deploy: a8bd9b7

AMBER/Tutorial-5.html

@@ -256,11 +256,9 @@ <h1>5.4. Run the simulation<a class="headerlink" href="#run-the-simulation" titl
 <h1>5.5. Visualizing the simulation<a class="headerlink" href="#visualizing-the-simulation" title="Link to this heading"></a></h1>
 <p>That’s it! Now you can analyze the trajectory.
 Process the output trajectory to account for the Periodic Boundary Conditions (PBC):</p>
-<blockquote>
-<div><div class="highlight-bash notranslate"><div class="highlight"><pre><span></span><span class="nb">echo</span><span class="w"> </span>-e<span class="w"> </span><span class="s2">&quot;autoimage\ngo\nquit\n&quot;</span><span class="w"> </span><span class="p">|</span><span class="w"> </span>cpptraj<span class="w"> </span>-p<span class="w"> </span>../1CRN_cg.prmtop<span class="w"> </span>-y<span class="w"> </span>1CRN_cg_md.nc<span class="w"> </span>-x<span class="w"> </span>1CRN_cg_md_pbc.nc<span class="w"> </span>--interactive
+<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span><span class="nb">echo</span><span class="w"> </span>-e<span class="w"> </span><span class="s2">&quot;autoimage\ngo\nquit\n&quot;</span><span class="w"> </span><span class="p">|</span><span class="w"> </span>cpptraj<span class="w"> </span>-p<span class="w"> </span>../1CRN_cg.prmtop<span class="w"> </span>-y<span class="w"> </span>1CRN_cg_md.nc<span class="w"> </span>-x<span class="w"> </span>1CRN_cg_md_pbc.nc<span class="w"> </span>--interactive
 </pre></div>
 </div>
-</div></blockquote>
 <p>Load the processed trajectory in VMD:</p>
 <div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">vmd</span> <span class="o">../</span><span class="mi">1</span><span class="n">CRN_cg</span><span class="o">.</span><span class="n">prmtop</span> <span class="o">../</span><span class="mi">1</span><span class="n">CRN_cg</span><span class="o">.</span><span class="n">ncrst</span> <span class="mi">1</span><span class="n">CRN_cg_md</span><span class="o">.</span><span class="n">nc</span> <span class="o">-</span><span class="n">e</span> <span class="o">../</span><span class="n">sirah</span><span class="o">.</span><span class="n">amber</span><span class="o">/</span><span class="n">tools</span><span class="o">/</span><span class="n">sirah_vmdtk</span><span class="o">.</span><span class="n">tcl</span>
 </pre></div>

AMBER/Tutorial-6.html

@@ -143,7 +143,7 @@ <h1>6.2. Prepare LEaP input<a class="headerlink" href="#prepare-leap-input" titl
 <span class="go">addIonsRand Lipid NaW 33 ClW 33</span>
 
 <span class="gp"># </span>Save<span class="w"> </span>Parms
-<span class="go">saveAmberParmNetcdf protein DMPC64_cg.prmtop DMPC64_cg.ncrst</span>
+<span class="go">saveAmberParmNetcdf Lipid DMPC64_cg.prmtop DMPC64_cg.ncrst</span>
 
 <span class="gp"># </span>EXIT
 <span class="go">quit</span>

AMBER/Tutorial-7.html

@@ -195,20 +195,26 @@ <h1>7.2. Prepare LEaP input<a class="headerlink" href="#prepare-leap-input" titl
 <span class="go">source leaprc.sirah</span>
 
 <span class="gp"># </span>Load<span class="w"> </span>model
-<span class="go">Lipid = loadpdb DMPC64_cg.pdb</span>
+<span class="go">ProtMem = loadpdb 2kyv_DMPC_cg.pdb</span>
+
+<span class="gp"># </span>Info<span class="w"> </span>on<span class="w"> </span>system<span class="w"> </span>charge
+<span class="go">charge ProtMem</span>
+
+<span class="gp"># </span>Prevent<span class="w"> </span>adding<span class="w"> </span>solvent<span class="w"> </span>molecules<span class="w"> </span>beyond<span class="w"> </span>the<span class="w"> </span>membrane<span class="w"> </span>boundaries
+<span class="go">setbox ProtMem centers 0</span>
 
 <span class="gp"># </span>Add<span class="w"> </span>solvent,<span class="w"> </span>counterions<span class="w"> </span>and<span class="w"> </span><span class="m">0</span>.15M<span class="w"> </span>NaCl
 <span class="gp"># </span>Tuned<span class="w"> </span>solute-solvent<span class="w"> </span>closeness<span class="w"> </span><span class="k">for</span><span class="w"> </span>best<span class="w"> </span>hydration
-<span class="go">solvateBox Lipid WT4BOX {0 0 40} 0.7</span>
-<span class="go">addIonsRand Lipid NaW 33 ClW 33</span>
+<span class="go">solvateBox ProtMem WT4BOX {0,0,27} 0.7</span>
+<span class="go">addIonsRand ProtMem NaW 109 ClW 124</span>
 
