Merge pull request #59 from luciannahss/lu-sirah-doc

Modificaciones Tutorial Amber

docs/source/AMBER/Tutorial-3.rst

@@ -152,7 +152,7 @@ The folder ``sirah.amber/tutorial/3/PMEMD.GPU/`` contains typical input files fo
 
 .. code-block:: bash
 
-   pmemd.cuda -O -i ../sirah.amber/tutorial/3/SANDER/em_HYB.in -p ../dna_hyb.prmtop -c ../dna_hyb.ncrst -o dna_hyb_em.out -r dna_hyb_em.ncrst &
+   pmemd.cuda -O -i ../sirah.amber/tutorial/3/PMEMD.GPU/em_HYB.in -p ../dna_hyb.prmtop -c ../dna_hyb.ncrst -o dna_hyb_em.out -r dna_hyb_em.ncrst &
 
 .. important::
 
@@ -167,7 +167,7 @@ The folder ``sirah.amber/tutorial/3/PMEMD.GPU/`` contains typical input files fo
 
     .. code-block:: bash
 
-        ln -s ../sirah.amber/tutorial/1/SANDER/dna_cg.RST
+        ln -s ../sirah.amber/tutorial/3/SANDER/dna_hyb.RST
     
     The file ``dna_cg.RST`` can only be read by ``sander``, ``pmemd`` reads a different restrain format.
 
@@ -177,13 +177,13 @@ The folder ``sirah.amber/tutorial/3/PMEMD.GPU/`` contains typical input files fo
 
 .. code-block:: bash
 
-   pmemd.cuda -O -i ../sirah.amber/tutorial/3/SANDER/eq_HYB.in -p ../dna_hyb.prmtop -c dna_hyb_em.ncrst -o dna_hyb_eq.out -r dna_hyb_eq.ncrst -x dna_hyb_eq.nc &
+   pmemd.cuda -O -i ../sirah.amber/tutorial/3/PMEMD.GPU/eq_HYB.in -p ../dna_hyb.prmtop -c dna_hyb_em.ncrst -o dna_hyb_eq.out -r dna_hyb_eq.ncrst -x dna_hyb_eq.nc &
 
 **Production (10ns):**
 
 .. code-block:: bash
 
-   pmemd.cuda -O -i ../sirah.amber/tutorial/3/SANDER/md_HYB.in -p ../dna_hyb.prmtop -c dna_hyb_eq.ncrst -o dna_hyb_md.out -r dna_hyb_md.ncrst -x dna_hyb_md.nc &
+   pmemd.cuda -O -i ../sirah.amber/tutorial/3/PMEMD.GPU/md_HYB.in -p ../dna_hyb.prmtop -c dna_hyb_eq.ncrst -o dna_hyb_md.out -r dna_hyb_md.ncrst -x dna_hyb_md.nc &
 
 
 

docs/source/AMBER/Tutorial-4.rst

@@ -20,7 +20,7 @@ Map the atomistic structure of the closed circular DNA to its CG representation:
 
 .. code-block:: bash
    
-   ./sirah.amber/tools/CGCONV/cgconv.pl -i ./sirah.amber/tutorial/4/ccdna.pdb | sed -e 's/DCX A 1/CW5 A 1/'  -e 's/DCX B 1/CW5 B 1/' -e 's/DGX A 100/GW3 A 100/' -e 's/DGX B 100/GW3 B 100/' > ccdna_cg.pdb
+   ./sirah.amber/tools/CGCONV/cgconv.pl -i ./sirah.amber/tutorial/4/ccdna.pdb | sed -e 's/DCX A   1/CW5 A   1/'  -e 's/DCX B   1/CW5 B   1/' -e 's/DGX A 100/GW3 A 100/' -e 's/DGX B 100/GW3 B 100/' > ccdna_cg.pdb
 
 .. note::
 

docs/source/AMBER/Tutorial-5.rst

@@ -19,7 +19,7 @@ _____________________________
 
 	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/>`_ and use the **PDB Reader & Manipulator** to prepare your system. 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. 
 
