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12 changes: 6 additions & 6 deletions AMBER/Tutorial-8.html
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Expand Up @@ -104,11 +104,11 @@ <h1>8.1. Build CG representations<a class="headerlink" href="#build-cg-represent
<p class="admonition-title">Caution</p>
<p>The mapping to CG requires the correct protonation state of each residue at a given pH. We recommend using the <a class="reference external" href="https://www.charmm-gui.org/">CHARMM-GUI server</a> with the <strong>Glycan Reader &amp; Modeler</strong> to prepare your system, choosing the output naming scheme of AMBER for best compatibility. An account is required to access any of the CHARMM-GUI Input Generator modules, and it can take up to 24 hours to obtain one.</p>
</div>
<p>This example use the structure of glycoprotein <a class="reference external" href="https://www.rcsb.org/structure/1GYA">1GYA</a>, using CHARMM-GUI server are obtained the files parm7 and rst7, this files are converted to pdb format with naming scheme of AMBER/GLYCAM using AmberTool as follow:</p>
<p>This example use the structure of glycoprotein <a class="reference external" href="https://www.rcsb.org/structure/1GYA">1GYA</a>, using CHARMM-GUI server are obtained the files parm7 and rst7, these files are converted to pdb format with the naming scheme of AMBER/GLYCAM using AmberTool as follow:</p>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>ambpdb<span class="w"> </span>-p<span class="w"> </span>./sirah.amber/tutorial/8/step3_input.parm7<span class="w"> </span>-c<span class="w"> </span>./sirah.amber/tutorial/8/step3_input.rst7<span class="w"> </span>&gt;<span class="w"> </span>1GYA_glycam.pdb
</pre></div>
</div>
<p>From the file 1GYA_glycam.pdb generated delete the solvent, rename to 1GYA_glycam_NoW.pdb and then map the protonated atomistic to its CG representation:</p>
<p>From the file 1GYA_glycam.pdb generated delete the solvent, rename to 1GYA_glycam_NoW.pdb and then map the protonated atomistic structure to its CG representation:</p>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>./sirah.amber/tools/CGCONV/cgconv.pl<span class="w"> </span>-i<span class="w"> </span>./sirah.amber/tutorial/8/1GYA_glycam_NoW.pdb<span class="w"> </span>-o<span class="w"> </span>1GYA_cg.pdb
</pre></div>
</div>
Expand All @@ -126,7 +126,7 @@ <h1>8.1. Build CG representations<a class="headerlink" href="#build-cg-represent
</div>
<div class="admonition important">
<p class="admonition-title">Important</p>
<p>By default charged termini are used, but it is possible to set them neutral by renaming the residues from <strong>s</strong>[code] to <strong>a</strong>[code] (Nt-acetylated) or <strong>m</strong>[code] (Ct-amidated) after mapping to CG, where [code] is the root residue name in SIRAH. For example, to set a neutral N-terminal Histidine protonated at epsilon nitrogen (<span class="math notranslate nohighlight">\(N_{\epsilon}\)</span>) rename it from “sHe” to “aHe”.</p>
<p>By default, charged termini are used. However, it is possible to set them neutral by renaming the residues from <strong>s</strong>[code] to <strong>a</strong>[code] (Nt-acetylated) or <strong>m</strong>[code] (Ct-amidated) after mapping to CG, where [code] is the root residue name in SIRAH. For example, to set a neutral N-terminal Histidine protonated at epsilon nitrogen (<span class="math notranslate nohighlight">\(N_{\epsilon}\)</span>) rename it from “sHe” to “aHe”.</p>
</div>
<p>Please check both PDBs structures using VMD:</p>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>vmd<span class="w"> </span>-m<span class="w"> </span>sirah.amber/tutorial/8/1GYA_glycam_NoW.pdb<span class="w"> </span>1GYA_cg.pdb
Expand Down Expand Up @@ -213,7 +213,7 @@ <h1>8.4. Run the simulation<a class="headerlink" href="#run-the-simulation" titl
</pre></div>
</div>
<p>The folder <code class="docutils literal notranslate"><span class="pre">sirah.amber/tutorial/8/</span></code> contains typical input files for energy minimization
(<code class="docutils literal notranslate"><span class="pre">em1_WT4.in</span></code> and <code class="docutils literal notranslate"><span class="pre">em2_WT4.in</span></code>), equilibration (<code class="docutils literal notranslate"><span class="pre">eq1_WT4.in</span></code> and <code class="docutils literal notranslate"><span class="pre">eq2_WT4.in</span></code>) and production (<code class="docutils literal notranslate"><span class="pre">md_WT4.in</span></code>) runs. Please check carefully the
(<code class="docutils literal notranslate"><span class="pre">em1_WT4.in</span></code> and <code class="docutils literal notranslate"><span class="pre">em2_WT4.in</span></code>), relaxation (or equilibration) (<code class="docutils literal notranslate"><span class="pre">eq1_WT4.in</span></code> and <code class="docutils literal notranslate"><span class="pre">eq2_WT4.in</span></code>) and production (<code class="docutils literal notranslate"><span class="pre">md_WT4.in</span></code>) runs. Please check carefully the
input flags therein, in particular the definition of flag <em>chngmask=0</em> at <em>&amp;ewald</em> section is <strong>mandatory</strong>.</p>
<div class="admonition tip">
<p class="admonition-title">Tip</p>
