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scoreopt

Elaine Meng, Brian Shoichet
scoreopt is an interactive program for stand-alone scoring of DOCK output. There are three options.

OPTION 1:
calculates contact scores for single or search mode output, given that the output is in standard PDB format up through the coordinates columns. Output from all versions fulfills this criterion. A grid for contact scoring, from distmap, is required.

OPTION 2:
calculates electrostatic interaction energies for single or search mode output, given that the output is in standard PDB format up through the coordinates columns, then has atomic charges in another F8.3 field right after the coordinates. Extended PDB format fulfills this criterion (see below). A Delphi (Klapper et al., 1986; Gilson, Sharp, and Honig, 1987) electrostatic potential map must be supplied.

OPTION 3:
calculates force field scores for single or search mode output, given that the output is in extended PDB format (includes charges and integer vdw type indicators) and given the grids from chemgrid and a vdw parameter file. Extended PDB format is produced when the database for searching is in version 3.x format, or when the ligand input for single mode is in a format that includes charges and atom type information (SYBYL MOL2 or extended PDB). The extended format is standard up through the coordinates columns, and then: F8.3 (atomic charges), F8.3 (electrostatic potential OR contact score per atom; not necessary for this program), and I3 (van der Waals type indicators). (Standard PDB format, which cannot be used for direct rescoring, can be obtained from DOCK by setting standard_pdb in the DOCKOPT file.) Option 3 is useful for getting the components of the force field scores of ligands found in search mode, rescoring using different grids (for instance, using a different dielectric function), or counting the number of atoms, if any, that fall outside the grid.

The names of necessary input files and an output file are requested. There may be many ligands in the input file, as long as each ends with a TER card. Electrostatic and force field scores are reported in kcal/mol.

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