grid_spacing¶

grid_spacing = spacing

This is the grid mesh given in Å. A value of 0.5 means there is 0.5 Å between two grid points. The lower this value is, the more accurate will be the result but the slower the program will be. We noticed that, below 0.5, the final volume variations are not very different from those obtained with 0.5 while the execution time exponentially increases.

The Maximum Englobbing Region (MER) where a pocket lies is defined using inclusion or exclusion spheres, boxes or cylinders. The final is MER is created by combining these objects using boolean operators. This concept is known as solid constructive geometry

See Epock error estimation section for more details on grid_spacing adequate value.

grid¶

grid = input_grid.pdb

Alternatively, Epock can use a grid stored as a PDB file.

include|exclude_sphere¶

include_sphere = x  y  z  r
exclude_sphere = x  y  z  r

Spheric include/exclude regions are defined by their center (x, y, z) and their radius r.

include|exclude_box¶

include_box = x  y  z  lx ly lz
exclude_box = x  y  z  lx ly lz

Cuboid include/exclude regions are defined by their center (x, y, z) and the length or each edge (lx, ly, lz)

include|exclude_cylinders¶

include_cylinder = x1 y1 z1 x2 y2 z2 r
exclude_cylinder = x1 y1 z1 x2 y2 z2 r

Cylindrical include/exclude regions are defined by the coordinates of the upper center (x1, y1, z1) and the lower center (x2, y2, z2) and and their radius r.

contiguous¶

contiguous = (ON|OFF) | (TRUE|FALSE) | (0|1)

Boolean that specify whether or not non-contiguous points should be removed.

contiguous_seed_sphere|box|cylinder¶

contiguous_seed_sphere = x  y  z  r
contiguous_seed_box = x  y  z  lx ly lz
contiguous_seed_cylinder = x1 y1 z1 x2 y2 z2 r

Seed region for non-contiguous points removal. At first, Epock will define as “free space points” every grid point that does not overlap any atom and that lies within the seed region within the seed region. The algorithm will then step by step add all grid points with a distance lower that a cutoff value (see contiguous_cutoff) and define them as “free space points”. All non-visited points are therefore non-free space.

The directives for defining the contiguous seed region share the same format than for the MER definition. Note however that contiguous seed regions cannot be composed of include and include regions. They are for now limited to a single inclusion region.

contiguous_cutoff¶

contiguous_cutoff = cutoff

The cutoff from non-contiguous points removal in Å.

contribution¶

contribution = (ATOM|RESIDUE) | (NONE|FALSE)

Calculate the residue contribution on the free space i.e. the number of of grid points that overlap a given residue. A high contribution value will therefore reflect that a residue is largely inside the grid while a lower contribution will reflect peripherical residues. The value of residue contribution is not very indicative itself but the evolution of this data over an MD simulation can help identifying residues that are peripherical at first and become more central at some point.

It is to be noted that contribution can be computed at the residue scale or at the atomic scale.

The output file produced by Epock will be named prefix_contribution.dat with prefix the cavity name has defined in the configuration file section header.

The data in the output file can be plotted thanks to the plot_contribution.py script distributed along with Epock.

profile¶

profile = (ON|OFF) | (TRUE|FALSE) | (0|1)

Calculate the profile of the pocket along the Z-axis. This feature can be enabled to calculated the profile of a channel pore. The trajectory is assumed to be aligned on the Z-axis. Pore profile can therefore be easily calculated using include cylinders.

The output file produced by Epock will be named prefix_profile.dat with prefix the cavity name has defined in the configuration file section header.

The data in the output file can be plotted thanks to the plot_profile.py script distributed along with Epock.

path¶

path = cavity_identifier

Epock can calculate if a path exists between two predefined cavities. For more informations about the algorithm used for path finding, refer to section path finding from the Algorithms page.

The output file produced by Epock will be named path_prefix1_prefix2.dat with prefix1 and prefix2 the cavity names has defined in the configuration file section header.

padding¶

padding = radius

Default value : 1.4 Å.

This parameter should be considered as a probe radius for free space detection. To be more specific, every grid point that lies within padding Å of any atom will not be considered as free space.

precision¶

precision = prec

This specifies the grid mesh for the volume calculation (the parameter grid_spacing defines the grid mesh for the free space detection). As this parameter is called “precision”, the higher the value is, the more accurate will be the calculation (so the unit is 1/Å). We recommand use the default value (2) as we did not observe a strong dependency of the result on this variable.

See Epock error estimation section for more details on precision adequate value.