Expand Down Expand Up @@ -246,15 +246,15 @@ <h1>8.4. Run the simulation<a class="headerlink" href="#run-the-simulation" titl
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>pmemd.cuda<span class="w"> </span>-O<span class="w"> </span>-i<span class="w"> </span>../sirah.amber/tutorial/8/em2_WT4.in<span class="w"> </span>-p<span class="w"> </span>../1GYA_cg.prmtop<span class="w"> </span>-c<span class="w"> </span>../1GYA_cg_em1.ncrst<span class="w"> </span>-o<span class="w"> </span>1GYA_cg_em2.out<span class="w"> </span>-r<span class="w"> </span>1GYA_cg_em2.ncrst<span class="w"> </span><span class="p">&amp;</span>
</pre></div>
</div>
<p><strong>Solvent Equilibration (NPT):</strong></p>
<p><strong>Solvent Relaxation (or equlibration) in NPT:</strong></p>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>pmemd.cuda<span class="w"> </span>-O<span class="w"> </span>-i<span class="w"> </span>../sirah.amber/tutorial/8/eq1_WT4.in<span class="w"> </span>-p<span class="w"> </span>../1GYA_cg.prmtop<span class="w"> </span>-c<span class="w"> </span>1GYA_cg_em2.ncrst<span class="w"> </span>-ref<span class="w"> </span>1GYA_cg_em2.ncrst<span class="w"> </span>-o<span class="w"> </span>1GYA_cg_eq1.out<span class="w"> </span>-r<span class="w"> </span>1GYA_cg_eq1.ncrst<span class="w"> </span>-x<span class="w"> </span>1GYA_cg_eq1.nc<span class="w"> </span><span class="p">&amp;</span>
</pre></div>
</div>
<div class="admonition caution">
<p class="admonition-title">Caution</p>
<p>Option <strong>restraintmask=:’1-114’</strong> in input file <code class="docutils literal notranslate"><span class="pre">eq1_WT4.in</span></code> must be set specifically for each system to embrace all glycoprotein’s residues.</p>
</div>
<p><strong>Soft equilibration to improve side chain and glycan solvation (NPT):</strong></p>
<p><strong>Soft Relaxation to improve side chain and glycan solvation (NPT):</strong></p>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>pmemd.cuda<span class="w"> </span>-O<span class="w"> </span>-i<span class="w"> </span>../sirah.amber/tutorial/8/eq2_WT4.in<span class="w"> </span>-p<span class="w"> </span>../1GYA_cg.prmtop<span class="w"> </span>-c<span class="w"> </span>1GYA_cg_eq1.ncrst<span class="w"> </span>-ref<span class="w"> </span>1GYA_cg_eq1.ncrst<span class="w"> </span>-o<span class="w"> </span>1GYA_cg_eq2.out<span class="w"> </span>-r<span class="w"> </span>1GYA_cg_eq2.ncrst<span class="w"> </span>-x<span class="w"> </span>1GYA_cg_eq2.nc<span class="w"> </span><span class="p">&amp;</span>
</pre></div>
</div>
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12 changes: 6 additions & 6 deletions Tutorials amber.html
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Expand Up @@ -1555,11 +1555,11 @@ <h3>8.1. Build CG representations<a class="headerlink" href="#id68" title="Link
<p class="admonition-title">Caution</p>
<p>The mapping to CG requires the correct protonation state of each residue at a given pH. We recommend using the <a class="reference external" href="https://www.charmm-gui.org/">CHARMM-GUI server</a> with the <strong>Glycan Reader &amp; Modeler</strong> to prepare your system, choosing the output naming scheme of AMBER for best compatibility. An account is required to access any of the CHARMM-GUI Input Generator modules, and it can take up to 24 hours to obtain one.</p>
</div>
<p>This example use the structure of glycoprotein <a class="reference external" href="https://www.rcsb.org/structure/1GYA">1GYA</a>, using CHARMM-GUI server are obtained the files parm7 and rst7, this files are converted to pdb format with naming scheme of AMBER/GLYCAM using AmberTool as follow:</p>
<p>This example use the structure of glycoprotein <a class="reference external" href="https://www.rcsb.org/structure/1GYA">1GYA</a>, using CHARMM-GUI server are obtained the files parm7 and rst7, these files are converted to pdb format with the naming scheme of AMBER/GLYCAM using AmberTool as follow:</p>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>ambpdb<span class="w"> </span>-p<span class="w"> </span>./sirah.amber/tutorial/8/step3_input.parm7<span class="w"> </span>-c<span class="w"> </span>./sirah.amber/tutorial/8/step3_input.rst7<span class="w"> </span>&gt;<span class="w"> </span>1GYA_glycam.pdb
</pre></div>
</div>
<p>From the file 1GYA_glycam.pdb generated delete the solvent, rename to 1GYA_glycam_NoW.pdb and then map the protonated atomistic to its CG representation:</p>
<p>From the file 1GYA_glycam.pdb generated delete the solvent, rename to 1GYA_glycam_NoW.pdb and then map the protonated atomistic structure to its CG representation:</p>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>./sirah.amber/tools/CGCONV/cgconv.pl<span class="w"> </span>-i<span class="w"> </span>./sirah.amber/tutorial/8/1GYA_glycam_NoW.pdb<span class="w"> </span>-o<span class="w"> </span>1GYA_cg.pdb
</pre></div>
</div>
Expand All @@ -1577,7 +1577,7 @@ <h3>8.1. Build CG representations<a class="headerlink" href="#id68" title="Link
</div>
<div class="admonition important">
<p class="admonition-title">Important</p>
<p>By default charged termini are used, but it is possible to set them neutral by renaming the residues from <strong>s</strong>[code] to <strong>a</strong>[code] (Nt-acetylated) or <strong>m</strong>[code] (Ct-amidated) after mapping to CG, where [code] is the root residue name in SIRAH. For example, to set a neutral N-terminal Histidine protonated at epsilon nitrogen (<span class="math notranslate nohighlight">\(N_{\epsilon}\)</span>) rename it from “sHe” to “aHe”.</p>