 <span class="gp"># </span>Save<span class="w"> </span>Parms
-<span class="go">saveAmberParmNetcdf protein DMPC64_cg.prmtop DMPC64_cg.ncrst</span>
+<span class="go">saveAmberParmNetcdf ProtMem 2kyv_DMPC_cg.prmtop 2kyv_DMPC_cg.ncrst</span>
 
 <span class="gp"># </span>EXIT
-<span class="go">quit</span>
 </pre></div>
 </div>
+<p>quit</p>
 <div class="admonition seealso">
 <p class="admonition-title">See also</p>
 <p>The available electrolyte species in SIRAH force field are: <code class="docutils literal notranslate"><span class="pre">Na⁺</span></code> (NaW), <code class="docutils literal notranslate"><span class="pre">K⁺</span></code> (KW) and <code class="docutils literal notranslate"><span class="pre">Cl⁻</span></code> (ClW) which represent solvated ions in solution. One ion pair (e.g., NaW-ClW) each 34 WT4 molecules results in a salt concentration of ~0.15M (see <a class="reference internal" href="../Tutorials%20amber.html#appendix"><span class="std std-ref">Appendix</span></a> for details). Counterions were added according to <a class="reference external" href="https://pubs.acs.org/doi/10.1021/acs.jctc.9b00953">Machado et al.</a>.</p>

Tutorials amber.html

@@ -1027,11 +1027,9 @@ <h3>5.4. Run the simulation<a class="headerlink" href="#id41" title="Link to thi
 <h3>5.5. Visualizing the simulation<a class="headerlink" href="#id42" title="Link to this heading"></a></h3>
 <p>That’s it! Now you can analyze the trajectory.
 Process the output trajectory to account for the Periodic Boundary Conditions (PBC):</p>
-<blockquote>
-<div><div class="highlight-bash notranslate"><div class="highlight"><pre><span></span><span class="nb">echo</span><span class="w"> </span>-e<span class="w"> </span><span class="s2">&quot;autoimage\ngo\nquit\n&quot;</span><span class="w"> </span><span class="p">|</span><span class="w"> </span>cpptraj<span class="w"> </span>-p<span class="w"> </span>../1CRN_cg.prmtop<span class="w"> </span>-y<span class="w"> </span>1CRN_cg_md.nc<span class="w"> </span>-x<span class="w"> </span>1CRN_cg_md_pbc.nc<span class="w"> </span>--interactive
+<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span><span class="nb">echo</span><span class="w"> </span>-e<span class="w"> </span><span class="s2">&quot;autoimage\ngo\nquit\n&quot;</span><span class="w"> </span><span class="p">|</span><span class="w"> </span>cpptraj<span class="w"> </span>-p<span class="w"> </span>../1CRN_cg.prmtop<span class="w"> </span>-y<span class="w"> </span>1CRN_cg_md.nc<span class="w"> </span>-x<span class="w"> </span>1CRN_cg_md_pbc.nc<span class="w"> </span>--interactive
 </pre></div>
 </div>
-</div></blockquote>
 <p>Load the processed trajectory in VMD:</p>
 <div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">vmd</span> <span class="o">../</span><span class="mi">1</span><span class="n">CRN_cg</span><span class="o">.</span><span class="n">prmtop</span> <span class="o">../</span><span class="mi">1</span><span class="n">CRN_cg</span><span class="o">.</span><span class="n">ncrst</span> <span class="mi">1</span><span class="n">CRN_cg_md</span><span class="o">.</span><span class="n">nc</span> <span class="o">-</span><span class="n">e</span> <span class="o">../</span><span class="n">sirah</span><span class="o">.</span><span class="n">amber</span><span class="o">/</span><span class="n">tools</span><span class="o">/</span><span class="n">sirah_vmdtk</span><span class="o">.</span><span class="n">tcl</span>
 </pre></div>
@@ -1101,7 +1099,7 @@ <h3>6.2. Prepare LEaP input<a class="headerlink" href="#id47" title="Link to thi
 <span class="go">addIonsRand Lipid NaW 33 ClW 33</span>
 
 <span class="gp"># </span>Save<span class="w"> </span>Parms
-<span class="go">saveAmberParmNetcdf protein DMPC64_cg.prmtop DMPC64_cg.ncrst</span>
+<span class="go">saveAmberParmNetcdf Lipid DMPC64_cg.prmtop DMPC64_cg.ncrst</span>
 
 <span class="gp"># </span>EXIT
 <span class="go">quit</span>
@@ -1380,20 +1378,26 @@ <h3>7.2. Prepare LEaP input<a class="headerlink" href="#id58" title="Link to thi
 <span class="go">source leaprc.sirah</span>
 
