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hbdata

Andrew Good

This program automatically runs Goodford's GRID program (version 11.01, Goodford, 1985) for a variety of probes, creating SYBYL contour files and files containing centers of favorable interaction energy for sphgen file creation. It also runs GRIN and will stop if GRIN encounters a problem with the PDB file. The program requires an input file called HBIN which should follow this example:

`3dfr`	name of parent protein (PDB file name - used for file naming)
`/bert/grid11.01`	root directory for GRID
`-12.0`	minimum x coordinate
`26.0`	minimum y coordinate
`4.0`	minimum z coordinate
`9.0`	maximum x coordinate
`48.0`	maximum y coordinate
`33.0`	maximum z coordinate
`1.0`	grid density - # of planes per Ångstrom of GRID map
`-7.0`	highest permitted interaction energy included in site point creation
`1.0`	exclusion sphere to remove local low energy pts. near each local minimum
`2`	# of probes in probe list that will be used - first two are N3+, O::

Notes for use in conjunction with mol2sph: The GRID energy of each point is assigned to the charge field for reference purposes and atom types are set to dummy. Both of these fields must be corrected, the sphgen file converted into PDB format using showsphere, the resulting atomtypes modified and combined within SYBYL before they can be written to MOL2 format in preparation for mol2sph conversion.

Curator: Daniel Gschwend, gschwend@cgl.ucsf.edu (rev. 1 September 1995)