<p>By default, charged termini are used. However, it is possible to set them neutral by renaming the residues from <strong>s</strong>[code] to <strong>a</strong>[code] (Nt-acetylated) or <strong>m</strong>[code] (Ct-amidated) after mapping to CG, where [code] is the root residue name in SIRAH. For example, to set a neutral N-terminal Histidine protonated at epsilon nitrogen (<span class="math notranslate nohighlight">\(N_{\epsilon}\)</span>) rename it from “sHe” to “aHe”.</p>
</div>
<p>Please check both PDBs structures using VMD:</p>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>vmd<span class="w"> </span>-m<span class="w"> </span>sirah.amber/tutorial/8/1GYA_glycam_NoW.pdb<span class="w"> </span>1GYA_cg.pdb
Expand Down Expand Up @@ -1664,7 +1664,7 @@ <h3>8.4. Run the simulation<a class="headerlink" href="#id73" title="Link to thi
</pre></div>
</div>
<p>The folder <code class="docutils literal notranslate"><span class="pre">sirah.amber/tutorial/8/</span></code> contains typical input files for energy minimization
(<code class="docutils literal notranslate"><span class="pre">em1_WT4.in</span></code> and <code class="docutils literal notranslate"><span class="pre">em2_WT4.in</span></code>), equilibration (<code class="docutils literal notranslate"><span class="pre">eq1_WT4.in</span></code> and <code class="docutils literal notranslate"><span class="pre">eq2_WT4.in</span></code>) and production (<code class="docutils literal notranslate"><span class="pre">md_WT4.in</span></code>) runs. Please check carefully the
(<code class="docutils literal notranslate"><span class="pre">em1_WT4.in</span></code> and <code class="docutils literal notranslate"><span class="pre">em2_WT4.in</span></code>), relaxation (or equilibration) (<code class="docutils literal notranslate"><span class="pre">eq1_WT4.in</span></code> and <code class="docutils literal notranslate"><span class="pre">eq2_WT4.in</span></code>) and production (<code class="docutils literal notranslate"><span class="pre">md_WT4.in</span></code>) runs. Please check carefully the
input flags therein, in particular the definition of flag <em>chngmask=0</em> at <em>&amp;ewald</em> section is <strong>mandatory</strong>.</p>
<div class="admonition tip">
<p class="admonition-title">Tip</p>
Expand Down Expand Up @@ -1697,15 +1697,15 @@ <h3>8.4. Run the simulation<a class="headerlink" href="#id73" title="Link to thi
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>pmemd.cuda<span class="w"> </span>-O<span class="w"> </span>-i<span class="w"> </span>../sirah.amber/tutorial/8/em2_WT4.in<span class="w"> </span>-p<span class="w"> </span>../1GYA_cg.prmtop<span class="w"> </span>-c<span class="w"> </span>../1GYA_cg_em1.ncrst<span class="w"> </span>-o<span class="w"> </span>1GYA_cg_em2.out<span class="w"> </span>-r<span class="w"> </span>1GYA_cg_em2.ncrst<span class="w"> </span><span class="p">&amp;</span>
</pre></div>
</div>
<p><strong>Solvent Equilibration (NPT):</strong></p>
<p><strong>Solvent Relaxation (or equlibration) in NPT:</strong></p>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>pmemd.cuda<span class="w"> </span>-O<span class="w"> </span>-i<span class="w"> </span>../sirah.amber/tutorial/8/eq1_WT4.in<span class="w"> </span>-p<span class="w"> </span>../1GYA_cg.prmtop<span class="w"> </span>-c<span class="w"> </span>1GYA_cg_em2.ncrst<span class="w"> </span>-ref<span class="w"> </span>1GYA_cg_em2.ncrst<span class="w"> </span>-o<span class="w"> </span>1GYA_cg_eq1.out<span class="w"> </span>-r<span class="w"> </span>1GYA_cg_eq1.ncrst<span class="w"> </span>-x<span class="w"> </span>1GYA_cg_eq1.nc<span class="w"> </span><span class="p">&amp;</span>
</pre></div>
</div>
<div class="admonition caution">
<p class="admonition-title">Caution</p>
<p>Option <strong>restraintmask=:’1-114’</strong> in input file <code class="docutils literal notranslate"><span class="pre">eq1_WT4.in</span></code> must be set specifically for each system to embrace all glycoprotein’s residues.</p>
</div>
<p><strong>Soft equilibration to improve side chain and glycan solvation (NPT):</strong></p>
<p><strong>Soft Relaxation to improve side chain and glycan solvation (NPT):</strong></p>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>pmemd.cuda<span class="w"> </span>-O<span class="w"> </span>-i<span class="w"> </span>../sirah.amber/tutorial/8/eq2_WT4.in<span class="w"> </span>-p<span class="w"> </span>../1GYA_cg.prmtop<span class="w"> </span>-c<span class="w"> </span>1GYA_cg_eq1.ncrst<span class="w"> </span>-ref<span class="w"> </span>1GYA_cg_eq1.ncrst<span class="w"> </span>-o<span class="w"> </span>1GYA_cg_eq2.out<span class="w"> </span>-r<span class="w"> </span>1GYA_cg_eq2.ncrst<span class="w"> </span>-x<span class="w"> </span>1GYA_cg_eq2.nc<span class="w"> </span><span class="p">&amp;</span>
</pre></div>
</div>
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12 changes: 6 additions & 6 deletions _sources/AMBER/Tutorial-8.rst.txt
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Expand Up @@ -19,13 +19,13 @@ _____________________________

