################################################

This repository is now archvived

################################################

Molecular Dynamics Carbohydrate Structure Analysis Module

1) Setup

This package should work on most unix based systems (Mac/Linux).

To get things running python3 is required and ensure the packages listed in requirements.txt are installed.

1.1) Basic setup (for Ubuntu)

• Within a terminal navigate to the directory you wish to clone the structure_analysis repo to;
• Run: git clone https://github.com/ztimol/structure_analysis.git
• Enter the cloned structure_analysis directroy: cd structure_analysis
• Setup a virtual environment then install the required pip packages

sudo apt install virtualenv
virtualenv venv -p python3
source venv/bin/activate
pip3 install -r requirements.txt

1.2) Minimum Requirements

• python3.5 or greater

2) Running the script

The entrypoint script is base.py. The path to the config file is a required flag:

python3 base.py -f config_files/example_run.conf

3) Multiprocessing

The underlying MDAnalysis libraries do not employ multiprocessing - see the MDAnalysis docs. The way trajectories are handled by MDAnalysis also do not make implementing multiprocessing on top of it trivial. There is a good reason for this - again google and the MDAnalysis docs provide more information.

4) Config file

4.1) Config Parameters

ALL CONFIG FILE PARAMETERS ARE STILL TO BE LISTED HERE.

• frames_per_ns

  • Optional: False
  • Acceptable value(s): numeric (integer)
  • Default value: n/a
  • Description: Used to calculate the trajectory length in time from the number of frames. Value must be specific in config_file.

• start_frame:

  • Optional: True
  • Acceptable value(s): numeric (integer)
  • Default value: 0
  • Description: Used as the trajectory start point in the analysis.

• dcd_file:

  • Optional: False
  • Acceptable value(s): string
  • Default value: n/a
  • Description: Absolute or relative file path to trajectory DCD file.

• psf_file:

  • Optional: False
  • Acceptable value(s): string
  • Default value: n/a
  • Description: Absolute or relative file path to structure file.

• amber:

  • Optional: True
  • Acceptable value(s): yes or no
  • Default value: no
  • Description: Absolute or relative file path to structure file.

4.2) Config file example

Below is an example config file that does the following:

• Measures the torsion angles for two sets of glycisidic linkages - phi and psi for each;
• Calculates the single point potential energies for the trajectory with the NAMD Amber force field parameters enabled;
• Calculates the Cremer-Pople ring pucker polar coordiates for two six membered rings.

start_frame 0
frames_per_ns 40

dcd_file /home/[user]/Studies/Dynamics/NAMD/MD/solution/general_structures/aLRha13_aDGlc14_bDGlcNAc/trajectories/aLRha13_aDGlc14_bDGlcNAc_glycam_0-1000ns.dcd
psf_file /home/[user]/Studies/Dynamics/NAMD/MD/solution/general_structures/aLRha13_aDGlc14_bDGlcNAc/trajectories/1_noWAT.psf

amber yes

parm7_file /home/[user]/Studies/Dynamics/NAMD/MD/solution/general_structures/aLRha13_aDGlc14_bDGlcNAc/trajectories/1_noWAT.parm7
rst7_file /home/[user]/Studies/Dynamics/NAMD/MD/solution/general_structures/aLRha13_aDGlc14_bDGlcNAc/trajectories/1_noWAT.rst7

torsion aLRha13bDGlcNAc phi "51 50 27 15"
torsion aLRha13bDGlcNAc psi "50 27 15 16"
torsion aLRha13bDGlcNAc scatter phi psi

torsion aDGlc14bDGlcNAc phi "29 28 14 12" # time series scatter of phi torsion
torsion aDGlc14bDGlcNAc psi "28 14 12 13" # time series scatter of psi torsion
torsion aDGlc14bDGlcNAc scatter phi psi # phi against psi scatter plot 

namd_path  /home/[user]/.NAMD_2.13_Linux-x86_64-multicore/namd2
namd_energy trisaccharide_PE potential_energy

ring_pucker GlcNAc "resid 2 and name O5 C1 C2 C3 C4 C5" # Calcualte the Cremer-Pople ring pucker parameters of the GlcNAc ring. Provides several graphs and data sets for the trajectory. 
ring_pucker Glc "resid 3 and name O5 C1 C2 C3 C4 C5"

5) Known Bugs

• Cannot run two or simulataneous simulations with namd_energy calc enabled.