Optional Parameters¶

Input File Options¶

-ligand <filename>
-l <filename>

[keyless parameter 2]

If an OEDesignUnit was used as input for the protein, and it contained a ligand the ligand from this will be used unless otherwise specified.

The format can be one that retains partial charges: OEBinary, Tripos .mol2, or DelPhi flavor PDB (where there is radii in the occupancy field and charge in the B-factor field).

Note

If no charges are present on the read molecule, AM1BCC charges and Zap9 radii are assigned to the molecule.

-warn_if_missing_hydrogens

If specified, missing hydrogens will not terminate the program, but will instead generate a warning message. Otherwise, missing hydrogens on the ligand or on more than 10 percent of the protein heavy atoms will cause szmap to fail.

-split_lig

Separate ligand file into individual molecules and run each individually.

Output File Options¶

-prefix <prefix>

Prefix used to name output files. Using -prefix FOO will create results in an OEBinary file named FOO.oeb.gz (see -output_mol). The table produced with -at_coords will be written to FOO.txt (see -table). Additionally, a parameter file named FOO.param (see -param) and a log file named FOO.log (see -log).

[default = szmap]

-output_mol <filename>
-o <filename>

[keyless parameter 3]

OEBinary output file (.oeb or .oeb.gz), with calculated results attached to a copy of the input -protein and any -ligand.

If not specified, -prefix will be used to name the output.

-table <filename>

A tab-delimited table of results from -at_coords calculations is written to this file. If specified, this will override the filename created from -prefix. Specify -table - to send to standard-output.

-std_box <filename>

Write standard (complex) grid bounding box to output ‘box molecule’ coordinate file.

File type Extension
OEBinary .oeb .oeb.gz
MacroModel .mmod .mmod.gz
MDL .mdl .mdl.gz
MOL2 .mol2 .mol2.gz
MOPAC .mopac .mopac.gz
PDB .pdb .ent .pdb.gz .ent.gz
SDF .sdf .mol .sdf.gz .mol.gz
XMol xyz .xyz .xyz.gz

To facilitate visualization, box corners are represented by nitrogen atoms and bonds define the box edges in formats that support bonds. Use -box_mol to select based on this file.

-lig_box <filename>

Write ligand grid bounding box to output ‘box molecule’ coordinate file.

File type Extension
OEBinary .oeb .oeb.gz
MacroModel .mmod .mmod.gz
MDL .mdl .mdl.gz
MOL2 .mol2 .mol2.gz
MOPAC .mopac .mopac.gz
PDB .pdb .ent .pdb.gz .ent.gz
SDF .sdf .mol .sdf.gz .mol.gz
XMol xyz .xyz .xyz.gz

To facilitate visualization, box corners are represented by nitrogen atoms and bonds define the box edges in formats that support bonds. Use -box_mol to select based on this file.

-apo_box <filename>

Write apo grid bounding box to output ‘box molecule’ coordinate file.

File type Extension
OEBinary .oeb .oeb.gz
MacroModel .mmod .mmod.gz
MDL .mdl .mdl.gz
MOL2 .mol2 .mol2.gz
MOPAC .mopac .mopac.gz
PDB .pdb .ent .pdb.gz .ent.gz
SDF .sdf .mol .sdf.gz .mol.gz
XMol xyz .xyz .xyz.gz

To facilitate visualization, box corners are represented by nitrogen atoms and bonds define the box edges in formats that support bonds. Use -box_mol to select based on this file.

Selection Options¶

If a -ligand is provided but none of the selection method’s options are specified, points are selected around the ligand when grids are generated, even for apo grids (see -distance_cutoff).

-at_coords <filename>
-coords <filename>

Perform calculations just at the coordinates of atoms in any molecules in the file. Write those molecules, with the (masked) results attached to the atoms, to the output file.

File type Extension
OEBinary .oeb .oeb.gz
MacroModel .mmod .mmod.gz
MDL .mdl .mdl.gz
MOL2 .mol2 .mol2.gz
MOPAC .mopac .mopac.gz
PDB .pdb .ent .pdb.gz .ent.gz
SDF .sdf .mol .sdf.gz .mol.gz
XMol xyz .xyz .xyz.gz

Text formats such as .xyz are easily modified in a text editor to specify an arbitrary set of coordinates.

The tags that will be used when assigning values to atoms are listed in Appendix 2: SZMAP Atom Properties.

A tab-delimited table of calculation results is printed to a text file (see -table). In the abbreviated column heading, n_ stands for neutral and v_ stands for vacuum. A mask value of 0 indicates that the intvdw value is above -mask_cutoff and this row of data should not be used.

-residue_number <number>
-res <number>

Select grid points around the selected residue (see -distance_cutoff).

