS\tSG\t1\tCYS\tSG\t1\t0.2\tCYS2\tCYS2\nCYS\tSG\t1\tHEM \tFE\t2\t0.25\tCYS2\tHEME\nCYS\tSG\t1\tHEM \tCAB\t1\t0.18\tCYS2\tHEME\nCYS\tSG\t1\tHEM \tCAC\t1\t0.18\tCYS2\tHEME\nHIS\tNE2\t1\tHEM \tFE\t1\t0.2\tHIS1\tHEME\nMET\tSD\t1\tHEM \tFE\t1\t0.24\tMET\tHEME\nCO      C       1       HEME    FE      1       0.19    CO      HEME\nCYM     SG      1       CYM     SG      1       0.2     CYS2    CYS2<\/pre>\n<pre class=\"command-line\"><code class=\"language-bash\" data-line=\"\">$ gmx pdb2gmx -f modeller.pdb -o conf.out -ignh<\/code><\/pre>\n<p>\u529b\u5834\u306f 9: CHARMM36 all-atom force field (November 2016)\uff0c<br \/>\n\u6c34\u306f1: TIP3P TIP 3-point, recommended, by default uses CHARMM TIP3 with LJ on H<br \/>\n\u3092\u9078\u3073\u307e\u3059\uff0e<\/p>\n<pre class=\"prettyprint\">Linking HIS-2 ND1-12 and ZN-53 ZN-410...\nLinking CYS-15 SG-129 and ZN-54 ZN-411...\nLinking CYS-18 SG-153 and ZN-54 ZN-411...\nLinking CYS-32 SG-257 and ZN-53 ZN-410...\nLinking CYS-35 SG-280 and ZN-53 ZN-410...\nLinking HIS-40 ND1-315 and ZN-54 ZN-411...\nLinking CYS-43 SG-342 and ZN-54 ZN-411...\nLinking CYS-51 SG-405 and ZN-53 ZN-410...<\/pre>\n<p>\u3068\u51fa\u529b\u3055\u308c\uff0c\u7d50\u5408\u304c\u4f5c\u3089\u308c\u3066\u3044\u308b\u3053\u3068\u304c\u78ba\u8a8d\u3067\u304d\u307e\u3057\u305f\uff0e\u3044\u3064\u3082\u901a\u308a\uff0c\u30b7\u30df\u30e5\u30ec\u30fc\u30b7\u30e7\u30f3BOX\u3092\u4f5c\u6210\u3057\uff0c\u6c34\u3092\u6492\u3044\u3066\uff0c\u30a4\u30aa\u30f3\u3092\u52a0\u3048\u3066\u96fb\u8377\u3092\u4e2d\u548c\u3057\u307e\u3059\uff0e<\/p>\n<pre class=\"command-line\"><code class=\"language-bash\" data-line=\"\">$ gmx editconf -f conf.gro -bt cubic -d 1 -o box.gro\n$ gmx solvate -cp box.gro -p topol.top -o solv.gro\n$ gmx grompp -f minim.mdp -c solv.gro -o ion.tpr\n$ gmx genion -s ion.tpr -p topol.top -o ion.gro -nname CL -neutral<\/code><\/pre>\n<p>\u30a4\u30aa\u30f3\u3068\u7f6e\u63db\u3059\u308b\u5206\u5b50\u306fGroup 15 SOL\u3092\u9078\u629e\uff0e<\/p>\n<p>\u30c8\u30dd\u30ed\u30b8\u30fc\u30d5\u30a1\u30a4\u30eb (topol.top) \u306e\u6700\u5f8c\u3092\u78ba\u8a8d\u3059\u308b\u3068\uff0cSOL\u3068CL\u304c\u8ffd\u52a0\u3055\u308c\u3066\u3044\u307e\u3057\u305f\uff0e<\/p>\n<pre class=\"prettyprint\">&#91; molecules &#93;\n; Compound        #mols\nProtein             1\nSOL         5840\nCL               1<\/pre>\n<p>\u30a8\u30cd\u30eb\u30ae\u30fc\u6700\u5c0f\u5316\u3092\u5b9f\u884c\u3057\u3066\u307f\u307e\u3059\uff0e<\/p>\n<pre class=\"command-line\"><code class=\"language-bash\" data-line=\"\">$ gmx grompp -f minim.mdp -c ion.gro -o