disordered_system_builder_driver.py Command Help
Command: $SCHRODINGER/run disordered_system_builder_gui_dir/disordered_system_builder_driver.py
usage: $SCHRODINGER/run disordered_system_builder_gui_dir/disordered_system_builder_driver.py
[-h] [-molecules NUMBER_OF_MOLECULES] [-density DENSITY]
[-scale_vdw VDW_SCALE_FACTOR] [-obey TARGET] [-maximize_density]
[-tries_per_mol TRIES] [-tries_per_dc TRIES]
[-composition COMPOSITION:COMPOSITION] [-no_system]
[-interface_buffer ANGSTROMS] [-forcefield FORCE_FIELD]
[-split_components] [-water_fftype WATER_TYPE]
[-rigid MONOMER INDEX,MONOMER INDEX] [-target_atoms TARGET ATOMS]
[-selection_type_count SELECTION_TYPE_COUNT] [-dihe_temperature KELVIN]
[-homogeneous] [-homo_by_comp] [-no_disordered_cell] [-ncells NUMBER]
[-pbc SOURCE] [-pbc_side ANGSTROMS] [-no_rotation] [-no_recolor]
[-substrate PATH] [-substrate_mode TYPE] [-interface_normal VECTOR]
[-interface_vacuum_buffer ANGSTROMS]
[-infinite_axis a_b_c_a,b_a,c_OR_b,c] [-grid] [-grow] [-grow_together]
[-minimize] [-pack] [-mc] [-mc_weights ROTATION:TRANSLATION]
[-mc_max_rotation DEGREES] [-mc_translation_mu MEAN]
[-mc_translation_sigma STDDEV] [-mc_temperatures TEMP:TEMP:TEMP]
[-mc_iterations ITERATIONS] [-mc_gravity] [-mc_gravity_weight WEIGHT]
[-mc_no_ff_term] [-pack_iterations ITERATIONS] [-preserve_res_info]
[-no_rezero] [-monomer_ff_q] [-seed SEED] [-HOST <hostname>]
input_file output_basename
Disorder system builder utility files. Copyright Schrodinger, LLC. All rights
reserved.
positional arguments:
input_file Input file. Structures for multiple components should
be in the same file and in the same order as the
composition values.
output_basename Output file basename - output file names will be
formed using this.
options:
-h, -help Show this help message and exit.
-molecules NUMBER_OF_MOLECULES
Number of molecules to place in the cell. Numbers
other than perfect cubes will result in unpopulated
gridpoints. The default is 64. (default: 64)
-density DENSITY The initial density target for building the cell. This
may subsequently be modified if the -obey flag is not
set to density. The density may also change if any of
the equilibration methods (-mc, -pack or -minimize) or
-maximize_density are used. (default: 0.5)
-scale_vdw VDW_SCALE_FACTOR
Scale factor for VDW radii to use when computing
clashes. The default is 1.0. (default: 1.0)
-obey TARGET When building the initial cell, either density or VdW
scale factor can be varied to find a cell with the
required number of molecules and no clashes. Use This
flag to specify which value is held constant. Choices
are "density" or "vdw". density specifies to keep the
density constant and vary the VdW scale factor, while
vdw specifies the opposite. The default is vdw.
(default: vdw)
-maximize_density If -obey is vdw, the density will be increased until a
successful cell can no longer be built. Not valid if
-obey is density. (default: False)
-tries_per_mol TRIES The number of times to try inserting a molecule into
an amorphous cell without clashes before the cell is
abandoned. (default: 50)
-tries_per_dc TRIES The number of attempts to make a cell at a specific
density and VdW scale factor before the adjustable
parameter is changed to make clashes less likely. See
also the -obey flag. (default: 20)
-composition COMPOSITION:COMPOSITION, -c COMPOSITION:COMPOSITION
Composition ratio for the structures in the input
file. Ratio values should be separated by a colon and
in the same order the structures appear in the input
file. If no composition is given, all structures will
be given equal ratio values. Examples of valid
composition ratios: 50:50, 2:1, 50:45:5, 66.7:33.3,
99:1, 25:2. Ratios that do not result in evenly
distributing the total number of molecules when
converted to integer molecules will raise an error -
such as 50:50 for an odd number of molecules. Maximum
number of components is 999. (default: None)
-no_system Produce a structure but do not assign a force field to
it. (default: False)
-interface_buffer ANGSTROMS
For interface scaffolds, buffer in angstroms between
scaffold and disordered system. (default: 0)
-forcefield FORCE_FIELD, -f FORCE_FIELD
Force field to specify in System Builder, default is
OPLS_2005. (default: OPLS_2005)
-split_components Split system in components when Desmond system is
built. This can speed up the the force field
assignment for systems that contain multiple identical
molecules. (default: False)
-water_fftype WATER_TYPE
Force field type for water molecules. Must be used
with -split_components. If using "none", the Residue
Name atom property is used instead. (default: SPC)
-rigid MONOMER INDEX,MONOMER INDEX
Monomers of these indexes are treated as rigid bodies
and are placed into the cell when using the tangled
chain method. Indexes refer to the order of the
monomers in the input file. This flag has no effect if
not using the tangled chain method. (default: None)
-target_atoms TARGET ATOMS
The maximum number of atoms in each disordered cell.
The number of molecules in each disordered cell will
be determined based on -target_atoms, -composition and
-selection_type_count. (default: None)
-selection_type_count SELECTION_TYPE_COUNT
The composition values for components with these
indexes are the fixed number of molecules in the final
system. Indexes refer to the order of the monomers in
the input file. Components not listed here are
considered to have composition values that can be
adjusted in a constant ratio to meet the
-target_atoms. (default: None)
-dihe_temperature KELVIN
With torsion energy surface, Boltzmann distribution of
dihedral angles is generated at this temperature. By
default, a uniform distribution is used. (default:
None)
-homogeneous Also create homogeneous cells for each component.
(default: False)
-homo_by_comp The number of molecules in each homogeneous cell will
be determined from the -composition and -molecules
flags, so each component will have the same number of
molecules as it would in the mixed cell. By default,
the number of molecules in each homogeneous cell is
determined solely by the -molecules so that each cell
contains the same number of molecules. (default:
False)
-no_disordered_cell By default, a system is created that is a mixtureof
all components - the "disordered" cell. Use this flag
to not create this system. (default: False)
-ncells NUMBER The number of cells of each type to produce. Each cell
of the same type will be generated starting with a
different random seed so that the cells have the same
composition but different distribution and
orientation. (default: 1)
-pbc SOURCE Whether to create a new, orthorhombic periodic
boundary condition or use existing periodic boundary
information on the scaffold structure. Choices are
"new", "new_cubic" and "existing". The default is
"existing" if a container or interface scaffold is
supplied that has PBC properties set in it, and also
for immersed scaffolds when the -infinite_axis flag is
supplied. The default is "new" in all other cases.An
existing PBC will be expanded in the case of interface
scaffolds to accomodate the components and vacuum
buffer, and also in the case immersed scaffolds.
(default: None)
-pbc_side ANGSTROMS For -pbc new_cubic, supply a single value that will
enforce a cubic PBC that has sides of this length. For
-pbc new, supply two comma-separated values that will
enforce the length of the a and b sides of the PBC,
while the length of the c side will be determined by
the initial density value. Use of this flag will force
-obey density. (default: None)
-no_rotation Do not randomly rotate molcules. All molecules will
have the same orientation as the input structure.
(default: False)
-no_recolor The default is to recolor molecules so that all
molecules of the same component have the same color.
Use this option to keep the original coloring of each
component. (default: False)
-substrate PATH The path to a structure file containing the scaffold
that the disordered system will be built on. See also
-substrate_mode. (default: None)
-substrate_mode TYPE The type of scaffold structure, must be one of
immersed, container or interface. immersed scaffolds
will be surrounded by the disordered system
components, such as a nanoparticle/solvent system.
container scaffolds will have the disordered system
created in its void space, such as a zeolite storage
system. interface scaffolds will have the disordered
system built on a surface plane of the scaffold, such
as organic materials deposited on a metal surface. For
interface scaffolds, -interface_atoms or
-interface_vector must also be supplied. (default:
None)
-interface_normal VECTOR
A colon-delimited list of 6 numbers that defines a
normal vector of the interface plane for an interface
scaffold. The disordered system will be built using
this plane as its base and extending in the direction
the vector points. The six numbers are
a:b:c:x:y:z,where (a,b,c) defines the origin of the
vector and(x,y,z) defines the vector itself. For
instance, to build a disordered system starting at the
Y=5 plane and extending into the +y direction, use
0:5:0:0:1:0. If the list begins with a negative
number, use the -interface_normal=list syntax rather
than -interface_normal list. For instance, instead of
"-interface_normal -1:5:0:0:1:0", use
"-interface_normal=-1:5:0:0:1:0". (default: None)
-interface_vacuum_buffer ANGSTROMS
For interface scaffolds, the number of angstroms to
expand the periodic boundary condition beyond the
components to create a vacuum buffer between the
disordered system and the mirror image of the
scaffold. (default: 0.0)
-infinite_axis a_b_c_a,b_a,c_OR_b,c
For immersed scaffolds, the axes in which the
substrate is infinite - i.e. the axes that should not
be expanded to contain the disordered system. Use of
this flag will automatically set -pbc to existing.
