compute_grids

boolean

no

Flag to compute scoring grids.

grid_spacing

real

0.3

The distance between grid points along each axis.

output_molecule

boolean

no

Flag to write out the coordinates of the receptor into a new, cleaned-up file. Atoms are resorted to put all residue atoms together. Terminal sybyl capping groups are merged with the terminal residues. This option can be useful to fix ligands also, so that hydrogens added by sybyl are put with the proper residue.

contact_score

boolean

no

Flag to construct contact grid.

contact_cutoff_distance

real

4.5

Maximum distance between heavy atoms for the interaction to be counted as a contact.

chemical_score

boolean

no

Flag to construct chemical grid.

energy_score

boolean

no

Flag to perform energy scoring.

energy_cutoff_distance

real

10

Maximum distance between two atoms for their contribution to the energy score to be computed.

atom_model

string

u

Flag for how to model of non-polar hydrogens.

• u = United atom model. Hydrogens attached to carbons are assigned a zero VDW well-depth and the partial charge is transferred to the carbon.
• a = All atom model. Hydrogens attached to carbons have regular VDW well-depth and partial charge is not modified.

attractive_exponent

integer

6

Exponent of attractive Lennard-Jones term for VDW potential. See Equation 1 on page 74 for context.

repulsive_exponent

integer

12

Exponent of repulsive Lennard-Jones term for VDW potential.

distance_dielectric

boolean

yes

Flag to make the dielectric depend linearly on the distance.

dielectric_factor

real

4

Coefficient of the dielectric.

bump_filter

boolean

no

Flag to screen each orientation for clashes with receptor prior to scoring and minimizing.

bump_overlap

real

0.75

Amount of VDW overlap allowed. If the probe atom and the receptor heavy atom approach closer than this fraction of the sum of their VDW radii, then the position is flagged as a bump.

• 0 = Complete overlap allowed.
• 1 = No overlap allowed.

receptor_file

receptor.mol2

Receptor coordinate file. Partial charges and atom types need to be present.

box_file

site_box.pdb

File containing showbox output file which specifies boundaries of grid.

vdw_definition_file

$PATH/vdw.defn

VDW parameter file.

chemical_definition_file

$PATH/chem.defn

Chemical label definition file for use when chemical_score set.

score_grid_prefix

grid

Core file name of grids (file extension will be appended automatically).

receptor_out_file

receptor_out.mol2

File for cleaned-up receptor when output_molecule set.