em.tpr\n$ gmx mdrun -v -deffnm em<\/code><\/pre>\n<p>\u554f\u984c\u306a\u304f\u52d5\u304d\u307e\u3057\u305f\uff0e\u4ee5\u5f8c\uff0cMD\u30b7\u30df\u30e5\u30ec\u30fc\u30b7\u30e7\u30f3\u3092\u884c\u3046\u6642\u306f\uff0cresiduetypes.dat\u30d5\u30a1\u30a4\u30eb\u3092\u30b3\u30d4\u30fc\u3057\u3066\u304d\u3066\uff0c\u4e9c\u925b\u3092\u30bf\u30f3\u30d1\u30af\u8cea\u3068\u3057\u3066\u6271\u3063\u305f\u65b9\u304c\u4f55\u304b\u3068\u4fbf\u5229\u3067\u3059\uff0e<\/p>\n<p>\u932f\u4f53\u306e\u96fb\u8377\u3092\u5206\u6563\u3055\u305b\u3066\u3044\u306a\u3044\u3053\u306e\u5f62\u5f0f\u3068\uff0c\u96fb\u8377\u3092\u5206\u6563\u3055\u305b\u305f\u5f62\u5f0f\u304b\u3089\u5f97\u3089\u308c\u305f\u7d50\u679c\u3067\u3069\u3093\u306a\u9055\u3044\u304c\u3042\u308b\u304b\u306f\u691c\u8a3c\u304c\u5fc5\u8981\u3067\u3059\uff0e<\/p>\n<h2>\u30ea\u30ac\u30f3\u30c9\u3092\u52a0\u3048\u308b<\/h2>\n<p>\u5143\u30d5\u30a1\u30a4\u30eb\u304b\u3089\u5206\u96e2\u3057\u3066\u3044\u305fPRB.pdb\u3092<a href=\"https:\/\/avogadro.cc\/\">Avogadro<\/a>\u3067\u958b\u304d\u307e\u3059\uff08\u03b2\u7248\u306e1.90.0\u3067\u306f\u306a\u304fver 1.2\uff09\uff0eBond order\u3092\u4fee\u6b63\u3057\u3066\uff0c\u6c34\u7d20\u7d50\u5408\u3092\u4ed8\u52a0\uff0cMMFF94s\u529b\u5834\u3067\u69cb\u9020\u6700\u9069\u5316\u3057\u305f\u5f8c\uff0cmol2\u5f62\u5f0f\u3067\u4fdd\u5b58\u3057\u307e\u3059\uff0ePRB.mol2\u30d5\u30a1\u30a4\u30eb\u3092\u30c6\u30ad\u30b9\u30c8\u30a8\u30c7\u30a3\u30bf\u3067\u958b\u3044\u3066\uff0c2\u884c\u76ee\u306e*****\u3092PRB\u3078\uff0c\u6b8b\u57fa\u540d\u306eLIG\u3092PRB\u3078\u66f8\u304d\u63db\u3048\u307e\u3059\uff0e<br \/>\n\u3053\u306emol2\u30d5\u30a1\u30a4\u30eb\u3092<a href=\"https:\/\/cgenff.paramchem.org\/\">CGenFF Server<\/a>\u3078\u30a2\u30c3\u30d7\u30ed\u30fc\u30c9\u3057\uff0cCharmm\u5f62\u5f0f\u306e\u30c8\u30dd\u30ed\u30b8\u30fc\u30d5\u30a1\u30a4\u30eb (PRB.str) \u3092\u5f97\u307e\u3059\uff0e\u4e0a\u8ff0\u3057\u305fMacKerell Lab\u3067\u914d\u5e03\u3055\u308c\u3066\u3044\u308bcgenff_charmm2gmx.py\u3092\u4f7f\u3063\u3066\uff0cGROMACS\u7528\u30c8\u30dd\u30ed\u30b8\u30fc\u306b\u5909\u63db\u3057\u307e\u3059\uff0e<\/p>\n<pre class=\"command-line\"><code class=\"language-bash\" data-line=\"\">$ cgenff_charmm2gmx.py PRB PRB.mol2 PRB.str $GMXPREFIX\/share\/gromacs\/top\/charmm36-nov2016.ff<\/code><\/pre>\n<p>\u3053\u306e\u30d1\u30e9\u30e1\u30fc\u30bf\u3092\u4f7f\u3063\u3066\u6700\u9069\u5316\u3057\u305f\u69cb\u9020\u3067\u3082\uff0cDFT\u8a08\u7b97\uff08M06-2X\/6-311++G(d,p) \u30ec\u30d9\u30eb\uff09\u3067\u5f97\u3089\u308c\u305f\u69cb\u9020\u3068\u6bd4\u8f03\u7684\u4e00\u81f4\u3057\u3066\u3044\u307e\u3057\u305f\uff08\u4e0b\u56f3\u5de6: