Mar 10 2017 Feedback.
Contents
 
Reference Guide
Getting Started
Protein Structure
Molecular Graphics
Slides & ActiveICM
Cheminformatics
Learn and Predict
MolScreen
3D Ligand Editor
 Setup Ligand and Receptor
 Preferences
 Display Options
 Score and Strain
 Edit Ligand
 Screen Replacement Group
 Scan
 Dock or Minimize
  Expand Pocket
 Dock Table
 Fragment Linking
 Restraints
 Flexible Groups
 Refinement
 Multiple Receptor Docking
 Covalent Docking
 Dock to APF
 Save Docked Complex
 Export Docking Project
 Close Project
Tables and Plots
Local Databases
KNIME
Tutorials
 
Index
PrevICM User's Guide
9.8 Dock or Minimize Ligand
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[ Expand Pocket ]

Available in the following product(s): ICM-Pro | ICM-VLS | ICM-Chemist-Pro

Video |

How to Dock or Minimize a Ligand in the Grid maps:

  • Setup the ligand and receptor.
  • Click on the dock or minimize button (see image above).
  • Check the Score and Strain in the top right panel.

How to undertake an all-atom minimization in cartesian coordinates:

  • Note this option is available in ICM 3.8-4 and higher.
  • Click and hold on the Minimize button.
  • Choose Minimize in Receptor.

9.8.1 Change the Size of the Docking Region


How to change the size of the docking region:

The purple box represents the region in which the energy maps are generated. If you want to change the size of this region you can do so by displaying the box (go to Advanced menu) and clicking and dragging on the corners of the puprle box. The maps will then be remade on the fly.


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