-residue_chain <letter>
-chain <letter>

Protein chain used with -residue_number. Case sensitive. Underscore (‘_’) stands for blank.

[default = ‘_’]

-residue_insert <letter>
-inscode <letter>

Protein insertion code used with -residue_number. Case sensitive. Underscore (‘_’) stands for blank.

[default = ‘_’]

-like_std <filename>

Select points in the same bounding box as the standard (complex) grids from the specified OEBinary (.oeb or .oeb.gz) file.

-like_lig <filename>

Select points in the same bounding box as the ligand grids from the specified OEBinary (.oeb or .oeb.gz) file.

-like_apo <filename>

Select points in the same bounding box as the apo grids from the specified OEBinary (.oeb or .oeb.gz) file.

-like_box <filename>

Select points in the same bounding box as the box_mol in the specified OEBinary (.oeb or .oeb.gz) file.

-around_mol <filename>
-around <filename>

Select points enclosing the atoms in the specified file (using -distance_cutoff to define how much extra space beyond the atoms is include).

File type Extension
OEBinary .oeb .oeb.gz
MacroModel .mmod .mmod.gz
MDL .mdl .mdl.gz
MOL2 .mol2 .mol2.gz
MOPAC .mopac .mopac.gz
PDB .pdb .ent .pdb.gz .ent.gz
SDF .sdf .mol .sdf.gz .mol.gz
XMol xyz .xyz .xyz.gz

Text formats such as .xyz are easily modified in a text editor to adjust the region of interest.

-box_mol <filename>

Select points in bounding box defined by atoms in the input ‘box molecule’ file (without a -distance_cutoff).

File type Extension
OEBinary .oeb .oeb.gz
MacroModel .mmod .mmod.gz
MDL .mdl .mdl.gz
MOL2 .mol2 .mol2.gz
MOPAC .mopac .mopac.gz
PDB .pdb .ent .pdb.gz .ent.gz
SDF .sdf .mol .sdf.gz .mol.gz
XMol xyz .xyz .xyz.gz

Text formats such as .xyz are easily modified in a text editor to adjust the region of interest.

-bounding_box <xmin> <ymin> <zmin> <xmax> <ymax> <zmax>
-bbox <xmin> <ymin> <zmin> <xmax> <ymax> <zmax>

Select points in the bounding box defined by minimum and maximum coordinate values.

-surface_points
-surf

Select grid points over the entire surface of the input molecule(s).

Warning

This usually results in very long run times.

-distance_cutoff <number>
-dcutoff <number>

Maximum distance from atoms of selected points, a margin around the focus region.

[default = 6.0 Å]

-value_cutoff <number>
-vcutoff <number>

Minimum FRED surface shape score value for selected points.

[default = 0.05]

-restrict_calc <level>

Control which points are used for calculations. Restricting calculations makes szmap run faster but make the that portion of the results less useful. In particular, restricting apo calculations may not be worth the speed increase because it prevents you from being able to analyze the full apo pocket.

Level Meaning
none Calculate full grids
ligand Restrict ligand calc to region from complex
apo Restrict apo calc to region from complex
both Restrict ligand & apo to region from complex

[default = ligand]

Grid/Coord Options¶

If a grid or coord request option is not specified, all apo results will be generated, and if a ligand is supplied, all std (complex) results as well.

-results_set <type>
-properties <type>
-grids <type>

Defines which sets of properties are included in grid or coordinate results.

Type Output
min Only the standard (complex) results; minimal grid output;
full coord output
default Both standard and apo results, if possible; minimal
grid output; full coord output
max Both standard and apo results, if possible; Full grid
and coord output

min or default used for a grid calculation produces the following properties:

• neut_diff_free_energy_grid (or the corresponding lig or apo grid)
• vdw_grid
• order_grid

See Appendix 1: SZMAP Grids for lists of properties.

[default = default]

-stabilization
-stbl

Generate (complex - (ligand + apo-pocket)) values that show where water is stabilized or destabilized upon ligand binding. This requires extra calculations with the ligand alone.

Points where the minimum interaction + van der Waals energy above this cutoff will be set to 0.0 in the output grids.

[default = 0.0 kcal/mol]

-grid_spacing <number>
-space <number>

Distance between grid points. We recommend this value be above 0.25 Å. szmap creates a grid by first building a temporary grid around the protein and/or ligand molecules that contains values of a function describing the space near the molecular surface. This temporary grid has the same grid spacing as the final grid, so using a very fine grid spacing can generate enormous temporary grids that fill memory.

[default = 0.5 Å]

-standard_grids
-std_grids
-cplx_grids
-std_coords

Generate all standard (holo-complex) grids or coords. The actual grids or coord data will depend on -results_set.

