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FAQs
View entire FAQ in fullFrequently Asked Questions (& Answers!)
| Sections |
|---|
| General Questions |
| Scientific Questions |
| Obtaining AutoDock |
| Installing AutoDock |
| Technical Questions |
| Running AutoDock |
| Running ADT |
| Virtual Screening |
| Analysing Results |
General Questions
View 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 Questions
View 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
Virtual Screening
View 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 Results
View 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