-	Other option is the `PDB2PQR server <https://server.poissonboltzmann.org/pdb2pqr>`_ and choosing the output naming scheme of AMBER for best compatibility. This server was utilized to generate the *PQR* file featured in this tutorial. Be aware that modified residues lacking parameters such as: MSE (seleno MET), TPO (phosphorylated THY), SEP (phosphorylated SER) or others are deleted from the PQR file by the server. In that case, mutate the residues to their unmodified form before submitting the structure to the server.
+	Other option is the `PDB2PQR server <https://server.poissonboltzmann.org/pdb2pqr>`_ and choosing the output naming scheme of AMBER for best compatibility. This server was utilized to generate the *PQR* file featured in this tutorial. Be aware that modified residues lacking parameters such as: MSE (seleno MET), TPO (phosphorylated TYR), SEP (phosphorylated SER) or others are deleted from the PQR file by the server. In that case, mutate the residues to their unmodified form before submitting the structure to the server.
 
 Map the protonated atomistic structure of protein `1CRN <https://www.rcsb.org/structure/1CRN>`_ to its CG representation:   
 
@@ -177,7 +177,7 @@ input flags therein, in particular the definition of flag *chngmask=0* at *&ewal
 
 .. code-block:: bash
 
-	pmemd.cuda -O -i ../sirah.amber/tutorial/5/em2_WT4.in -p ../1CRN_cg.prmtop -c ../1CRN_cg_em1.ncrst -o 1CRN_cg_em2.out -r 1CRN_cg_em2.ncrst &
+	pmemd.cuda -O -i ../sirah.amber/tutorial/5/em2_WT4.in -p ../1CRN_cg.prmtop -c 1CRN_cg_em1.ncrst -o 1CRN_cg_em2.out -r 1CRN_cg_em2.ncrst &
 
 **Solvent Equilibration (NPT):**
 

docs/source/AMBER/Tutorial-8.rst

@@ -23,13 +23,13 @@ This example use the structure of glycoprotein `1GYA <https://www.rcsb.org/struc
 
 .. code-block:: bash
 
-  ambpdb -p ./sirah.amber/tutorial/8/step3_input.parm7 -c ./sirah.amber/tutorial/8/step3_input.rst7 > 1GYA_glycam.pdb
+	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 structure to its CG representation:   
 
 .. code-block:: bash
 
-  ./sirah.amber/tools/CGCONV/cgconv.pl -i ./sirah.amber/tutorial/8/1GYA_glycam_NoW.pdb -o 1GYA_cg.pdb  
+	./sirah.amber/tools/CGCONV/cgconv.pl -i ./sirah.amber/tutorial/8/1GYA_glycam_NoW.pdb -o 1GYA_cg.pdb  
   
 The input file ``-i`` 1GYA_glycam_NoW.pdb contains the atomistic representation of `1GYA <https://www.rcsb.org/structure/1GYA>`_ structure at pH **7.0**, while the output ``-o`` 1GYA_cg.pdb is its SIRAH CG representation.
 
@@ -111,7 +111,8 @@ Use a text editor to create the file ``gensystem.leap`` including the following
     The above also applies to each disulfide bond, e.g.: “*bond unit.ri.BSG unit.rj.BSG*”. You can try the command *pdb4amber* to get those indexes from the atomistic structure, but be aware that it may not work if the Cysteine residues are too far away (in this case result in an empty file):
 
     .. code-block:: bash
-	   pdb4amber -i sirah.amber/tutorial/8/1GYA_glycam_NoW.pdb -o 1GYA_aa.pdb && cat 1GYA_aa_sslink
+
+		pdb4amber -i sirah.amber/tutorial/8/1GYA_glycam_NoW.pdb -o 1GYA_aa.pdb && cat 1GYA_aa_sslink
 
 
 

docs/source/AMBER/installation.rst

@@ -62,7 +62,7 @@ You will get the folder ``sirah_[version].amber/`` containing the force field de
 
 .. caution::
 
-  Remember to change **X.X** to the number that corresponds to the tutorial you are going to do.
+	Remember to change **X.X** to the number that corresponds to the tutorial you are going to do.
 
 Make a new folder for this tutorial in your working directory:
 
@@ -80,7 +80,9 @@ Create the following symbolic link in the folder tutorialX.X:
 
     SIRAH Force Field is also distributed with `AMBER <https://ambermd.org/index.php>`_ and `AmberTools <https://ambermd.org/AmberTools.php>`_ official releases. To use the native AMBER version of SIRAH, create a symbolic link located in $AMBERHOME:
 
-    ln -s $AMBERHOME/dat/SIRAH sirah.amber
+    .. code-block:: bash
+	
+		ln -s $AMBERHOME/dat/SIRAH sirah.amber
 
     Check the `AMBER Manual <https://ambermd.org/doc12/Amber23.pdf>`_ section **3.11.2** for more details.