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* Grid preparation submitted * Grid preparation running

...processes. It has been tested to obtain similar results compared with the grid-based free energy model but with much less computation efforts. o gbsa_zou_vdw_grid_prefix [grid] (string):

...raction energy between the ligand and the receptor is calculated from this grid. For more information please see the [http://dock.compbio.ucsf.edu/DOCK_6/d To create a DelPhi electrostatic grid (phimap) you will need:

* Design of a grid service based platform for in silico protein-ligand screenings. Levesque

USAGE: grid -i grid.in [-stv] [-o grid.out] - i input_file #Input parameters extracted from input_file, or grid.in if not specified

specify the margin to perform grid generation ...ritten out in the OUTDOCK file, DOCK will use the intersections of all the grid boxes.

Desolvation grid: ../dockfiles/ligand.desolv.heavy Additional hydrogen desolvation grid: ../dockfiles/ligand.desolv.hydrogen

...ds at all, although you have to option of using the grids generated by the GRID accessory to calculate the vdw term.

* MakeDOCK automates the process of sphere and grid generation for a target. * Automatically displays non-fatal WARNINGS that occurred during grid generation, which often lead to incorrect docking results.

(if you want a finer grid size you can specify it after the pdb file, the default is 1 angstrom/grid)

* [[Understanding MakeDOCK, which automates sphere and grid generation]]

...ctric regions and a description of an ion-accessible volume and produces a grid of electrostatic potentials. From this, transfer energies between different *** pbsa_vdw_grid_prefix [grid] (string):

...ar as the "sampling" I am not sure what this means, but I assume it is the grid size. In any case, it seemed that in the 2.B. set there was a greater diver

Grid Score: -29.223606

...the location and size of the grids that will be calculated by the program grid , using any graphics program that can display PDB format. The user is asked

Run blastermaster for flexible grid generation: xtal-lig.pdb (--xdist) 5) Grid IDs (--flexgrids) 6) Ground state grid

...W well-depth values are used in molecular mechanics-scoring functions (see Grid). The valence is the value for the maximum number of atoms that can be atta

...heres (generated by sphgen) with ligand atoms and uses scoring grids (from grid) to evaluate ligand orientations (Kuntz, et al. J. Mol. Biol. 1982 and Shoi ...these sphere centers. Or, a grid may be generated within the site and each grid point may be considered as a sphere center. Our sphere centers, however, at

- '''box''' (we use this to trim down the electrostatics grid to the size of the van der Waals and ligand desolvation grids) Next, copy your new "trim.electrostatics.phi" grid into your "dockfiles/" folder. Make sure that your INDOCK file has the corr

centers. Or, a grid may be generated within the site and each grid grids in order to minimize the overall computational time. At each grid