 <span class="gp"># </span>Load<span class="w"> </span>model
-<span class="go">Lipid = loadpdb DMPC64_cg.pdb</span>
+<span class="go">ProtMem = loadpdb 2kyv_DMPC_cg.pdb</span>
+
+<span class="gp"># </span>Info<span class="w"> </span>on<span class="w"> </span>system<span class="w"> </span>charge
+<span class="go">charge ProtMem</span>
+
+<span class="gp"># </span>Prevent<span class="w"> </span>adding<span class="w"> </span>solvent<span class="w"> </span>molecules<span class="w"> </span>beyond<span class="w"> </span>the<span class="w"> </span>membrane<span class="w"> </span>boundaries
+<span class="go">setbox ProtMem centers 0</span>
 
 <span class="gp"># </span>Add<span class="w"> </span>solvent,<span class="w"> </span>counterions<span class="w"> </span>and<span class="w"> </span><span class="m">0</span>.15M<span class="w"> </span>NaCl
 <span class="gp"># </span>Tuned<span class="w"> </span>solute-solvent<span class="w"> </span>closeness<span class="w"> </span><span class="k">for</span><span class="w"> </span>best<span class="w"> </span>hydration
-<span class="go">solvateBox Lipid WT4BOX {0 0 40} 0.7</span>
-<span class="go">addIonsRand Lipid NaW 33 ClW 33</span>
+<span class="go">solvateBox ProtMem WT4BOX {0,0,27} 0.7</span>
+<span class="go">addIonsRand ProtMem NaW 109 ClW 124</span>
 
 <span class="gp"># </span>Save<span class="w"> </span>Parms
-<span class="go">saveAmberParmNetcdf protein DMPC64_cg.prmtop DMPC64_cg.ncrst</span>
+<span class="go">saveAmberParmNetcdf ProtMem 2kyv_DMPC_cg.prmtop 2kyv_DMPC_cg.ncrst</span>
 
 <span class="gp"># </span>EXIT
-<span class="go">quit</span>
 </pre></div>
 </div>
+<p>quit</p>
 <div class="admonition seealso">
 <p class="admonition-title">See also</p>
 <p>The available electrolyte species in SIRAH force field are: <code class="docutils literal notranslate"><span class="pre">Na⁺</span></code> (NaW), <code class="docutils literal notranslate"><span class="pre">K⁺</span></code> (KW) and <code class="docutils literal notranslate"><span class="pre">Cl⁻</span></code> (ClW) which represent solvated ions in solution. One ion pair (e.g., NaW-ClW) each 34 WT4 molecules results in a salt concentration of ~0.15M (see <a class="reference internal" href="#appendix"><span class="std std-ref">Appendix</span></a> for details). Counterions were added according to <a class="reference external" href="https://pubs.acs.org/doi/10.1021/acs.jctc.9b00953">Machado et al.</a>.</p>

_sources/AMBER/Tutorial-5.rst.txt

@@ -210,7 +210,7 @@ ________________________________
 That’s it! Now you can analyze the trajectory.
 Process the output trajectory to account for the Periodic Boundary Conditions (PBC):
 
-  .. code-block:: bash
+.. code-block:: bash
 
       echo -e "autoimage\ngo\nquit\n" | cpptraj -p ../1CRN_cg.prmtop -y 1CRN_cg_md.nc -x 1CRN_cg_md_pbc.nc --interactive
 

_sources/AMBER/Tutorial-6.rst.txt

@@ -69,7 +69,7 @@ Use a text editor to create the file ``gensystem.leap`` including the following
     addIonsRand Lipid NaW 33 ClW 33
 
     # Save Parms
-    saveAmberParmNetcdf protein DMPC64_cg.prmtop DMPC64_cg.ncrst
+    saveAmberParmNetcdf Lipid DMPC64_cg.prmtop DMPC64_cg.ncrst
 
     # EXIT
     quit

_sources/AMBER/Tutorial-7.rst.txt

@@ -135,20 +135,26 @@ Use a text editor to create the file ``gensystem.leap`` including the following
     # Load SIRAH force field
     addPath ./sirah.amber
     source leaprc.sirah
-
+    
     # Load model
-    Lipid = loadpdb DMPC64_cg.pdb
+    ProtMem = loadpdb 2kyv_DMPC_cg.pdb
+
+    # Info on system charge
+    charge ProtMem
+
+    # Prevent adding solvent molecules beyond the membrane boundaries
+    setbox ProtMem centers 0
 
     # Add solvent, counterions and 0.15M NaCl
     # Tuned solute-solvent closeness for best hydration
-    solvateBox Lipid WT4BOX {0 0 40} 0.7
-    addIonsRand Lipid NaW 33 ClW 33
+    solvateBox ProtMem WT4BOX {0,0,27} 0.7
+    addIonsRand ProtMem NaW 109 ClW 124
 
     # Save Parms
-    saveAmberParmNetcdf protein DMPC64_cg.prmtop DMPC64_cg.ncrst
-
+    saveAmberParmNetcdf ProtMem 2kyv_DMPC_cg.prmtop 2kyv_DMPC_cg.ncrst
+    
     # EXIT
-    quit
+quit
 
 .. seealso::