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• Visualize docking grids
  1) Convert grids into a format that Chimera can read in 2) Visualize grids in Chimera
  909 bytes (142 words) - 00:26, 25 May 2024

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• Tutorial on running DOCK3.7 with blury-GIST
  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:
  774 bytes (123 words) - 19:39, 17 November 2017
• Blastermaster files
  == scoring grids == === VdW (ChemGrid) scoring grids ===
  2 KB (294 words) - 15:10, 25 March 2014
• Delphi electrostatics
  ...components and stored on grids. However only the steric interaction energy grids are used in DOCK 6 as a part of Dock3.5 Score. For calculating the electros === Creating DelPhi electrostatic grids ===
  2 KB (254 words) - 00:22, 25 May 2024
• Grid-convert
  ...nvert grids generated by chemgrid, solvgrid and DelPhi into DOCK6 readable grids.
  485 bytes (65 words) - 01:02, 11 March 2014
• Visualize docking grids
  1) Convert grids into a format that Chimera can read in 2) Visualize grids in Chimera
  909 bytes (142 words) - 00:26, 25 May 2024
• Qnifft DOCK 3.6 conversion
  If you're using DOCK Blaster, you can make the new electrostatic grids by typing: make grids/rec+sph.qnifft.phi
  2 KB (388 words) - 20:32, 8 October 2012
• Ligand desolvation
  === Creating SOLVMAP grids === [[Category:Grids]]
  1 KB (231 words) - 00:23, 25 May 2024
• How to protonate a receptor for docking?
  ...SA does not require grids at all, although you have to option of using the grids generated by the GRID accessory to calculate the vdw term.
  746 bytes (128 words) - 18:15, 2 May 2024
• Docktools
  ...used to generate steric, electrostatic and ligand and receptor desolvation grids. Dock3.5 scoring functionality in DOCK 6 is an alternate scoring approach t
  732 bytes (106 words) - 20:11, 8 October 2012
• Zou-GBA Score
  # The path to the pairwise GB grids #The path to the SA grids
  2 KB (242 words) - 20:33, 8 October 2012
• Solvgrid
  ...id program creates bulk (or receptor) and explicit (or ligand) desolvation grids using the occupancy desolvation method (Luty et. al., J. Comp. Chem, 1995; ...lvgrid program during docking. It requires the calculation of two separate grids:
  3 KB (475 words) - 00:26, 25 May 2024
• Solvmap
  ...restatement of input parameters; messages pertaining to calculation of the grids * solvmap #ligand desolvation grids
  2 KB (278 words) - 00:26, 25 May 2024
• DOCK Accessories
  generates the scoring grids <ref name='bks1992' >[http://onlinelibrary.wiley.com/doi/abs/10.1002/jcc.54 scoring grids (from [[grid]] to
  2 KB (229 words) - 22:43, 10 January 2019
• Understanding MakeDOCK, which automates sphere and grid generation
  ...MakeDOCK Makefile, you simply type 'make' to generate all the spheres and grids. ...art up a residue in grids/rec+sph.crg and type 'make' to regenerate delphi grids.
  3 KB (488 words) - 02:43, 13 March 2014
• Dock Ligand Clustering
  ...ay need a distmap file in your grids directory (just type 'distmap' in the grids directory and it should be created automatically, this will not be used in distmap_file ../grids/distmap
  3 KB (308 words) - 20:11, 8 October 2012
• DOCK 3.6 User Manual
  ...nergies. So be aware of the DOCK version being used and the Electrostatic grids generation method. solvmap_file ../../grids/solvmap_sev
  7 KB (721 words) - 22:17, 2 January 2019
• Delphi
  ...w Delphi is used to score ligands, see this page on [[visualizing delphi]] grids.
  540 bytes (81 words) - 00:25, 25 May 2024
• Analysing the results
  For default grids *run <tt>'$mud/doscoreopt.csh your.eel1 ../path/to/grids'</tt>
  5 KB (949 words) - 18:10, 8 October 2012
• BKS lab Structure preparation
  ...f the receptors and needs parameters so that Electrostatic, Solvation, VDW grids can be calculated. To calculate the VDW types and charges call the followin which you should add the the prot.table in grids and then run:
  2 KB (395 words) - 12:42, 14 March 2014
• Chemgrid
  ...nted in the Grid section above. However only the steric interaction energy grids are used in DOCK 6 as a part of Dock3.5 Score. The electrostatic interactio ...restatement of input parameters; messages pertaining to calculation of the grids
  3 KB (365 words) - 05:24, 13 March 2014