2024 update

_episodes/09-Amber_flowchart.md

@@ -68,7 +68,7 @@ AMBER package includes two utilities for simulation preparation: tLEaP and xLEaP
 A package of AMBER includes two MD engines: SANDER and PMEMD. Serial and parallel versions are available for both programs. AMBER also provides a GPU-accelerated version of PMEMD. Along with the topology file and the coordinate or resume file, you will also need an input file describing the parameters of your simulation, such as integrator, thermostat, barostat, time step, cut-off distance, etc. It's also possible to use bond and distance constraints derived from NMR experiments. PMEMD and SANDER can run multiple simulations, including replica exchange and constant pH. Parameters for such simulations are contained in a special groupfile. A simulation program will save energy components and MD trajectories. 
 {: .instructor_notes}
 
-PMEMD is faster than SANDER, but there are limitations to the simulation types available in PMEND. Some algorithms (such as DFT QM-MM with GPU-accelerated DFT code QUICK) are only available in SANDER.
+PMEMD is faster than SANDER, but there are limitations to the simulation types available in PMEMD. Some algorithms (such as DFT QM-MM with GPU-accelerated DFT code QUICK) are only available in SANDER.
 {: .instructor_notes}
 
 

_episodes/10-Checking_PDB_Files.md

@@ -88,6 +88,12 @@ Let's consider some example protein PDB files. The first step is to connect to t
 - **no GPUs**
 <br>
 
+#### Workshop data: 
+
+/project/def-sponsor00/workshop_amber_2024.tar.gz  
+
+wget https://github.com/ComputeCanada/molmodsim-amber-md-lesson/releases/download/workshop-2021-04/workshop_amber_2024.tar.gz
+
 ### Checking a molecular structure 
 [Check_structure](https://pypi.org/project/biobb-structure-checking/) is a command-line utility from [BioBB project](https://github.com/bioexcel/biobb) for exhaustive structure quality checking (residue chirality, amide orientation, vdw clashes, etc.).  Using this utility, you can perform manipulations with structures, such as selecting chains or conformations, removing components, mutating residues, adding missing atoms, adding hydrogens, etc. 
 {: .instructor_notes}  
@@ -161,7 +167,7 @@ check_structure -i 2qwo.pdb -o protein.pdb ligands --remove all
 >>quit
 >>~~~
 >>{: .vmd}
->>The first line of code loads a new molecule from 1ERT.pdb. Using the **atomselect** method, we then select all protein atoms from the top molecule. Finally, we save the selection in the file "protein.pdb".  
+>>The first line of code loads a new molecule from 2qwo.pdb. Using the **atomselect** method, we then select all protein atoms from the top molecule. Finally, we save the selection in the file "protein.pdb".  
 >>The Atom Selection Language has many capabilities. You can learn more about it by visiting the following [webpage](https://www.ks.uiuc.edu/Research/vmd/vmd-1.3/ug/node132.html). 
 >>
 >{: .solution}
@@ -210,6 +216,7 @@ Check conformations
 cd ~/scratch/workshop_amber/example_02
 check_structure -i 1ert.pdb checkall
 ~~~
+{: .language-bash}
 
 ~~~
 ASP A20
@@ -231,6 +238,7 @@ Select conformers A ASP20 and B HIS43.
 ~~~
 check_structure -i 1ert.pdb -o output.pdb altloc --select A20:A,A43:B,A90:B 
 ~~~
+{: .language-bash}
 
 
 >## Selecting Alternate Conformations with VMD

_episodes/11-Protonation_State.md

@@ -95,7 +95,7 @@ What protonation states are appropriate for simulating Asp79 and His53 at pH 6?
 A more consistent and convenient way to select the desired form of amino acid is to change its name in the structure file before generating a topology. The neutral states of LYS, ASP, and GLU can be chosen by renaming them  LYN, ASH, and GLH, respectively.  You can select the appropriate form of HIS by renaming HIS to HIE (proton on NE2), HID (proton on ND1), or HIP (both protons).
 {: .instructor_notes}
 
-- Change residue name in the structure file
+-  To change the form of an amino acid, change its name in the structure file
 
 ```
 LYS (+1) - LYN  (0)  
@@ -169,6 +169,7 @@ The use of constant protonation states in molecular dynamics simulations has its
 
 ### Combining all structure preparation steps in one check_structure script
 ~~~
+cd ~/scratch/workshop_amber/example_03
 check_structure -i 1rgg.pdb -o 1RGG_chain_A_prot.pdb \
 command_list --list "\
 chains --select A;\

_episodes/12-Adding_Ions.md

@@ -45,7 +45,7 @@ Let's neutralize 1RGG protein using the *leap* module. We will add ions prior to
 
 ~~~
 cd ~/scratch/workshop_amber/example_04
-module load gcc/12.3 openmpi/4.1.5 cuda/12.2 amber
+module load StdEnv/2023 amber
 tleap
 ~~~
 {: .language-bash}

code/run_setup.sh

@@ -4,7 +4,7 @@
 mkdir amber
 cd amber
 module purge
-module load nixpkgs/16.09  intel/2016.4 vmd/1.9.3
+module load StdEnv/2023 vmd
 # Save VMD commands in the variable 'script'
 script="$(cat << EOF
 # Load 1RGG.pdb into a new (top) molecule
@@ -37,7 +37,7 @@ vmd -e <<<"${script}" /dev/stdin
 
 # >>>>>  Prepare the system using LEaP + pbd2gmx <<<<<
 module purge
-module load nixpkgs/16.09  gcc/5.4.0  openmpi/2.1.1 amber/18
+module load StdEnv/2023 amber
 # Save LeaP commands in the variable 'script'
 script="$(cat << EOF
 # Load spce water model
@@ -68,7 +68,7 @@ mkdir gromacs_A
 cp amber/1RGG_chain_A_solvated.pdb gromacs_A
 cd gromacs_A
 module purge
-module load gcc/7.3.0 openmpi/3.1.2 gromacs/2019.3
+module load StdEnv/2023 gromacs
 # Rename ions for GROMACS and assign them to chain B
 sed s/"Cl-  Cl-  "/" CL  CL  B"/g 1RGG_chain_A_solvated.pdb | sed s/"Na+  Na+  "/" NA  NA  B"/g > 1RGG_chain_A_solvated_gro.pdb
 # Save GROMACS topology and coordinate files
@@ -82,7 +82,7 @@ mkdir gromacs_B
 cp amber/1RGG_chain_A_prot.pdb gromacs_B
 cd gromacs_B
 module purge
-module load gcc/7.3.0 openmpi/3.1.2 gromacs/2019.3
+module load StdEnv/2023 gromacs
 # Generate GROMACS topology and coordinate files
 gmx pdb2gmx -f 1RGG_chain_A_prot.pdb -ff amber99sb-ildn -water spce -ignh -chainsep id -ss << EOF >log
 y