{"id":5016,"date":"2025-06-26T11:16:35","date_gmt":"2025-06-26T02:16:35","guid":{"rendered":"https:\/\/www.ag.kagawa-u.ac.jp\/charlesy\/?p=5016"},"modified":"2025-06-26T13:36:09","modified_gmt":"2025-06-26T04:36:09","slug":"conformational-search-of-small-molecules-using-gromacs","status":"publish","type":"post","link":"https:\/\/www.ag.kagawa-u.ac.jp\/charlesy\/2025\/06\/26\/conformational-search-of-small-molecules-using-gromacs\/","title":{"rendered":"Conformational Search of Small Molecules Using GROMACS"},"content":{"rendered":"\n<figure class=\"wp-block-image aligncenter size-large\"><img loading=\"lazy\" decoding=\"async\" width=\"1024\" height=\"397\" src=\"https:\/\/www.ag.kagawa-u.ac.jp\/charlesy\/wp\/wp-content\/uploads\/2016\/10\/ILVconformationseyecatch-1024x397.png\" alt=\"\" class=\"wp-image-370\" srcset=\"https:\/\/www.ag.kagawa-u.ac.jp\/charlesy\/wp\/wp-content\/uploads\/2016\/10\/ILVconformationseyecatch-1024x397.png 1024w, https:\/\/www.ag.kagawa-u.ac.jp\/charlesy\/wp\/wp-content\/uploads\/2016\/10\/ILVconformationseyecatch-300x116.png 300w, https:\/\/www.ag.kagawa-u.ac.jp\/charlesy\/wp\/wp-content\/uploads\/2016\/10\/ILVconformationseyecatch-768x297.png 768w, https:\/\/www.ag.kagawa-u.ac.jp\/charlesy\/wp\/wp-content\/uploads\/2016\/10\/ILVconformationseyecatch-360x139.png 360w, https:\/\/www.ag.kagawa-u.ac.jp\/charlesy\/wp\/wp-content\/uploads\/2016\/10\/ILVconformationseyecatch.png 1420w\" sizes=\"auto, (max-width: 1024px) 100vw, 1024px\" \/><\/figure>\n\n\n\n<p class=\"wp-block-paragraph\">GROMACS\u306eSimulated annealing method\u3092\u4f7f\u7528\u3057\u3066\uff0c\u771f\u7a7a\u4e2d\u3067\u306e\u4f4e\u5206\u5b50\u5316\u5408\u7269\u306e\u914d\u5ea7\u63a2\u7d22\u3092\u884c\u3046\uff0e<br>This tutorial assumes you are using a GROMACS version in the 2025 series with AmberTools 25.<br>Updated on June&nbsp;26, 2025. <\/p>\n\n\n\n<ul style=\"list-style-type: square;\">\n<li>OS: macOS Sequoia 15.5, Chip: Apple M4, RAM: 16 GB\uff0e<\/li>\n<li>AmberTools 25<\/li>\n<li>GROMACS 2025.1<\/li>\n<li>VMD 1.9.4a57-arm64-Rev12<\/li>\n<\/ul>\n\n\n\n<p class=\"wp-block-paragraph\">\uff082016\u5e7410\u670817\u65e5\u306b\u56fa\u5b9a\u30da\u30fc\u30b8\u3068\u3057\u3066\u516c\u958b\u30022025\u5e746\u670826\u65e5\u306b\u56fa\u5b9a\u30da\u30fc\u30b8\u304b\u3089\u8a18\u4e8b\u306b\u79fb\u884c\u3057\u3001\u8a18\u8ff0\u5185\u5bb9\u3092\u66f4\u65b0\u3057\u305f\u3002\uff09<\/p>\n\n\n\n<p class=\"wp-block-paragraph\">\u6ce8\u610f: \u4ee5\u4e0b\u306e\u65b9\u6cd5\u306f\u6c34\u4e2d\u3067\u306e\u30b7\u30df\u30e5\u30ec\u30fc\u30b7\u30e7\u30f3\u306b\u6700\u9069\u5316\u3055\u308c\u305f\u529b\u5834\u30d1\u30e9\u30e1\u30fc\u30bf\u3092\u4f7f\u3063\u3066\u771f\u7a7a\u4e2d\u3067\u306e\u30b7\u30df\u30e5\u30ec\u30fc\u30b7\u30e7\u30f3\u3092\u884c\u3046\u3082\u306e\u3067\uff0c\u6b63\u78ba\u306a\u30b7\u30df\u30e5\u30ec\u30fc\u30b7\u30e7\u30f3\u3067\u306f\u306a\u304f\u69d8\u3005\u306a\u914d\u5ea7\u3092\u767a\u751f\u3055\u305b\u308b\u3053\u3068\u3092\u76ee\u7684\u3068\u3057\u3066\u3044\u307e\u3059\uff0e\u672c\u6765\u3053\u3046\u3044\u3063\u305f\u76ee\u7684\u306b\u306fSpartan\u3084Macromodel\u3067\u4f7f\u308f\u308c\u308b\u30e2\u30f3\u30c6\u30ab\u30eb\u30ed\u6cd5\u304c\u3042\u308a\u307e\u3059\u304c\uff0c\u7121\u511f\u306eGromacs\u3067\u4f3c\u305f\u3053\u3068\u3092\u3067\u304d\u306a\u3044\u304b\u3068\u3084\u3063\u3066\u307f\u305f\u3082\u306e\u3067\u3059\uff0eSimulated annealing\u306e\u6e29\u5ea6\u306e\u5024\u3084\u4e0a\u3052\u65b9\uff0c\u4e0b\u3052\u65b9\uff0c\u6642\u9593\u306b\u3064\u3044\u3066\u8a73\u7d30\u306f\u691c\u8a0e\u3057\u3066\u3044\u307e\u305b\u3093\uff0e<\/p>\n\n\n\n<h2 class=\"wp-block-heading\">Step 1: Building a small molecule<\/h2>\n\n\n\n<p class=\"wp-block-paragraph\">\u307e\u305a\uff0c<a href=\"https:\/\/avogadro.cc\/\" title=\"\">Avogadro<\/a>\u3092\u4f7f\u7528\u3057\u3066\u4f4e\u5206\u5b50\u306e3\u6b21\u5143\u69cb\u9020\u3092\u4f5c\u6210\u3059\u308b\uff0e\u3053\u306e\u30c1\u30e5\u30fc\u30c8\u30ea\u30a2\u30eb\u3067\u306f\uff0c\u4f8b\u3068\u3057\u30669\u54e1\u74b0\u30e9\u30af\u30bf\u30e0\u3067\u3042\u308bindolactam-V (ILV) \u3092\u53d6\u308a\u4e0a\u3052\u308b (<a href=\"https:\/\/www.ag.kagawa-u.ac.jp\/charlesy\/wp\/wp-content\/uploads\/2016\/10\/ILV.mol2_.txt\">ILV.mol2<\/a>).GAFF\u529b\u5834\u306fTIP3P\u6c34\u30e2\u30c7\u30eb\u4e2d\u3067\u306e\u4f7f\u7528\u304c\u9069\u5207\u3060\u304c\uff0c\u4eca\u56de\u306f\u30a8\u30cd\u30eb\u30ae\u30fc\u969c\u58c1\u3092\u8d85\u3048\u3066\u30b3\u30f3\u30db\u30e1\u30fc\u30b7\u30e7\u30f3\u3092\u751f\u6210\u3059\u308b\u3053\u3068\u304c\u76ee\u7684\u306a\u306e\u3067\u771f\u7a7a\u4e2d\u3067\u8a08\u7b97\u3059\u308b (\u8a08\u7b97\u3082\u65e9\u304f\u7d42\u308f\u308b)\uff0e<\/p>\n\n\n\n<h2 class=\"wp-block-heading\">Step 2: Preparing the small molecule topology<\/h2>\n\n\n\n<p class=\"wp-block-paragraph\"><a href=\"https:\/\/ambermd.org\/AmberTools.php\" title=\"\">AmberTools<\/a>\uff08\u7121\u6599\u3001<a href=\"https:\/\/qiita.com\/Ag_smith\/items\/9526142858f8ea5248c1\" title=\"\">macOS 15\u3078\u306e\u30a4\u30f3\u30b9\u30c8\u30fc\u30eb\u65b9\u6cd5<\/a>\uff09\u306b\u542b\u307e\u308c\u308bantechamber\u3092\u4f7f\u7528\u3059\u308b\uff0e<\/p>\n\n\n<div class=\"wp-block-syntaxhighlighter-code command-line language-bash\"><pre class=\"brush: bash; title: ; notranslate\" title=\"\">\n$ antechamber -fi mol2 -fo prepi -i ILV.mol2 -o ILV.prep -c bcc -at gaff2 -rn ILV\n$ parmchk2 -i ILV.prep -o ILV.frcmod -f prepi -s gaff2\n$ tleap\n&gt; source leaprc.gaff2\n&gt; loadamberprep ILV.prep\n&gt; loadamberparams ILV.frcmod\n&gt; mol = loadpdb NEWPDB.PDB\n&gt; saveamberparm mol ILV.prmtop ILV.inpcrd\n&gt; quit\n<\/pre><\/div>\n\n\n<p class=\"wp-block-paragraph\">tleap\u306e\u5b9f\u884c\u306f\u4e0b\u8a18\u306e\u30b9\u30af\u30ea\u30d7\u30c8\u3092\u4fdd\u5b58\u3057\u3066\u5b9f\u884c\u3057\u3066\u3082\u3088\u3044\uff0e<br><code class=\"\" data-line=\"\">tleap.in<\/code><\/p>\n\n\n\n<pre class=\"prettyprint\">source leaprc.gaff2\nloadamberprep ILV.prep\nloadamberparams ILV.frcmod\nmol = loadpdb NEWPDB.PDB\nsaveamberparm mol ILV.prmtop ILV.inpcrd\nquit<\/pre>\n\n\n<div class=\"wp-block-syntaxhighlighter-code command-line language-bash\"><pre class=\"brush: plain; title: ; notranslate\" title=\"\">\n$ tleap -s -f tleap.in &gt; tleap.out\n<\/pre><\/div>\n\n\n<p class=\"wp-block-paragraph\">AmberTools\u4ed8\u5c5e\u306eParmEd\u3092\u4f7f\u7528\u3057\u3066\uff0cAmber\u5f62\u5f0f\u306e\u30d5\u30a1\u30a4\u30eb\u3092GROMACS\u5f62\u5f0f\u3078\u5909\u63db\u3059\u308b\uff0e<br>\u4ee5\u4e0b\u306escript (ambergromacs.py) \u3092\u5b9f\u884c\u3059\u308b\uff0e<\/p>\n\n\n\n<pre class=\"prettyprint\">import parmed as pmd\n# Load AMBER format\namber = pmd.load_file(&#39;ILV.prmtop&#39;,xyz=&#39;ILV.inpcrd&#39;)\n# Save a GROMACS topology and GRO files\namber.save(&#39;gromacs.top&#39;)\namber.save(&#39;gromacs.gro&#39;)<\/pre>\n\n\n<div class=\"wp-block-syntaxhighlighter-code command-line language-bash\"><pre class=\"brush: plain; title: ; notranslate\" title=\"\">\n$ $AMBERHOME\/miniconda\/bin\/python .\/ambergromacs.py\n<\/pre><\/div>\n\n\n<p class=\"wp-block-paragraph\">gromacs.top\u3068gromacs.gro\u304c\u66f8\u304d\u51fa\u3055\u308c\u307e\u3059\uff0e<\/p>\n\n\n\n<p class=\"wp-block-paragraph\">antechamber\u3067\u751f\u6210\u3057\u305f\u30c8\u30dd\u30ed\u30b8\u30fc\u3067\u306f\uff0c\u539f\u5b50\u96fb\u8377\u306e\u7dcf\u548c\u304c0\u304b\u3089\u305a\u308c\u308b\u6642\u304c\u3042\u308b\uff0e\u305d\u3046\u3044\u3063\u305f\u5834\u5408\u306f\uff0cGROMACS\u306etop\u30d5\u30a1\u30a4\u30a4\u30eb\u3092\u30c6\u30ad\u30b9\u30c8\u30a8\u30c7\u30a3\u30bf\u3067\u958b\u304d\uff0c\u539f\u5b50\u96fb\u8377\u306e\u7dcf\u548c\u304c0\u306b\u306a\u308b\u3088\u3046\u306b\u4fee\u6b63\u3059\u308b\uff0e\u5927\u62b5\u306f\u96fb\u8377\u306e\u305a\u308c\u3066\u3044\u308b\u5206\u3092\u5168\u539f\u5b50\u306b\u5747\u7b49\u306b\u5272\u308a\u632f\u308b\uff0e<\/p>\n\n\n\n<h2 class=\"wp-block-heading\">Step 3: Running simulated annealing protocol<\/h2>\n\n\n\n<p class=\"wp-block-paragraph\">Preparing mdp file for a test run (sa5cycles.mdp).