| Dock |
 Introduction Overview Installation Quickstart Hints and tips Utilities PVM version | | usage: cat cmd.cex protein.cex spheres.cex molecules.cex | dock > docked.cex Dock docks small molecules from "molecules.cex" into the protein from "protein.cex" in two stages:
During the optimization, optional user specified distance constraints can be applied. A reference conformation (e.g. the crystallographically determined bound ligand) is specified by adding coordinates for the molecule and a REMARK field of "1 LIGAND REFERENCE" (this is done automatically by pdb2site). The RMS difference between each docked conformation and the reference conformation will be reported, along with the reference conformation's score. Including hydrogens (setting ADDH to TRUE) will typically at least double the amount of CPU time required, but hydrogens produce higher-quality ligand geometries, especially for molecules with flexible rings and aliphatic chains. If the output CEX file is too large during large docking runs (for example, if it exceeds the 2GB file limit on Linux), the simplest solution is to pipe the output of dock into either gzip or split. The CEX output compresses well, so gzip is usually a good solution. Dock options are specified in "cmd.cex", which is a simple text file. For now, the only way to change these options is to edit this file. The first section of "cmd.cex" defines CEX datatypes for each command option and should not be changed. Editable command options begin after $MSG<"dock options">. Frequently changed commands are:
The following commands are rarely modified (an additional third stage of refinement is added if hydrogens are included using ADDH):
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