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DOCK FAQ

A DOCKumentation supplement

rev. 31 August 1995

To address the needs of our customers, we are slowly putting together a FAQ which may aid in getting set up for using DOCK and with problem areas in DOCK's operation. If you feel there are issues which haven't been appropriately addressed here, please let me know. If you feel this is a useful effort on my part, that'd give me a warm, fuzzy feeling too. Bear in mind, this thing's still under construction!

CONTENTS

A. Prospective DOCK Customers

  1. Where can I get more information on DOCK?
  2. What are the system requirements for DOCK?
  3. How is DOCK distributed?
  4. What comes in the DOCK package?
  5. What else do I need to get?
  6. What ligand databases are supported?
  7. What modeling packages best interface with DOCK?
  8. Like, how long does it take to do a DOCK run?

B. Current DOCK Clients - Specific Questions

  1. Do I really need QCPE's version of MS? Where can I get it?
  2. Do I need to use SPHGEN? What are some alternative methods of generating site points?
  3. How do I get QCPE MS to recognize standard PDB files?
  4. What is the status on using Delphi electrostatic scoring with DOCK?
  5. What about hydrogens in molecular surfaces, docking, and scoring?
  6. What's all this stuff in my CHEMGRID OUTPARM file?
  7. What about using the Cambridge Structural Database with DOCK?
  8. Bugs in sortDOCKout??
  9. How in the world do I use chemical matching (a.k.a. coloring)?!
  10. Are there standard bin sizes? 

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Curator: Daniel Gschwend, gschwend@cgl.ucsf.edu (web page born 25 August 1995)