(default: None)
-grid Distribute the components on a grid and do not
equilibrate. (default: False)
-grow Grow the molecules in cell if the structures have
rotatable bonds. (default: False)
-grow_together Grow all the molecules together. Otherwise,
sequentially grow molecules based on the volume,
flexibility, and count. (default: False)
-minimize Minimize the system using the requested force field.
The default is not to minimize the system. There are
three equilibration methods: Monte Carlo simulated
annealing (-mc), steric pack (-pack) and minimization
(-minimize). Any or all of the methods may be used
together and those chosen are performed in the
following order: simulated annealing, steric pack,
minimization. (default: False)
-pack, -p Condense the molecules towards the center of the cell
to minimize volume. The default is not to pack. There
are three equilibration methods: Monte Carlo simulated
annealing (-mc), steric pack (-pack) and minimization
(-minimize). Any or all of the methods may be used
together and those chosen are performed in the
following order: simulated annealing, steric pack,
minimization. (default: False)
-mc After the initial system is generated, use Monte Carlo
simulated annealing to equilibrate the system. The
default is not to anneal. See the options starting
with -mc_ for additional options for this method.
There are three equilibration methods: Monte Carlo
simulated annealing (-mc), steric pack (-pack) and
minimization (-minimize). Any or all of the methods
may be used together and those chosen are performed in
the following order: simulated annealing, steric pack,
minimization. (default: False)
-mc_weights ROTATION:TRANSLATION
A colon-delimited list of 2 numbers that defines the
relative frequency of rotations and translations
during Monte Carlo annealing, with the first value
being the weight for rotations.Rotation rotates a
molecule randomly, keeping the center of the molecule
fixed. Translation moves the molecule randomly,
keeping the rotation fixed. A value of 0 for any
weight means that type of move will not be performed.
The default value of 0.5:0.5 indicates that rotation
and translation are equally likely. (default: 0.5:0.5)
-mc_max_rotation DEGREES
The maximum rotation in degrees allowed when
performing a rotation step in the Monte Carlo
annealing. The default is 360.0. (default: 360.0)
-mc_translation_mu MEAN
The value of mu in the log-normal distribution that
determines the translation step size. mu gives the
mean value of the distribution. The default mu and
sigma values of 0.25 and 1.00 give maximum probability
to values around 0.5 Angstrom, 40 percent chance of
translations of 1 Angstrom or less, and about a 5
percent chance of translations larger than 7 Angstrom.
(default: 0.25)
-mc_translation_sigma STDDEV
The value of sigma in the log-normal distribution that
determines the translation step size. sigma gives the
standard deviation of the distribution. The default mu
and sigma values of 0.25 and 1.00 give maximum
probability to values around 0.5 Angstrom, 40 percent
chance of translations of 1 Angstrom or less, and
about a 5 percent chance of translations larger than 7
Angstrom. (default: 1.0)
-mc_temperatures TEMP:TEMP:TEMP
A colon-delimited list of temperatures in K that the
Monte Carlo simulated annealing should be run at. The
number of iterations at each step is given by
-mc_iterations. (default: 900:600:300)
-mc_iterations ITERATIONS
The number of Monte Carlo iterations to run at each
temperature during Monte Carlo annealing. (default:
3000)
-mc_gravity Include a gravity term in the Monte Carlo simulated
annealing. This energy term favors movements that
decrease the distance between molecules and the
scaffold, or between molecules and the center of the
cell if no scaffold is used. If no force field term is
used, a hard sphere model is used to avoid steric
.clashes. See also the -mc_gravity_weight flag.
(default: False)
-mc_gravity_weight WEIGHT
In simulated annealing stages that use -mc_gravity,
This factor is multiple times the distance between the
moving molecule and the scaffold or center of the
cell. The default value is 4.0 kcal/mol. (default:
4.0)
-mc_no_ff_term Do not include a force field energy term in the Monte
Carlo simulated annealing stage. If this term is
turned off, -mc_gravity must be used. (default: False)
-pack_iterations ITERATIONS
Number of X-Y-Z packing iterations to perform. Default
is 1. Regardless of this setting, the calculation will
not continue past any iteration that resulted in no
change. (default: 1)
-preserve_res_info Do not overwrite residue information from the input
files when forming the final structure. (default:
False)
-no_rezero Re-zero system when Desmond system is built. (default:
False)
-monomer_ff_q Use forcefield charges computed for the monomer for
the polymer. This option is particularly useful for
S-OPLS, which uses OPLS_2005 charges by default for
molecules larger than 100 heavy atoms. (default:
False)
-seed SEED Seed for random number generator. (default: 1234)
Job Control Options:
-HOST <hostname> Run job remotely on the indicated host entry.
(default: localhost)