-lig_grids
-lig_coords

Generate all ligand grids or coords. The actual grids or coord data will depend on -results_set.

The std and/or apo grids will still be generated as usual even if this option is specified.

-apo_grids
-apo_coords

Generate all apo grids or coords. The actual grids or coord data will depend on -results_set.

-point_grid

Generate the grid of test points where the calculation is done (1 = test, 0 otherwise). If a ligand is provided, values are for the protein/ligand complex.

-lig_point_grid

Generate the grid of test points where the calculation is done (1 = test, 0 otherwise). Values are for the ligand without the protein.

-apo_point_grid

Generate the grid of test points where the calculation is done (1 = test, 0 otherwise). If a ligand is provided, values are for the protein without the ligand.

Calculation Options¶

-num_orientations <number>
-rot <number>

Number of probe-molecule orientations to sample at each grid point. If this number is set to 24, 60, 216, 360, or 648 then the set of rotations will be symmetric. Otherwise, they will be random and may have lopsided gaps in coverage. For most purposes, 60 is the minimum required for reliable energy calculations and 360 generates robust results.

[default = 60]

-dielectric_model <type>
-model <type>

Type of surface defining the boundary between -inner_dielectric and -outer_dielectric values.

Type Meaning
gaussian Dielectric value changes smoothly over
a distance of approximately 2 Å.
molecular Dielectric changes abruptly at molecular
surface

[default = gaussian]

-inner_dielectric <number>
-eps_in <number>

Dielectric value used inside the protein and ligand atom surface (see -dielectric_model).

[default = 1.0]

-outer_dielectric <number>
-eps_out <number>

Dielectric value used outside the protein and ligand atom surface (see -dielectric_model). This is the dielectric of bulk solvent.

[default = 80.0]

-salt_conc <number>
-salt <number>

Salt concentration in Poisson Boltzmann calculation (units: moles/liter).

[default = 0.05 M]

-zap_spacing <number>

Distance between grid points within the ZAP calculation. To avoid excessive memory requirements and ensure stability during the PB calculation, it is usually best for ZAP spacing to be greater than 0.25 Å.

[default = 0.5 Å]

-boundary_spacing <number>
-boundary <number>

Extra buffer outside the extents of the selection molecule.

[default = 4.0 Å]

Size of probe for boundary calculation.

[default = 1.4 Å]

-water_charge <type>

Which charges are used on the probe water: scaled or am1bcc. Scaled means scale AM1BCC charges to match the water dipole.

[default = scaled]

-vdw_scale <number>

Scale for van der Waals between probe atoms and other atoms.

[default = 1.0]

-use_apo_from <filename>

Use the apo grids in the .oeb results file from a previous szmap run rather than calculating them. This can speed up calculations for a series of ligands docked to a single ligand.

This option is also useful when the apo protein and the complex adopt slightly different states. For example, a key amino acid may have an ionized sidechain in the apo protein and a neutral sidechain in the complex.

MPI Options¶

These options control how MPI is used. Unless one of these options is specified, szmap will run in single processor mode.

-mpi_np <number>

Run szmap calculations in MPI multiprocessor mode using the specified number of processors. If an MPI hostfile is not specified with the -mpi_hostfile option all processor will be launched on the local machine.

-mpi_hostfile <filename>

Run szmap calculations in MPI multihost mode using the specified MPI hostfile. If an MPI hostfile is not specified all processes will be run on the local machine. The hostfile format is a text file with each line specifying a machine and the number of processes to launch on it.

The following example hostfile specified 3 hosts that can run up to 4, 2 and 5 processes respectively.

host1.mydomain.com slots=4
host2.mydomain.com slots=2
host3.mydomain.com slots=5


This example hostfile would typically be used with -mpi_np 11 to make use of all the processors (4+2+5=11).

Note that multiprocessor is only supported on the local machine under Windows, and in homogeneous environments for other architectures (i.e., machines with the same operating system environment).

Other Options¶

-param <filename>

Defines the control parameter file. This file can contain a collection of parameters which can be used instead of writing each parameter to the command-line. In addition, the parameter file written by any szmap run (see -prefix) can be used with the -param flag in subsequent szmap runs. Any command given explicitly on the command line will supersede any command found in a file specified with the -param flag.

-logfile <filename>
-log <filename>

If specified, this will override the filename created from -prefix. Specify “-log - ” (dash) to send to standard-output.

-progress <style>

How to display progress information:

Style Output
none no progress shown
dots print a period (.) for every point tested
percent print percentage complete every 10 points
log print percentage to log file

[default = percent]

-verbose
-v

Print additional information to log during calculations.