Merge pull request #65 from luciannahss/lu-sirah-doc

Background and Gromacs Tutorial 7
SIRAHFF · Jun 3, 2024 · 1d9f052 · 1d9f052
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diff --git a/docs/images/Fuerza_100pN.png b/docs/images/Fuerza_100pN.png
diff --git a/docs/images/TutorialSMD1.png b/docs/images/TutorialSMD1.png
diff --git a/docs/images/TutorialSMD2.png b/docs/images/TutorialSMD2.png
diff --git a/docs/images/cg-phospholipids.jpg b/docs/images/cg-phospholipids.jpg
diff --git a/docs/images/mousepad-old-amino.png b/docs/images/mousepad-old-amino.png
diff --git a/docs/images/mousepad-old-dna.png b/docs/images/mousepad-old-dna.png
diff --git a/docs/images/mousepad-old-solvent.png b/docs/images/mousepad-old-solvent.png
diff --git a/docs/images/mousepad-old.png b/docs/images/mousepad-old.png
diff --git a/docs/images/virus-cg.jpg b/docs/images/virus-cg.jpg
diff --git a/docs/source/AMBER/installation.rst b/docs/source/AMBER/installation.rst
@@ -1,6 +1,6 @@
 .. note:: 
 
-    SIRAH Force Field is distributed with `AMBER <https://ambermd.org/index.php>`_ and `AmberTools <https://ambermd.org/AmberTools.php>`_ offical releases.
+    SIRAH Force Field is distributed with `AMBER <https://ambermd.org/index.php>`_ and `AmberTools <https://ambermd.org/AmberTools.php>`_ official releases.
 
 Required Software
 __________________

diff --git a/docs/source/Background SIRAH.rst b/docs/source/Background SIRAH.rst
diff --git a/docs/source/Background SIRAH_complete.rst b/docs/source/Background SIRAH_complete.rst
diff --git a/docs/source/FAQ.rst b/docs/source/FAQ.rst
@@ -139,7 +139,7 @@ General questions
 
 .. _g21:    
 
-- **sirah_ss assign some residues as coil, does it means they are unfold or randomly moving?** .. _g21:   
+- **sirah_ss assign some residues as coil, does it means they are unfold or randomly moving?**   
 
 	Not necessarily, the strict definition of coil used by *sirah_ss* is *“not helix nor extended sheet”*, which means a residue that can not satisfy either condition. Importantly, the secondary structure is assigned according to the Ramachandran and the hydrogen bond network. Particularly, the later is very sensitive to small fluctuation around the distance criteria used to define the interaction. Hence, transient coil states may be more likely to point the lost of hydrogen bonds in well folded proteins, rather that shifts in the conformational space.
 

diff --git a/docs/source/Further reading.rst b/docs/source/Further reading.rst
@@ -26,6 +26,7 @@ SIRAH Applications
 
 .. |Review2-cit| image:: https://img.shields.io/endpoint?url=https%3A%2F%2Fapi.juleskreuer.eu%2Fcitation-badge.php%3Fshield%26doi%3D10.1021%2Facs.jctc.3c00733
    :alt: Citation
+   :target: https://scholar.google.com.uy/scholar?cites=14982031192725054357
 
 *    **Protein-DNA complexes** and **Membrane Proteins**:   
 

diff --git a/docs/source/GROMACS/Tutorial-3.rst b/docs/source/GROMACS/Tutorial-3.rst
@@ -223,7 +223,7 @@ Generate restraint files for the backbone *GN* and *GO* beads:
 
 When prompted, choose the group *GN_GO*
 
-Add restraints to ``topol.top``
+Add the restraints to ``topol.top``:
 
 .. list-table:: 
    :align: center
@@ -305,7 +305,7 @@ Make a new folder for the run:
 
 .. code-block:: bash 
 
-	gmx grompp -f ../sirah.ff/tutorial/3/GPU/eq1_CGPROT.mdp -p ../topol.top -po eq1.mdp -n ./1CRN_cg_ion.ndx -c 1CRN_cg_em2.gro -r 1CRN_cg_em2.gro -o 1CRN_cg_eq1.tpr
+	gmx grompp -f ../sirah.ff/tutorial/3/GPU/eq1_CGPROT.mdp -p ../topol.top -po eq1.mdp -n ../1CRN_cg_ion.ndx -c 1CRN_cg_em2.gro -r 1CRN_cg_em2.gro -o 1CRN_cg_eq1.tpr
 
 .. code-block:: bash 
 
@@ -388,8 +388,10 @@ When prompted, choose *Protein* as both the group for calculation and the output
 	 gmx sasa -surface 'group "A"' -output '"Hydrophobic" group "A" and charge {-0.2 to 0.2}; "Hydrophilic" group "B" and not charge {-0.2 to 0.2}; "Total" group "B"'
 