DFT, \u53f3: CGenFF\uff09\uff0e<\/p>\n<p><img loading=\"lazy\" decoding=\"async\" class=\"size-medium wp-image-1131 alignright\" src=\"https:\/\/www.ag.kagawa-u.ac.jp\/charlesy\/wp\/wp-content\/uploads\/2017\/06\/prb_em_ini-300x225.png\" alt=\"\" width=\"300\" height=\"225\" srcset=\"https:\/\/www.ag.kagawa-u.ac.jp\/charlesy\/wp\/wp-content\/uploads\/2017\/06\/prb_em_ini-300x225.png 300w, https:\/\/www.ag.kagawa-u.ac.jp\/charlesy\/wp\/wp-content\/uploads\/2017\/06\/prb_em_ini-360x270.png 360w, https:\/\/www.ag.kagawa-u.ac.jp\/charlesy\/wp\/wp-content\/uploads\/2017\/06\/prb_em_ini.png 640w\" sizes=\"auto, (max-width: 300px) 100vw, 300px\" \/><img loading=\"lazy\" decoding=\"async\" class=\"size-medium wp-image-1130 alignright\" src=\"https:\/\/www.ag.kagawa-u.ac.jp\/charlesy\/wp\/wp-content\/uploads\/2017\/06\/prb_dft-300x225.png\" alt=\"\" width=\"300\" height=\"225\" srcset=\"https:\/\/www.ag.kagawa-u.ac.jp\/charlesy\/wp\/wp-content\/uploads\/2017\/06\/prb_dft-300x225.png 300w, https:\/\/www.ag.kagawa-u.ac.jp\/charlesy\/wp\/wp-content\/uploads\/2017\/06\/prb_dft-360x270.png 360w, https:\/\/www.ag.kagawa-u.ac.jp\/charlesy\/wp\/wp-content\/uploads\/2017\/06\/prb_dft.png 640w\" sizes=\"auto, (max-width: 300px) 100vw, 300px\" \/><\/p>\n<p>PRB.str\u30d5\u30a1\u30a4\u30eb\u3092\u898b\u3066\u307f\u308b\u3068\uff0c\u30b7\u30af\u30ed\u30d7\u30ed\u30d1\u30f3\u74b0\u3084\u6a4b\u982d\u4f4d\u306e\u70ad\u7d20\u539f\u5b50\uff08CG3RC1\uff09\u306b\u7d50\u5408\u3057\u305f\u9178\u7d20\u539f\u5b50\uff08OG302\uff09\u304c\u95a2\u4e0e\u3059\u308b\u7d50\u5408\u89d2\u306e\u30d1\u30e9\u30e1\u30fc\u30bf\u304c\u70ad\u7d20-\u70ad\u7d20-\u70ad\u7d20\u306e\u30d1\u30e9\u30e1\u30fc\u30bf\u304b\u3089\u6d41\u7528\u3055\u308c\u3066\u3044\u305f\u306e\u3067\uff0c\u3053\u308c\u3089\u306e\u7d50\u5408\u89d2\u306e\u30d1\u30e9\u30e1\u30fc\u30bf\u3092\u4fee\u6b63\u3057\u307e\u3057\u305f\uff0e<br \/>\nAtom types\u306f<\/p>\n<ul>\n<li>\nCG3C31 &#8211; cyclopropyl carbon<\/li>\n<li>\nCG3RC1 &#8211; bridgehead in bicyclic systems containing at least one 5-membered or smaller ring<\/li>\n<li>OG302 &#8211; ester -O-<\/li>\n<\/ul>\n<p>\u3067\u3059\uff0e<\/p>\n<pre class=\"prettyprint\">&#91; bondtypes &#93;\n&#91; angletypes &#93;\n;      i        j        k  func       theta0       ktheta          ub0          kub\n   CG311   CG3RC1    OG302     5   113.500000   488.272800   0.25610000      9338.69\n   CG321   CG3RC1    OG311     5   113.500000   488.272800   0.25610000      9338.69\n  CG3C31   