FAQsView entire FAQ in full
Frequently Asked Questions (& Answers!)
General QuestionsView section in full
- How can I learn more about how to use Cygwin/Linux/Mac OS X?
- How do I join the ADL (AutoDock mailing list)?
- How do I search the ADL (AutoDock mailing list) archives?
- How do I report a bug?
- Is there a graphical user interface to AutoGrid and AutoDock?
- Can't find or open a file?
- Where can I find the Python scripts for preparing and analysing AutoDock dockings?
- How should I prepare a ligand for docking with AutoDock?
- How to cite AutoDock?
Scientific QuestionsView section in full
- Can AutoDock be used for "Blind Docking"?
- Where do I set the AutoDock 4 force field parameters?
- Should I always use polar hydrogens?
- How can I set up the protonation state of my histidine sidechains?
- How do I add new atom types to AutoDock 4?
- How Autodock 4 converts binding energy (kcal/mol) into Ki
- Missing atom types (“Why atom type 'X' is not recognized?”)
- Water: my target crystal structure has some waters in the active site, what should I do with them?
- Side Chain Alternate Confirmations
- Co-factors and Nucleic Acids
- Metal Charges
- Lowest energy or Largest Cluster? How to evaluate docking results
Obtaining AutoDockView section in full
Installing AutoDockView section in full
Technical QuestionsView section in full
Running AutoDockView section in full
Running ADTView section in full
Virtual ScreeningView section in full
- Which library should I use for virtual screening?
- How many dockings and energy evaluations should I use for each compound?
- How do I know which docking results are "hits"?
- What's the best way to analyze the results?
- Will I need to visualize the virtual screening results?
- How do I run virtual screening on Windows?
Analysing ResultsView section in full
- How do I visualise the docking results in the AutoDock log file?
- How do I evaluate AutoDock's clustering results?
- I used "get-dockings" to extract the docked conformations. Where is the macromolecule?
- I get very high Reference RMSD values in my DLG; what went wrong?
- Is there a way to save a protein-ligand complex as a PDB file in AutoDock?
- What should I look for when I visualize a docked compound?
- In a flexible receptor docking in AutoDock 4, which atoms are used in the clustering?
- Why do the results differ when multiple dockings are done with the same input?
by morris — last modified 2007-07-19 17:31
Contributors: Ruth Huey, Garrett M. Morris, Sargid Dallakyan, Stefano Forli