# Optional Parameters¶

## Input 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.

## Output 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). Additionally, a parameter file named FOO.param (see -param) and a log file named FOO.log (see -log).

[default = gameplan]

-output <filename>
-o <filename>

[keyless parameter 3]

OEBinary output file (.oeb or .oeb.gz), containing calculated results.

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

## Parameters¶

-merge <number>

[default = 0.35 Å]

Distance cutoff for merging two sample points.

-sp3_aromatic <bool>
-sp3aromatic <bool>

Sample sp3 hybridization at each aromatic ligand atom.

[default = false]

-stabilization <bool>
-stbl <bool>

Search for regions where water is stabilized or destabilized by in the protein/ligand complex.

[default = true]

-clean <bool>

Remove temporary files written by SZMAP during this run of gameplan.

[default = true]

-light_background
-light_bkg

If specified, annotation colors will be adjusted to better match a white background. By default, they are chosen to match a dark background.

-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 gameplan to fail.

-num_orientations <number>
-rot <number>

Number of orientations for the SZMAP probe.

[default = 60]

## MPI Options¶

-szmap_mpi_np <number>

Run GamePlan 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.

-szmap_mpi_hostfile <filename>

Run GamePlan 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 -szmap_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 gameplan run (see -prefix) can be used with the -param flag in subsequent gameplan 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 - to send to standard-output.

-progress <style>

How to display SZMAP 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 = dots]

-verbose
-v

Print additional information to log during calculations.