The mapping to CG requires the correct protonation state of each residue at a given pH. We recommend using the `CHARMM-GUI server <https://www.charmm-gui.org/>`_ with the **Glycan Reader & Modeler** to prepare your system, choosing the output naming scheme of AMBER for best compatibility. An account is required to access any of the CHARMM-GUI Input Generator modules, and it can take up to 24 hours to obtain one.

This example use the structure of glycoprotein `1GYA <https://www.rcsb.org/structure/1GYA>`_, using CHARMM-GUI server are obtained the files parm7 and rst7, this files are converted to pdb format with naming scheme of AMBER/GLYCAM using AmberTool as follow:
This example use the structure of glycoprotein `1GYA <https://www.rcsb.org/structure/1GYA>`_, using CHARMM-GUI server are obtained the files parm7 and rst7, these files are converted to pdb format with the naming scheme of AMBER/GLYCAM using AmberTool as follow:

.. code-block:: bash
ambpdb -p ./sirah.amber/tutorial/8/step3_input.parm7 -c ./sirah.amber/tutorial/8/step3_input.rst7 > 1GYA_glycam.pdb
From the file 1GYA_glycam.pdb generated delete the solvent, rename to 1GYA_glycam_NoW.pdb and then map the protonated atomistic to its CG representation:
From the file 1GYA_glycam.pdb generated delete the solvent, rename to 1GYA_glycam_NoW.pdb and then map the protonated atomistic structure to its CG representation:

