MDLovoFit.jl

Julia interface for the MDLovoFit package for analyzing the mobility of structures in MD simulations.

Installation

1. Install Julia using the juliaup installer, on your platform.

2. Install the necessary packages with:

juila> import Pkg; Pkg.activate("MDLovoFit", shared=true) 

julia> Pkg.add(["MDLovoFit", "Plots"])

These commands will create an environment with the MDLovoFit and Plots packages installed, within which the following example can be run.

Example

Computing the fraction of atoms that can be aligned at each precision

julia> import Pkg; Pkg.activate("MDLovoFit", shared=true) # activate environment

julia> using MDLovoFit, Plots

# PDB file of the system
julia> pdbfile = MDLovoFit.Testing.pdb_file 
# Loading a trajectory: Gromacs XTC in this example
julia> trajectory = MDLovoFit.Testing.trajectory_file # Gromacs trajecotry

julia> mf = map_fractions("protein and name CA", pdbfile, trajectory)
------------------
MapFractionsResult
------------------
Greatest fraction for which the RMSD-low is smaller than 1: 0.89

fraction contains the fraction of atoms considered in the alignment.
rmsd_low contains the RMSD of the fraction of the structure with the lowest RMSD.
rmsd_high contains the RMSD of the fraction not considered for the alignment.
rmsd_all contains the RMSD of the whole structure.

julia> plot(
           mf.fraction,
           [mf.rmsd_low mf.rmsd_high mf.rmsd_all],
           label=["low" "high" "all"],
           xlabel="fraction of aligned atoms",
           ylabel="RMSD",
           linewidth=2, framestyle=:box
       )

Will produce the following plot:

Aligning the trajectory

In the plot above, we see that about 90% of the atoms can be aligned with an RMSD of less than 1 Angstrom. Now we align the complete trajectory using this fraction as a criterium:

julia> r = mdlovofit(
           "protein and name CA", pdbfile, 
           trajectory, 
           fraction = 0.9, 
           output_pdb="aligned.pdb"
       )
---------------
MDLovoFitResult
---------------

Aligned pdb file: aligned.pdb
Number of frames considered: 26
Average RMSD of all atoms: 1.18
Average RMSD of the 90.0% atoms of lowest RMSD: 0.96
Average RMSD of the 10.0% atoms of highest RMSD: 3.09

Frame indices availabe in result.iframe
RMSD data availabe in rmsd_low, rmsd_high, and rmsd_all

RMSF data availabe in result.rmsf (Number of atoms: 76)

julia> plot(
           r.iframe,
           [r.rmsd_low r.rmsd_high r.rmsd_all],
           label=["low" "high" "all"],
           xlabel="trajectory frame",
           ylabel="RMSD",
           linewidth=2, framestyle=:box
       )

Which will produce the following figure:

Showing the RMSD as a function of the step of the trajectory for each subset of the protein.

The aligned.pdb file produced in the execution of mdlovofit above contains the frames aligned, and th occupancy field of the atoms indicate if they are, or not, used in the alignment. Visualizing the frames superimposed in VMD, and colored by occupancy, we get:

which illustrates the low and high mobility regions of the protein.

For additional information go to MDLovoFit.

Reference

Please cite the following reference if MDLovoFit was useful:

• L. Martínez, Automatic identification of mobile and rigid substructures in molecular dynamics simulations and fractional structural fluctuation analysis. PLoS One 10(3): e0119264, 2015. [LINK]