<\/p>\n\n\n\n<p class=\"wp-block-paragraph\"><span style=\"font-weight: bold;\">sa5cycles.mdp<\/span><\/p>\n\n\n\n<pre class=\"prettyprint\">; Run parameters\nintegrator\t= md\t\t; leap-frog integrator\nnsteps\t\t= 25000\t\t; 1 * 25000 = 25 ps; 5 cycles\ndt\t\t= 0.001\t\t; 1 fs\n; Output control\nnstxout\t\t= 100\t\t; save coordinates every 0.2 ps\nnstvout\t\t= 100\t\t; save velocities every 0.2 ps\nnstenergy\t= 100\t\t; save energies every 0.2 ps\nnstlog\t\t= 100\t\t; update log file every 0.2 ps\n; Bond parameters\ncontinuation\t= no\t\t; first dynamics run\nconstraint_algorithm = lincs\t; holonomic constraints \nconstraints\t= all-bonds\t; all bonds (even heavy atom-H bonds) constrained\ncomm_mode       = angular\nlincs_iter\t= 1\t\t; accuracy of LINCS\nlincs_order\t= 4\t\t; also related to accuracy\nlincs-warnangle = 90\n; Neighborsearching\ncutoff-scheme   = Verlet\t\npbc\t\t= xyz\n; Temperature coupling is on\ntcoupl\t\t= V-rescale\t; modified Berendsen thermostat\ntc-grps\t\t= Other\t; two coupling groups - more accurate\ntau_t\t\t= 0.1\t; time constant, in ps\nref_t\t\t= 300 \t; reference temperature, one for each group, in K\n; Velocity generation\n; SIMULATED ANNEALING CONTROL\nannealing       =  periodic\nannealing_npoints  = 6\nannealing_time  = 0 1 2 3 4 5\nannealing_temp  = 1500 1500 1500 100 0 0\n<\/pre>\n\n\n\n<p class=\"wp-block-paragraph\">Generate .tpr file.<\/p>\n\n\n<div class=\"wp-block-syntaxhighlighter-code command-line language-bash\"><pre class=\"brush: plain; title: ; notranslate\" title=\"\">\n$ gmx editconf -f gromacs.gro -bt cubic -d 1 -o box.gro\n$ gmx grompp -f sa5cycles.mdp -c box.gro -p gromacs.top -o sa_test.tpr -maxwarn 1\n<\/pre><\/div>\n\n\n<p class=\"wp-block-paragraph\">Run test simulation.<\/p>\n\n\n<div class=\"wp-block-syntaxhighlighter-code command-line language-bash\"><pre class=\"brush: plain; title: ; notranslate\" title=\"\">\n$ gmx mdrun -v -deffnm sa_test -ntmpi 1 -ntomp 1\n<\/pre><\/div>\n\n\n<p class=\"wp-block-paragraph\">\u6e29\u5ea6\u304c\u8a2d\u5b9a\u901a\u308a\u5909\u5316\u3057\u3066\u3044\u308b\u304b\u3092gmx energy\u3067\u78ba\u8a8d\uff0e<\/p>\n\n\n<div class=\"wp-block-syntaxhighlighter-code command-line language-bash\"><pre class=\"brush: plain; title: ; notranslate\" title=\"\">\n$ gmx energy -f sa_test.edr -o temperature.xvg\n$ xmgrace temperature.xvg # \u306a\u3044\u5834\u5408\u306f brew install grace\n<\/pre><\/div>\n\n\n<p class=\"wp-block-paragraph\">Type \u201c12 0\u201d and enter.<br>Visualize temperature.xvg file.<\/p>\n\n\n<div class=\"wp-block-syntaxhighlighter-code command-line language-bash\"><pre class=\"brush: plain; title: ; notranslate\" title=\"\">\n$ xmgrace temperature.xvg\n<\/pre><\/div>\n\n\n<figure class=\"wp-block-image alignright\"><img loading=\"lazy\" decoding=\"async\" width=\"300\" height=\"232\" src=\"https:\/\/www.ag.kagawa-u.ac.jp\/charlesy\/wp\/wp-content\/uploads\/2016\/10\/temperature-300x232.png\" alt=\"temperature\" class=\"wp-image-393\" srcset=\"https:\/\/www.ag.kagawa-u.ac.jp\/charlesy\/wp\/wp-content\/uploads\/2016\/10\/temperature-300x232.png 