DOCK 4.0 Frequently Asked Questions

Parameter Path Error
Backwards Compatibility
Flexible Ligand Database

Last modified July 18, 1997

ERROR efopen: Unable to open UPDATE_PARAMETER_PATH_IN_DEFINE.H/vdw.defn. Terminating execution."

The compilation instructions in the README files left out an important step. This will be updated immediately. Go to ~dock4/source/dock and perform these steps:

Before compiling for the first time, edit the PARAMETER_PATH variable in define.h. Set it to the unix path for the directory containing the dock parameters.

Existing setting:
#define PARAMETER_PATH "UPDATE_PARAMETER_PATH_IN_DEFINE.H/"

Example setting: #define PARAMETER_PATH "/applications/dock4/parameter/"

Perform this update whenever the location of the parameter files is changed.

"We just upgraded to DOCK4.0 from 3.5, and I was wondering about compatability with the old sphere and grid files (from distmap and chemgrid). This isn't explicitly addressed in the manual."

DOCK4 BACKWARDS FILE COMPATIBILITY

dock3.5 file	compatible?	comment
sphere	yes	but only first cluster read
chemgrid	yes	must specify grid_version = 3.5
distmap	no	to perform contact scoring, use grid v4.0
database	no	use mol2 instead

"Since DOCK 4.0 can perform a conformation search of flexible molecules, is there a new procedure to build the ligand database?"

All detection of flexibility is performed on the fly, as each ligand is read in. Therefore no preprocessing of the database is necessary.

Just use the recommended MOL2 format for the database, with 3D structures built by CONCORD (or similar procedure). You can modify the way flexibility is treated by editing the parameter files (flex.defn and flex_drive.tbl).