.. code-block:: bash
Expand All @@ -48,7 +48,7 @@ The input file ``-i`` 1GYA_glycam_NoW.pdb contains the atomistic representation

.. important::

By default charged termini are used, but it is possible to set them neutral by renaming the residues from **s**\[code\] to **a**\[code\] (Nt-acetylated) or **m**\[code\] (Ct-amidated) after mapping to CG, where \[code\] is the root residue name in SIRAH. For example, to set a neutral N-terminal Histidine protonated at epsilon nitrogen (:math:`N_{\epsilon}`) rename it from “sHe” to “aHe”.
By default, charged termini are used. However, it is possible to set them neutral by renaming the residues from **s**\[code\] to **a**\[code\] (Nt-acetylated) or **m**\[code\] (Ct-amidated) after mapping to CG, where \[code\] is the root residue name in SIRAH. For example, to set a neutral N-terminal Histidine protonated at epsilon nitrogen (:math:`N_{\epsilon}`) rename it from “sHe” to “aHe”.


Please check both PDBs structures using VMD:
Expand Down Expand Up @@ -159,7 +159,7 @@ Make a new folder for the run:
mkdir -p run; cd run
The folder ``sirah.amber/tutorial/8/`` contains typical input files for energy minimization
(``em1_WT4.in`` and ``em2_WT4.in``), equilibration (``eq1_WT4.in`` and ``eq2_WT4.in``) and production (``md_WT4.in``) runs. Please check carefully the
(``em1_WT4.in`` and ``em2_WT4.in``), relaxation (or equilibration) (``eq1_WT4.in`` and ``eq2_WT4.in``) and production (``md_WT4.in``) runs. Please check carefully the
input flags therein, in particular the definition of flag *chngmask=0* at *&ewald* section is **mandatory**.

.. tip::
Expand Down Expand Up @@ -195,7 +195,7 @@ input flags therein, in particular the definition of flag *chngmask=0* at *&ewal
pmemd.cuda -O -i ../sirah.amber/tutorial/8/em2_WT4.in -p ../1GYA_cg.prmtop -c ../1GYA_cg_em1.ncrst -o 1GYA_cg_em2.out -r 1GYA_cg_em2.ncrst &
**Solvent Equilibration (NPT):**
**Solvent Relaxation (or equlibration) in NPT:**

.. code-block:: bash
Expand All @@ -205,7 +205,7 @@ input flags therein, in particular the definition of flag *chngmask=0* at *&ewal

Option **restraintmask=:'1-114'** in input file ``eq1_WT4.in`` must be set specifically for each system to embrace all glycoprotein’s residues.

**Soft equilibration to improve side chain and glycan solvation (NPT):**
**Soft Relaxation to improve side chain and glycan solvation (NPT):**

.. code-block:: bash
Expand Down
2 changes: 1 addition & 1 deletion searchindex.js
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