 
-Use Grace to plot the results::
-	
+Use Xmgrace to plot the results:
+
+.. code-block:: bash
+
 	xmgrace -nxy area.xvg
 
 ..

diff --git a/docs/source/GROMACS/Tutorial-6.rst b/docs/source/GROMACS/Tutorial-6.rst
@@ -48,7 +48,7 @@ The input file ``-i`` 2kyv.pqr contains the atomistic representation of `2KYV <h
     ./sirah.ff/tools/CGCONV/cgconv.pl -h
 	
 
-6.2. Embed the protein in a lipid bilayer
+6.1.1. Embed the protein in a lipid bilayer
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
 We will show one possible way to do it by starting from a pre-equilibrated CG membrane patch.
@@ -68,7 +68,7 @@ Luckily, we already oriented the protein inside the membrane. For setting up you
    **Figure 1.** Protein oriented inside the membrane from the OPM database with dummy atoms represented as orange spheres.
 
 
-6.2.1. Delete close contact lipid molecules
+6.1.2. Delete close contact lipid molecules
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
 We need to use VMD to to delete lipid molecules in close contact with the protein. For a proper treatment and visualization of the system in VMD you must first generate the molecular topology and initial coordinate files.
@@ -124,7 +124,7 @@ To save the refined protein-membrane system, in the VMD main window click on ``2
 
 From now on it is just normal GROMACS stuff!
 
-6.3. PDB to GROMACS format
+6.2. PDB to GROMACS format
 __________________________
 
 Use ``pdb2gmx`` to convert your PDB file into GROMACS format: 
@@ -149,7 +149,7 @@ When prompted, choose *SIRAH force field* and then *SIRAH solvent models*.
   mapping step. In that case, check your atomistic and mapped structures and do not carry on the
   simulation until the problem is solved.
 
-6.4. Solvate the system
+6.3. Solvate the system
 _______________________
 
 
@@ -293,7 +293,7 @@ Use VMD to check how the CG system looks like:
   VMD assigns default radius to unknown atom types, the script ``sirah_vmdtk.tcl`` sets the right ones, according to the CG representation. It also provides a kit of useful selection macros, coloring methods and backmapping utilities.
   Use the command ``sirah_help`` in the Tcl/Tk console of VMD to access the manual pages. To learn about SIRAH Tools' capabilities, you can also go to the :ref:`SIRAH Tools tutorial <SIRAH tools>`.
 
-6.5. Generate position restraint files
+6.4. Generate position restraint files
 _______________________________________
 
 To achive a proper interaction between the protein and bilayer, we will perform a equilibration step applying restraints over the protein backbone and lipids' phosphate groups.
@@ -408,15 +408,15 @@ Edit ``topol_Lipid_chain_F.itp`` to include the new position restraints and defi
        | #include "posre_Pz.itp" 
        | #endif
 
-6.6. Run the simulation
+6.5. Run the simulation
 ________________________
 
 .. important:: 
 
   By default in this tutorial we will use input files for GROMACS on GPU (``sirah.ff/tutorial/6/GPU``). Example input files for using GROMACS on CPU can be found at: ``sirah.ff/tutorial/6/CPU``.
 
 The folder ``sirah.ff/tutorial/6/GPU/`` contains typical input files for energy minimization
-(``em_CGLIPROT.mdp``), equilibration (``eq_CGLIPROT.mdp``) and production (``md_CGLIPROT.mdp``) runs. Please
+(``em1_CGLIPROT.mdp`` and ``em2_CGLIPROT.mdp``), equilibration (``eq1_CGLIPROT.mdp`` and ``eq2_CGLIPROT.mdp``) and production (``md_CGLIPROT.mdp``) runs. Please
 check carefully the input flags therein.
 
 Make a new folder for the run:
@@ -447,7 +447,7 @@ Make a new folder for the run:
 
 **Equilibration 1**:
 
-Position restraints are defined in ``eq_CGLIPROT.mdp`` file for protein backbone in xyz and phosphate groups (BFO beads) in z coordinate by setting keywords ``-DPOSREBB`` and ``-DPOSREZ``, respectively.
+Position restraints are defined in ``eq1_CGLIPROT.mdp`` file for protein backbone in xyz and phosphate groups (BFO beads) in z coordinate by setting keywords ``-DPOSREBB`` and ``-DPOSREZ``, respectively.
 
 .. code-block:: bash
 
@@ -477,7 +477,7 @@ Position restraints are defined in ``eq_CGLIPROT.mdp`` file for protein backbone
 
   gmx mdrun -deffnm 2kyv_DMPC_cg_md &> MD.log & 
 
-6.7. Visualizing the simulation
+6.6. Visualizing the simulation
 ________________________________
 
 That’s it! Now you can analyze the trajectory.