/pyloxr_old

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pyLOXr README

pyLOXr is a set of Python scripts based on MDAnalysis Python package, which are useful for analysing Molecular Dynamics trajectories calculated using AMBER and to prepare the required files for carrying out QM/MM calculations using ChemShell. It is presented as an option-based program (as-simple-as-possible command-line UI), but it is also possible to use it as a set of modules in order to integrate it in any other program.

Modules

pyLOXr is divided into 6 different modules, some of them depending on other ones.

  1. Trajectory summariser: generates a short txt file where the basic characteristics of the trajectroy are specified.
  2. Plots and histograms of distances: generates the plots and histograms of the distances between groups of two atoms.
  3. RMSD: generates a plot of the RMSD of the backbone of the protein or of the substrate.
  4. Frame selector: selects the frames of the trajectory which satisfy a given criteria(on). This(These) criterion can be either a cut-off distance (specified by user) between two specified atoms or the difference of distance between two different bonds.
  5. QM/MM models: it generates a cropped model where only a pseudospherical drop of solvent molecules are kept. As a results, the module gives a pdb file which can be used on ChemShell. Moreover, it lets crop also the topology and parameters and coordinates files using the ParmEd package.

Dependencies

pyLOXr depends on the following Python packages: