Kuntz Home / DOCK Home / FAQ Contents
DOCK FAQ

A DOCKumentation supplement

rev. 31 August 1995

Prospective DOCK Customers

  1. Where can I get more information on DOCK?

  2. What are the system requirements for DOCK?

    3. DOCK is written in Fortran 77 and developed on Silicon Graphics machines. We now compile all code on the IRIX 5.x OS, but code can be recompiled on IRIX 4.0.5. Compilation on other Unix platforms generally works fine with only minor code changes. Successful operation is rumoured to have occurred on IBM RS/6000's, HP 9000's, a DEC alpha, and Crays. The DOCK software suite requires on the order of 50Mb of disk space, and will probably run with 32Mb RAM but 48Mb RAM or more is recommended. DOCK has no graphical component - input and output is strictly via ASCII files.

  3. How is DOCK distributed?

    4. DOCK is distributed either by email, ftp, or by tape cartridge (8mm or QIC150). Email is the most efficient method, and particularly preferred for international customers. Email transfer requires at least 5Mb free space on your mail partition.

  4. What comes in the DOCK package?

    5. The dock distribution comes with the core programs, SPHGEN, CHEMGRID, and DOCK, and close to 50 other utilities which help with various aspects of the docking process. A newly revised and indexed 120 page manual includes descriptions of core programs and all utilities, information on file format interchange, feature descriptions, a beginner's guide, and more. Example files illustrating some of DOCK's features are also provided with an accompanying walkthrough.

  5. What else do I need to get?

  6. What ligand databases are supported?

    7. We routinely use MDL databases such as the ACD (Available Chemicals Directory), CMC, and MDDR. Please contact them for information on availability:

    Direct interfaces are supported for MDL's SDF file format. Because conversion from MDL's SDF format to dockable databases is robust, SDF is the ideal format for working with in-house compound libraries.

    Another commonly-used database is the Cambridge Structural Database:

  7. What modeling packages best interface with DOCK?

    8. DOCK's fullest features are enabled through the use of SYBYL's MOL2 format. Features such as force-field scoring and chemical matching rely heavily upon interfaces to MOL2 format files. Sybyl atom typing is versatile and descriptive. Thus, Sybyl is the ideal software package to accompany a DOCK study and will probably give you less of a headache with reformatting issues. Other software (e.g. MSI's Insight II) is often capable of supporting an interface to MOL2 format - this is a very useful feature. Conceivably, any program (commercial or user-written) that can generate either DOCK database format files or MOL2 format files with appropriate charges and atom types will be sufficient.

  8. How long does it take to do a DOCK run?

    9. How long is a piece of string? DOCK runtimes depend on many variables, including the number of ligands you are interested in exploring, the size of the ligands, the size of the target site to be investigated, and user-controlled sampling parameters. It can take anywhere from a few seconds for a single ligand to a number of days for large databases. 

Dock Home 

Contents 

Continue
Curator: Daniel Gschwend, gschwend@cgl.ucsf.edu