How do I sample flexible ring conformations (boat, chair etc..) during docking?
MolSoft’s ICM docking algorithm has flexible ring sampling included on the fly. Just set ring sampling level to 1 (flex ring only in pre-sampling step) or 2 (throughout the simulation). To do this: • Set up the docking project (http://www.molsoft.com/gui/start- dock.html#docking-start) • Before running the docking simulation go to Docking/Preferences/ General and change the flexible ring sampling level to 1 or 2. • Now run the docking simulation (http://www.molsoft.com/gui/start- dock.html#begin-docking-simulation) OR, If you want to generate the conformations before docking and you have ICM-Pro + ICM-Chemistry then you can use the conformation generator algorithm described here: http://www.molsoft.com/gui/conf-gen.
MolSoft’s ICM docking algorithm has flexible ring sampling included on the fly. Just set ring sampling level to 1 (flex ring only in pre-sampling step) or 2 (throughout the simulation). To do this: • Set up the docking project (http://www.molsoft.com/gui/start- dock.html#docking-start) • Before running the docking simulation go to Docking/Preferences/ General and change the flexible ring sampling level to 1 or 2.
Related Questions
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- How do I sample conformations of flexible rings in docked ligands, for example, a "chair-boat" transition?
- How do I sample flexible ring conformations (boat, chair etc..) during docking?