CG3RC1    OG302     5   111.000000   446.432800   0.25610000      6694.40\n  CG3RC1   CG3RC1    OG302     5   111.000000   446.432800   0.25610000      6694.40\n\n\u4ee5\u4e0b\u306e\u3088\u3046\u306b\u4fee\u6b63\n   CG311   CG3RC1    OG302     5   110.000000   633.457600   0.00000000         0.00\n   CG321   CG3RC1    OG311     5   113.500000   633.457600   0.00000000         0.00\n  CG3C31   CG3RC1    OG302     5   111.000000   633.457600   0.00000000         0.00\n  CG3RC1   CG3RC1    OG302     5   114.500000   633.457600   0.00000000         0.00<\/pre>\n<p>Open Babel\u3092\u4f7f\u3063\u3066\u751f\u6210\u3055\u308c\u305fprb_ini.pdb\u3092gromacs\u5f62\u5f0f\u306b\u5909\u63db\u3057\u307e\u3059\uff0e<br \/>\n$ obabel -ipdb prb_ini.pdb -Oprb_ini.gro<\/p>\n<p>\u524d\u7bc0\u306e\u51e6\u7406\u9014\u4e2d\u306econf.gro\u306e\u5192\u982d\u306e\u539f\u5b50\u6570\u306bPRB\u5206\u5b50\u306e\u539f\u5b50\u6570\u3092\u8db3\u3057\u3066\uff08805\u2192864\uff09\uff0c\u30d5\u30a1\u30a4\u30eb\u306e\u6700\u5f8c\u306bprb_ini.gro\u4e2d\u306e\u5ea7\u6a19\u90e8\u5206\u3092\u304f\u3063\u3064\u3051\u307e\u3059 (conf_ligand.gro\u3068\u3057\u3066\u4fdd\u5b58)\uff0e<\/p>\n<pre class=\"prettyprint\">\u9014\u4e2d\u304b\u3089\n   53ZN      ZN  804   2.174   1.867   4.287\n   54ZN      ZN  805   1.196   1.317   3.294\n    1PRB     C1    1   1.345   2.964   2.324\n    1PRB     C2    2   1.438   3.077   2.292\n    1PRB     O1    3   1.227   3.011   2.371\n\uff08\u4e2d\u7565\uff09\n    1PRB    H29   58   1.137   2.370   2.862\n    1PRB    H30   59   1.319   2.314   2.651\n   2.74916   2.64127   2.90824<\/pre>\n<p>topol.top\u306e\u6700\u521d\u306e\u65b9\u3067\u30ea\u30ac\u30f3\u30c9\u306e\u30c8\u30dd\u30ed\u30b8\u30fc\u3092\u8aad\u307f\u8fbc\u3080\u304b\uff0c\u66f8\u304d\u8fbc\u307f\u307e\u3059\uff0e\u6700\u5f8c\u306e [ molecules ] \u30bb\u30af\u30b7\u30e7\u30f3\u306bPRB\u5206\u5b50\u3092\u52a0\u3048\u307e\u3059\uff0e<\/p>\n<pre class=\"prettyprint\">; Include forcefield parameters\n#include &#34;charmm36-nov2016.ff&#47;forcefield.itp&#34;\n\n#include &#34;prb.prm&#34;\n\n#include &#34;prb.itp&#34;\n\n&#91; moleculetype &#93;\n; Name            nrexcl\nProtein             3\n\n\uff08\u4e2d\u7565\uff09\n\n&#91; molecules &#93;\n; Compound        #mols\nProtein             1\nPRB\t\t    1<\/pre>\n<pre class=\"command-line\"><code class=\"language-bash\" data-line=\"\">$ gmx editconf -f conf_ligand.gro -bt cubic -d 1 -o box_ligand.gro\n$ gmx solvate -cp box_ligand.gro -p topol.top -o solv_ligand.gro\n$ gmx grompp -f minim.mdp -c solv_ligand.gro -o ion.tpr<\/code><\/pre>\n<p>\u4ee5\u4e0b\u306e\u3088\u3046\u306a\u30a8\u30e9\u30fc\u304c\u51fa\u307e\u3059\uff0e<\/p>\n<pre class=\"prettyprint\">ERROR 1 &#91;file prb.prm, line 81&#93;:\n  Encountered a second block of parameters for dihedral type 9 for the same\n  atoms, with either different parameters and&#47;or the first block has\n  multiple lines. This is not supported.