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dock 3.5 ligand database format
In DOCK 3.5 the ligand database format has changed. The new ligand database
format (a) handles a variable number of chemical labels, (b) incorporates
fields for conformational entropy and solvation correction, although they are
not currently used by DOCK, (c) includes all the fields of the version 3.0
database, and (d) has been reorganized so that all the information pertaining
to a particular atom is grouped together. This new format takes a little more
space than the 3.0 format (which omitted fields that were 0), but it is easier
to understand.
After the header line (DOCK 3.5 ligand_atoms) comes the color (label) table -
a list of color names, one per line (format A30). Next come the ligands, in the
format below. The label (color) for each ligand atom is simply an index into
the color table (i.e. 1 for the first color listed, 2 for the second
color listed, etc.).
For an example molecule, see here.
Curator: Daniel Gschwend, gschwend@cgl.ucsf.edu (rev. 1 September 1995)