Tutorial on running DOCK3.7 with blury-GIST

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first we truncate the grids. That is we cap the max magnitude any on voxel can contribute to the score. Use the following command to truncated the GIST grids:

python /path/GIST_DX_tools/src/dx-remove_extrema.py input.dx value ouput_prifix > truncate.log

if value = 3.0 kcal/mol/anstroms^3 then the max any on voxel can contribute is 0.375 kcal/mol.

Use the following python script to blur GIST grids:

python /path/GIST_DX_tools/src/dx-gist_precalculate_sphere_gausian.py infile sphradius divider pad_radius outfileprefix

Note that the blurring process will shrink the grids slightly by the sphere radius.

  • set divider to 2.0

We will generate two grids one for heavy atoms and one for hydrogens:

  • radius = 1.8, pad_radius = 1.8
  • radius = 1.0, pad_radius = 1.8