<\/pre>\n<p>CGenFF server\u306e\u529b\u5834\u306e\u30d0\u30fc\u30b8\u30e7\u30f3\u306f3.0.3\u3067\u3059\u304c\uff0ccharmm36-nov2016.ff\u306b\u542b\u307e\u308c\u308bCGenFF\u306e\u30d0\u30fc\u30b8\u30e7\u30f3\u306f4.0\u306b\u30a2\u30c3\u30d7\u30c7\u30fc\u30c8\u3055\u308c\u3066\u3044\u308b\u306e\u3067\uff0c\u30d1\u30e9\u30e1\u30fc\u30bf\u304c\u91cd\u8907\u3057\u3066\u3044\u307e\u3057\u305f\uff0eprb.prm\u30d5\u30a1\u30a4\u30eb\u306e81-83\u884c\u76ee\u3092\u30b3\u30e1\u30f3\u30c8\u30a2\u30a6\u30c8\u304b\u524a\u9664\u3057\u307e\u3059\uff0e<\/p>\n<pre class=\"command-line\"><code class=\"language-bash\" data-line=\"\">$ gmx grompp -f minim.mdp -c solv.gro -o ion.tpr\n$ gmx genion -s ion.tpr -p topol.top -o ion_ligand.gro -nname CL -neutral\n$ gmx grompp -f minim.mdp -c ion_ligand.gro -o em_ligand.tpr\n$ gmx mdrun -v -deffnm em_ligand\n$ gmx trjconv -f em_ligand.gro -s em_ligand.tpr -o em_ligand.pdb<\/code><\/pre>\n<p><img loading=\"lazy\" decoding=\"async\" src=\"https:\/\/www.ag.kagawa-u.ac.jp\/charlesy\/wp\/wp-content\/uploads\/2017\/06\/charmm-300x225.png\" alt=\"\" width=\"300\" height=\"225\" class=\"aligncenter size-medium wp-image-1137\" srcset=\"https:\/\/www.ag.kagawa-u.ac.jp\/charlesy\/wp\/wp-content\/uploads\/2017\/06\/charmm-300x225.png 300w, https:\/\/www.ag.kagawa-u.ac.jp\/charlesy\/wp\/wp-content\/uploads\/2017\/06\/charmm-360x270.png 360w, https:\/\/www.ag.kagawa-u.ac.jp\/charlesy\/wp\/wp-content\/uploads\/2017\/06\/charmm.png 640w\" sizes=\"auto, (max-width: 300px) 100vw, 300px\" \/><\/p>\n<p>(\u4e86)<\/p>\n","protected":false},"excerpt":{"rendered":"<p>\u74b0\u5883: macOS Sierra 10.12.4, Grom &#8230;<\/p>\n","protected":false},"author":1,"featured_media":1131,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","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":""},"categories":[5],"tags":[],"class_list":["post-1115","post","type-post","status-publish","format-standard","has-post-thumbnail","hentry","category-5","ja"],"aioseo_notices":[],"aioseo_head":"\n\t\t<!-- All in One SEO 4.9.8 - aioseo.com -->\n\t<meta name=\"description\" content=\"\u74b0\u5883: macOS Sierra 10.12.4, Gromacs 2016.3. 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