300w, https:\/\/www.ag.kagawa-u.ac.jp\/charlesy\/wp\/wp-content\/uploads\/2016\/10\/temperature-768x593.png 768w, https:\/\/www.ag.kagawa-u.ac.jp\/charlesy\/wp\/wp-content\/uploads\/2016\/10\/temperature-349x270.png 349w, https:\/\/www.ag.kagawa-u.ac.jp\/charlesy\/wp\/wp-content\/uploads\/2016\/10\/temperature.png 792w\" sizes=\"auto, (max-width: 300px) 100vw, 300px\" \/><\/figure>\n\n\n\n<p class=\"wp-block-paragraph\">Simulated annealing\u304c\u5b9f\u884c\u3067\u304d\u3066\u3044\u308b\u3068\u78ba\u8a8d\u3067\u304d\u305f (\u53f3\u56f3) \u306e\u3067100\u30b5\u30a4\u30af\u30eb\u306esimulated annealing\u3092\u5b9f\u884c\u3059\u308b\uff0e\u5404\u30b5\u30a4\u30af\u30eb\u6bce\u306b\u69cb\u9020\u304a\u3088\u3073\u30a8\u30cd\u30eb\u30ae\u30fc\u3092\u4fdd\u5b58\u3059\u308b (sa.mdp)\uff0e<br><span style=\"font-weight: bold;\">sa.mdp<\/span><\/p>\n\n\n\n<pre class=\"prettyprint\">; Run parameters\nintegrator\t= md\t\t; leap-frog integrator\nnsteps\t\t= 500000        ; 1 * 500000 = 500 ps; 100 cycles\ndt\t\t= 0.001\t\t; 1 fs\n; Output control\nnstxout\t\t= 5000\t\t; save coordinates every 0.2 ps\nnstvout\t\t= 5000\t\t; save velocities every 0.2 ps\nnstenergy\t= 5000\t\t; save energies every 0.2 ps\nnstlog\t\t= 5000\t\t; update log file every 0.2 ps\n; Bond parameters\ncontinuation\t= no\t\t; first dynamics run\nconstraint_algorithm = lincs\t; holonomic constraints \nconstraints\t= all-bonds\t; all bonds (even heavy atom-H bonds) constrained\ncomm_mode       = angular\nlincs_iter\t= 1\t\t; accuracy of LINCS\nlincs_order\t= 4\t\t; also related to accuracy\nlincs-warnangle = 90\n; Neighborsearching\ncutoff-scheme   = Verlet\t\npbc\t\t= xyz\n; Temperature coupling is on\ntcoupl\t\t= V-rescale\t; modified Berendsen thermostat\ntc-grps\t\t= Other\t; two coupling groups - more accurate\ntau_t\t\t= 0.1\t; time constant, in ps\nref_t\t\t= 300 \t; reference temperature, one for each group, in K\n; Velocity generation\n; SIMULATED ANNEALING CONTROL\nannealing       =  periodic\nannealing_npoints  = 6\nannealing_time  = 0 1 2 3 4 5\nannealing_temp  = 1500 1500 1500 100 0 0\n<\/pre>\n\n\n\n<p class=\"wp-block-paragraph\">\u3042\u308b\u7a0b\u5ea6\u9ad8\u3044\u6e29\u5ea6\u306e\u5834\u5408\uff0c\u70ad\u7d20-\u70ad\u7d20\u4e8c\u91cd\u7d50\u5408\u3092\u6301\u3064\u5206\u5b50\u3067\u306f\u30b7\u30b9-\u30c8\u30e9\u30f3\u30b9\u7570\u6027\u5316\u304c\u8d77\u3053\u3063\u3066\u3057\u307e\u3046\u306e\u3067\u6ce8\u610f\u3059\u308b\u3053\u3068\uff0e<\/p>\n\n\n<div class=\"wp-block-syntaxhighlighter-code command-line language-bash\"><pre class=\"brush: plain; title: ; notranslate\" title=\"\">\n$ gmx grompp -f sa.mdp -c box.gro -p gromacs.top -o sa.tpr -maxwarn 1\n$ gmx mdrun -v -deffnm sa -ntmpi 1 -ntomp 1\n<\/pre><\/div>\n\n\n<p class=\"wp-block-paragraph\">7\u79d2\u7a0b\u3067\u8a08\u7b97\u7d42\u4e86\uff0e<\/p>\n\n\n\n<h2 class=\"wp-block-heading\">Step 4: \u7d50\u679c\u306e\u89e3\u6790<\/h2>\n\n\n\n<p class=\"wp-block-paragraph\">Gromacs\u4ed8\u5c5e\u306eg_cluster\u3082\u4f7f\u7528\u3067\u304d\u308b\u304c\uff0cVMD\u306eextension\u3092\u4f7f\u7528\u3059\u308b (<a href=\"https:\/\/github.com\/luisico\/clustering\">clustering<\/a>).<br>Clustering 2.0\u3092\u30c0\u30a6\u30f3\u30ed\u30fc\u30c9\u3057\u3066\u89e3\u51cd\u3059\u308b\uff0e\u9069\u5f53\u306a\u5834\u6240\u306bdirectory\u3092\u30b3\u30d4\u30fc\uff0e~\/.vmdrc\u306b\u4ee5\u4e0b\u306e\u3088\u3046\u306b\u66f8\u3044\u3066\u304a\u304f\uff0e<\/p>\n\n\n<div class=\"wp-block-syntaxhighlighter-code command-line language-bash\"><pre class=\"brush: plain; title: ; notranslate\" title=\"\">\nmenu main on\nset auto_path &#x5B;linsert $auto_path 0 {clustering\u30d5\u30a9\u30eb\u30c0\u306e\u5834\u6240}]\nvmd_install_extension clustering clustering &quot;WMC PhysBio\/Clustering&quot;\n<\/pre><\/div>\n\n\n<p class=\"wp-block-paragraph\">VMD\u3092\u8d77\u52d5\u3057\u3066\u5148\u7a0b\u306esimulated annealing\u306etrajectory\u3092\u8868\u793a\uff0e<\/p>\n\n\n<div class=\"wp-block-syntaxhighlighter-code command-line language-bash\"><pre class=\"brush: plain; title: ; notranslate\" title=\"\">\n$ vmd sa.gro sa.trr # vmd: aliased to \/Applications\/VMD\\ 1.9.4a57-arm64-Rev12.app\/Contents\/vmd\/vmd_MACOSXARM64\n<\/pre><\/div>\n\n\n<p class=\"wp-block-paragraph\">Extensions\u2192Analysis\u2192RMSD Trajectory Tool<br>selection\u3092protein\u304b\u3089resname ILV\u306b\u66f8\u304d\u63db\u3048\uff0cAlign\u30dc\u30bf\u30f3\u3092\u30af\u30ea\u30c3\u30af\u3059\u308b\u3068\u521d\u671f\u69cb\u9020\u3092\u57fa\u6e96\u306b\u5206\u5b50\u306e\u5411\u304d\u304c\u63c3\u3046\uff0e<br>Extensions\u2192WMC PhysBio\u2192Clustering \u3092\u8d77\u52d5\u3057\u3066\u30af\u30e9\u30b9\u30bf\u30fc\u89e3\u6790\u3092\u884c\u3046\uff0e<br>selection\u3092resname ILV\u306b\u66f8\u304d\u63db\u3048\u308b\uff0enoh\u306e\u30c1\u30a7\u30c3\u30af\u3092\u306f\u305a\u3059\uff0enum\u309220\u306b\u5909\u66f4\u3059\u308b\uff0e<br>Use measure cluster\u306eCutoff\u30921\u304b\u30890.9\u306b\u5909\u66f4\u3057\u3066\uff0cCalculate\u30dc\u30bf\u30f3\u3092\u30af\u30ea\u30c3\u30af\u3059\u308b\u3068\u4e0b\u90e8\u306b\u30af\u30e9\u30b9\u30bf\u30fc\u304c\u8272\u5206\u3051\u3055\u308c\u3066\u8868\u793a\u3055\u308c\u308b\uff0e\u7d50\u679c\u3092\u76ee\u3067\u898b\u3066\u89e3\u6790\u3059\u308b\uff0e<br>ILV\u306f\u6eb6\u6db2\u4e2d\u30672\u3064\u306e\u5b89\u5b9a\u30b3\u30f3\u30db\u30de\u30fc\uff08<span style=\"font-style: italic;\">cis<\/span>-amide\u578b\u3068<span style=\"font-style: