Additional options: the DOCKOPT file

keyword	variable name	allowed values	default
write_coordinates	wrt	yes, no	yes
standard_pdb	stdpdb	yes, no	no
normalization_type	nrmtyp	n, sqrt(n)	n
focus_ratio	fratio	real	1.0
vdw_minimum	vdwmin	real	-1.0e+10
electrostatic_limit	eslim	real	1.0e+10

write_coordinates

is used to save disk space when it is anticipated that a large number of orientations will result from a SINGLE run. no: coordinates will not be output for the orientations; only the REMARK lines, which contain the scores, will be written; yes: coordinates and REMARK lines will be written. write_coordinates does not affect SEARCH runs.

standard_pdb

allows the user to specify standard PDB format output, with charges in the temperature factor field. no: output will be in extended PDB format; yes: output will be in standard PDB format. This option affects both SINGLE and SEARCH mode runs. The advantage of extended PDB format is that it allows the output to be rescored with different contact, Delphi, and/or force-field maps. The advantage of standard PDB format with charges in the temperature factor column is that it should be displayable by virtually all modeling packages, and that the atoms may often be colored according to the values in the temperature factor column.

normalization_type

controls the normalization factor to be used during a SEARCH run. n or 0 (default): normalize by the number of heavy atoms; sqrt(n) or 1: normalize by the square root of the number of heavy atoms.

focus_ratio

is the minimum ratio of number of orientations found in a zooming cycle to number of orientations found previously (either without zooming or in the previous cycle) needed to trigger a further cycle of zooming. focus_ratio cannot override focus_cycles, which ultimately controls the number of nested zooming cycles that may be performed. Only runs with zooming are affected by focus_ratio. The default value is 1.0.

vdw_minimum

is the minimum VDW interaction energy a ligand atom can receive. If a ligand atom receives a lower VDW interaction energy, the energy will be reset to this value. Any resetting represents a departure from the standard molecular mechanics interaction energy. However, this variable is mainly useful for similarity docking, in which only the attractive part of the VDW potential is being used (vdw.parms.norepuls in the subdirectory parms is the vdw_parameter_file being used). In such cases, the scores do not have physical meaning, at least as energies.

electrostatic_limit

is the maximum absolute value of electrostatic interaction energy that a ligand atom can receive. If the absolute magnitude of a ligand atom's electrostatic interaction energy exceeds electrostatic_limit, it will be set to this value (but the sign will not be changed). Again, any resetting represents a departure from the standard molecular mechanics interaction energy. However, this variable is generally useful only for similarity docking, in which the "electrostatic interaction energy" is scaled by -1.0 (see electrostatic_scale) so that charge similarity rather than complementarity is favored; the scores do not have physical meaning, at least as energies. electrostatic_limit must be positive; if a negative value is specified, its sign is changed.

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