Ligand preparation

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NB these instructions appear to refer to a version that is local to UCSF and not part of the DOCK 3.7 distribution YET

Ligand preparation has been modified to use mol2db2 instead of mol2db for database generation. Many other features have also been integrated. To build a set of ligands from SMILES on the cluster, use:

db2start.e.csh input.smi ref

Or to build on a standalone machine, use

db2gen.e.csh input.smi ref

Note that many programs must be properly installed and available or this script will fail. The most troublesome is EPIK. For this reason, among others, Dahlia Weiss has helped get Marvin's Chemaxon cxcalc running in lieu of EPIK. This is probably the preferred way to build molecules. Run it on the cluster with:

db2start.e.cxcalc.csh input.smi

The format of the input file here is a two column file with one column being a SMILES string and the other column being an ID. Any length IDs are valid, but only 16 characters will get carried into the DOCKing phase of the operation, see Mol2db2_Format_2 for more details.

Once the jobs have finished, you can run name

To build dockable name-XXXXXX.db2.gz files.

This pertains strictly to preparing mol2db2 format files for docking using DOCK 3.7. Look elsewhere for database preparation for previous versions.

This work is licensed under the Creative Commons Attribution-ShareAlike 3.0 Unported License. To view a copy of this license, visit This page is adapted from "DOCK3.7 Documentation" by Ryan G. Coleman. Based on a work at