italic;\">trans<\/span>-amide\u578b\uff09\u306e\u5e73\u8861\u6df7\u5408\u7269\u3068\u3057\u3066\u5b58\u5728\u3057\u3066\u304a\u308a\uff0cNMR\u3067\u306f\u305d\u308c\u305e\u308c\u306e\u30b3\u30f3\u30db\u30de\u30fc\u306e\u30b7\u30b0\u30ca\u30eb\u304c\u89b3\u6e2c\u3055\u308c\u308b\uff0e\u4eca\u56de\u306e\u30b7\u30df\u30e5\u30ec\u30fc\u30b7\u30e7\u30f3\u306b\u8907\u6570\u56de\u73fe\u308f\u308c\u305f\u30b3\u30f3\u30db\u30e1\u30fc\u30b7\u30e7\u30f3\u306e\u30af\u30e9\u30b9\u30bf\u30fc\u306f\u4ee5\u4e0b\u306e\u901a\u308a (Conformers are classified on the basis of <a href=\"http:\/\/dx.doi.org\/10.1021\/jo00049a020\" title=\"\">Itai\u2019s nomenclature<\/a>)\uff0e<\/p>\n\n\n\n<ul class=\"wp-block-list\">\n<li>Cluster 0 (23): Sofa conformer with <span style=\"font-style: italic;\">trans<\/span>-amide. <strong>NMR\u30b9\u30da\u30af\u30c8\u30eb\u3068\u4e00\u81f4\u3059\u308b\uff0e\u203b\u521d\u671f\u69cb\u9020<\/strong><\/li>\n\n\n\n<li>Cluster 1 (11): &nbsp;Sofa conformer. Cluster 0\u3068\u306f12\u4f4d\u306e\u30a4\u30bd\u30d7\u30ed\u30d4\u30eb\u57fa\u306e\u914d\u5ea7\u304c\u7570\u306a\u308b\uff0e<\/li>\n\n\n\n<li>Cluster 2&nbsp;(5): &nbsp;Sofa conformer. Cluster 0\u3068\u306f\u30d2\u30c9\u30ed\u30ad\u30b7\u30e1\u30c1\u30eb\u57fa\u306e\u914d\u5ea7\u304c\u7570\u306a\u308b\u306e\u307f\u3067\u5b9f\u8cea\u540c\u3058\uff0e<\/li>\n\n\n\n<li>Cluster 3&nbsp;(5): <span style=\"font-style: italic;\">r<\/span>&#8211;<span style=\"font-style: italic;\">Cis<\/span>-sofa conformer. NMR\u3067\u306f\u89b3\u6e2c\u3055\u308c\u306a\u3044\uff0e<\/li>\n\n\n\n<li>Cluster 4&nbsp;(4): Twist conformer with <span style=\"font-style: italic;\">cis<\/span>-amide. <strong>NMR\u30b9\u30da\u30af\u30c8\u30eb\u3068\u4e00\u81f4\u3059\u308b<\/strong>\uff0e<\/li>\n\n\n\n<li>Cluter 5 (2):&nbsp;<span style=\"font-style: italic;\">r<\/span>&#8211;<span style=\"font-style: italic;\">Trans<\/span>-fold conformer.<\/li>\n<\/ul>\n\n\n\n<p class=\"wp-block-paragraph\">\u5b89\u5b9a\u30b3\u30f3\u30db\u30de\u30fc\u304c\u540c\u5b9a\u3067\u304d\u306a\u3044\u5834\u5408\u306f\uff0c\u4ed6\u306e\u529b\u5834\u3084MO\u8a08\u7b97\u3067\u30a8\u30cd\u30eb\u30ae\u30fc\u6bd4\u8f03\u3092\u884c\u3046\uff0e\u307e\u305f\uff0c\u8907\u6570\u306e\u30b3\u30f3\u30db\u30de\u30fc\u3092Docking simulation\u306b\u4f7f\u7528\u3057\u3066\u3082\u3088\u3044\uff0e<\/p>\n","protected":false},"excerpt":{"rendered":"","protected":false},"author":1,"featured_media":370,"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":"ja","_original_post":"https:\/\/www.ag.kagawa-u.ac.jp\/charlesy\/?p=5016","footnotes":""},"categories":[5],"tags":[],"class_list":["post-5016","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 4.9.9 - aioseo.com -->\n\t<meta name=\"description\" content=\"GROMACS\u306eSimulated annealing 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