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<div class="section" id="sampling-a-backbone-only-configuration-ensemble">
<h1>Sampling a backbone-only configuration ensemble<a class="headerlink" href="#sampling-a-backbone-only-configuration-ensemble" title="Permalink to this headline">ΒΆ</a></h1>
<div class="highlight-python"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre> 1
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50</pre></div></td><td class="code"><div class="highlight"><pre><span class="c"># Generate an ensemble of backbone configurations for a protein using</span>
<span class="c"># a simplified protein model which consists only of the C_alpha atoms.</span>
<span class="c"># The ensemble is written to a trajectory file.</span>
<span class="c">#</span>
<span class="kn">from</span> <span class="nn">MMTK</span> <span class="kn">import</span> <span class="o">*</span>
<span class="kn">from</span> <span class="nn">MMTK.Proteins</span> <span class="kn">import</span> <span class="n">Protein</span>
<span class="kn">from</span> <span class="nn">MMTK.ForceFields</span> <span class="kn">import</span> <span class="n">CalphaForceField</span>
<span class="kn">from</span> <span class="nn">MMTK.NormalModes</span> <span class="kn">import</span> <span class="n">NormalModes</span>
<span class="kn">from</span> <span class="nn">MMTK.Random</span> <span class="kn">import</span> <span class="n">gaussian</span>
<span class="kn">from</span> <span class="nn">MMTK.Trajectory</span> <span class="kn">import</span> <span class="n">Trajectory</span><span class="p">,</span> <span class="n">SnapshotGenerator</span><span class="p">,</span> <span class="n">TrajectoryOutput</span>
<span class="c"># Construct the system. The scaling factor of 0.1 for the CalphaForceField</span>
<span class="c"># was determined empirically for a C-phycocyanin dimer at 300 K; its value</span>
<span class="c"># is expected to depend at least on the protein and the temperature,</span>
<span class="c"># but the order of magnitude should be right for mid-sized proteins.</span>
<span class="n">universe</span> <span class="o">=</span> <span class="n">InfiniteUniverse</span><span class="p">(</span><span class="n">CalphaForceField</span><span class="p">(</span><span class="mf">2.5</span><span class="p">,</span> <span class="mf">0.1</span><span class="p">))</span>
<span class="n">universe</span><span class="o">.</span><span class="n">protein</span> <span class="o">=</span> <span class="n">Protein</span><span class="p">(</span><span class="s">'insulin.pdb'</span><span class="p">,</span> <span class="n">model</span><span class="o">=</span><span class="s">'calpha'</span><span class="p">)</span>
<span class="c"># Set all masses to the same value, since we don't want</span>
<span class="c"># mass-weighted sampling.</span>
<span class="k">for</span> <span class="n">atom</span> <span class="ow">in</span> <span class="n">universe</span><span class="o">.</span><span class="n">atomList</span><span class="p">():</span>
<span class="n">atom</span><span class="o">.</span><span class="n">setMass</span><span class="p">(</span><span class="mf">1.</span><span class="p">)</span>
<span class="c"># Calculate normal modes. Note that the normal modes are automatically</span>
<span class="c"># scaled to their vibrational amplitudes at a given temperature.</span>
<span class="n">modes</span> <span class="o">=</span> <span class="n">NormalModes</span><span class="p">(</span><span class="n">universe</span><span class="p">,</span> <span class="mf">300.</span><span class="o">*</span><span class="n">Units</span><span class="o">.</span><span class="n">K</span><span class="p">)</span>
<span class="c"># Create trajectory</span>
<span class="n">trajectory</span> <span class="o">=</span> <span class="n">Trajectory</span><span class="p">(</span><span class="n">universe</span><span class="p">,</span> <span class="s">"insulin_backbone.nc"</span><span class="p">,</span> <span class="s">"w"</span><span class="p">,</span>
<span class="s">"Monte-Carlo sampling for insulin backbone"</span><span class="p">)</span>
<span class="c"># Create the snapshot generator</span>
<span class="n">snapshot</span> <span class="o">=</span> <span class="n">SnapshotGenerator</span><span class="p">(</span><span class="n">universe</span><span class="p">,</span>
<span class="n">actions</span> <span class="o">=</span> <span class="p">[</span><span class="n">TrajectoryOutput</span><span class="p">(</span><span class="n">trajectory</span><span class="p">,</span>
<span class="p">[</span><span class="s">"all"</span><span class="p">],</span> <span class="mi">0</span><span class="p">,</span> <span class="bp">None</span><span class="p">,</span> <span class="mi">1</span><span class="p">)])</span>
<span class="c"># Generate an ensemble of 100 configurations. The scaling factor for</span>
<span class="c"># each mode is half the vibrational amplitude, which explains the</span>
<span class="c"># factor 0.5.</span>
<span class="n">minimum</span> <span class="o">=</span> <span class="n">copy</span><span class="p">(</span><span class="n">universe</span><span class="o">.</span><span class="n">configuration</span><span class="p">())</span>
<span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="mi">100</span><span class="p">):</span>
<span class="n">conf</span> <span class="o">=</span> <span class="n">minimum</span>
<span class="k">for</span> <span class="n">j</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="mi">6</span><span class="p">,</span> <span class="nb">len</span><span class="p">(</span><span class="n">modes</span><span class="p">)):</span>
<span class="n">conf</span> <span class="o">=</span> <span class="n">conf</span> <span class="o">+</span> <span class="n">gaussian</span><span class="p">(</span><span class="mf">0.</span><span class="p">,</span> <span class="mf">0.5</span><span class="p">)</span><span class="o">*</span><span class="n">modes</span><span class="p">[</span><span class="n">j</span><span class="p">]</span>
<span class="n">universe</span><span class="o">.</span><span class="n">setConfiguration</span><span class="p">(</span><span class="n">conf</span><span class="p">)</span>
<span class="n">snapshot</span><span class="p">()</span>
<span class="c"># Close trajectory</span>
<span class="n">trajectory</span><span class="o">.</span><span class="n">close</span><span class="p">()</span>
</pre></div>
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