Parameter Table

keyword	variable name	allowed values	default
scoring_option	versn	1, contact 2, contact+delphi 3, contact+forcefield 4, forcefield	contact
# (if scoring_option = 1,2,3) distmap_file	mapnam	filename	none
# (if scoring_option = 2) delphi_file	phifil	filename	none
# (if scoring_option = 3,4) chemgrid_file_prefix interpolate vdw_parameter_file vdw_maximum electrostatic_scale vdw_scale	prefix interp vdwfil vdwmax escale vscale	filename yes, no filename real real real	none yes none 1.0e+10 1.0 1.0

Parameter Descriptions

scoring_option

may be given either traditionally, as an integer, or as a character string: 1: contact scoring only, 2: contact scoring plus Delphi electrostatic scoring, 3: contact scoring plus force field scoring, 4: force field scoring only. Any other values are reset to the default value, 1 (contact scoring only).

distmap_file

specifies the grid for contact scoring, created by distmap. This file is necessary for scoring options 1, 2, and 3.

delphi_file

specifies the name of the map of the receptor electrostatic potential, calculated with the Delphi program (Klapper et al., 1986; Gilson, Sharp, and Honig, 1987). This file is only necessary for Delphi electrostatic scoring.

chemgrid_file_prefix

states the prefix name for the force-field grid files created using chemgrid. For example, if the files are named foo.bmp, foo.esp, and foo.vdw, chemgrid_file_prefix is foo. The value of chemgrid_file_prefix should be the same as the value of grdfil used for running chemgrid.

interpolate

indicates whether or not trilinear interpolation will be used for calculating force-field scores. no: the values for the nearest grid point will be used; yes: the values will be obtained by trilinear interpolation of the values for the eight surrounding grid points.

vdw_parameter_file

gives the van der Waals parameters file name. The file vdw.parms.amb and related parameter files (Appendix 2) are located in the parms subdirectory and contains AMBER all-atom and united-atom parameters (Weiner et al., 1984; Weiner, et al., 1986). This table consists of comment lines and lines containing SQRT(A) and SQRT(B) for each van der Waals type. The lines must be in order of type, without any skipped integers.

vdw_maximum

specifies the maximum van der Waals interaction energy a ligand atom can receive. If a ligand atom receives a higher (less favorable) VDW interaction energy, the energy will be reset to this value. Any resetting represents a departure from the standard molecular mechanics interaction energy. If resetting is not desired, vdw_maximum should be set very high; the default value is 1.0E+10 kcal/mol. Lower values allow orientations that make fairly close contacts to receive better force-field scores; in effect, the sensitivity of the 6-12 potential to small changes in interatomic distances can be counteracted by limiting the magnitude of steric penalties.

electrostatic_scale

is a scaling factor for the electrostatic component of the force field score. The default is 1.0 (no scaling); other values represent a departure from the standard molecular mechanics interaction energy. This feature allows the user to adjust the relative weights of the electrostatic and VDW terms. The electrostatic component can also be scaled by varying esfact when running chemgrid. Only through electrostatic_scale, however, can the electrostatic component be scaled to 0.0. Either electrostatic_scale or esfact may be used to change the sign of the electrostatic term.

vdw_scale

is a scaling factor for the VDW component of the force field score. The default is 1.0 (no scaling); other values represent a departure from the standard molecular mechanics interaction energy. This feature allows the user to adjust the relative weights of the electrostatic and VDW terms. vdw_scale may be positive, negative, or equal to 0.0.