strain_rescore.py Command Help
Command: $SCHRODINGER/run strain_rescore.py
Usage: $SCHRODINGER/run strain_rescore.py <structure_file> [<options>]
Calculates penalties for poses with internal strain. For each ligand pose in
the input file, a tightly constrained minimization and an unconstrained
minimization are performed with MacroModel. The minimizations are performed
with a distance-dependent dielectric, r=4, potential energy surface. The
energy difference is used to determine the Glide gscore penalty. The input
file can be either a 'pv.mae' file, with a receptor as the first structure,
or a 'lib.mae' file that contains only ligand poses. The output file will
contain the original properties plus: 1) the potential energy of the
restrained geometry, calculated without restraints (bound). 2) the
potential energy of the minimized geometry, starting from the restrained
optimization's coordinates (free). 3) the difference between these two
potentials (strain). Note that this is dependent on the restraint type. When
using Cartesian restraints the 'free' minimization uses restraints with a wide
half-width (1.0 angstroms). When using torsional restraints the 'free'
minimization is unrestrained. Copyright Schrodinger, LLC. All rights
reserved.
Options:
-v, -version Show the program's version and exit.
-h, -help Show this help message and exit.
-f FFLD, -ffld FFLD Force field. Default is OPLS_2005. Must be one of the
following: MM2|MM3|AMBER|AMBER94|OPLS|OPLS_2005|S-
OPLS|MMFF94|MMFF94s
-s SCALE_FACTOR, -scale_factor SCALE_FACTOR
Penalty scale factor. Default is 0.25
-e ENERGY_OFFSET, -energy_offset ENERGY_OFFSET
Ignored strain energy threshold. Default is 4.00
kcal/mol
-E, -energy_offset_per_rotor
Optionally calculate the amount of ignored strain
energy based on the number of rotors. total_offset =
energy_offset * num_rotors. If this optin is used the
energy_offset may need to be reduced. A value around
0.7 kcal/mol is a possible starting point.
-c FORCE_CONSTANT, -force_constant FORCE_CONSTANT
Restraint force constant. By default cartesian
constraints are used and the force constant is 120.00
kcal/mol/angstrom**2. If torsional restraints are
requested, then the force constant default is 10
kcal/mol/deg**2. MacroModel natively constrains
torsions by scaling V1, in units of kJ/mol. A
harmonic potential (kcal/mol/deg**2) is approximated
by multiplying the torsion_constraint value by
13744.45, with a maximum V1 value of 999999999.
kJ/mol.
-w BOUND_HALF_WIDTH, -bound_half_width BOUND_HALF_WIDTH
Half-width of flat-bottom restraint potential applied
to the 'bound' state, in units of a tenth of an
angstrom. Default is 3 (0.3 angstroms). If torsional
restraints are requested, then the default is 15
degrees
-t, -torsional_restraints
Use torsional restraints instead of Cartesian
constraints.
-n NJOBS, -NJOBS NJOBS
Divide each task into this many subjobs. By default
it is the number of cpus.
-csearch Run conformational search and report the energy
difference between the restrained input minimization
("bound" state) and the global minimum found by the
search.
-csearch_mode CSEARCH_MODE
Run a ConfGen search (fast mode), or a 100 step/rotor
Monte Carlo/Low-Mode conformation search in GB/SA
water solvent. Default is "CONFGEN". Must be one of
the following: CONFGEN|MCMMLMOD
-j JOBNAME, -o JOBNAME, -JOBNAME JOBNAME
Optional jobname for the output and log file.
-r, -calculate_rmsd Calculate the heavy-atom, in-place RMSD between the
input conformation and the "unbound" conformation.
This calculation can be slow with large gzipped
Maestro files, relative to uncompressed file input.
-solvation SOLVATION Solvation model treatment. The default is to perform
the search with 4RDDD solvation model. Must be one of
4RDDD|WATER|VACUUM
Job Control Options:
-HOST <hostname> Run job remotely on the indicated host entry.
-WAIT Do not return a prompt until the job completes.
-LOCAL Do not use a temporary directory for job files. Keep
files in the current directory.
-NOJOBID Run the job directly, without Job Control layer.