ligand_strain Command Help
Command: $SCHRODINGER/ligand_strain
usage:
To run the ligand_strain script, use the following command:
$SCHRODINGER/ligand_strain <mae> [options]
Calculate the estimated strain of a bound ligand.
Given a structure file containing a bound ligand, the ligand strain is calculated by
comparing the energy of the ligand in the bound conformation to that of the ligand
in its "free" conformation. The script uses a combination of conformational searching
and energy minimization to find the lowest energy ligand conformation in the free state.
The free and bound states then undergo energy minimization to find the lowest energy
conformations. The strain energy is then calculated as the difference in energy between
the free and the bound states.
In its default mode, the script performs a conformational search of the ligand to generate
a set of diverse conformations. Conformational sampling aims to generate conformations that
avoid "collapsed" states. Conformations can be sampled in either in 'global', 'global_enhanced'
or 'local' mode. In the default 'global' mode, the conformational search is performed using
Macromodel. In the 'global_enhanced' mode, a two-stage conformational search is performed using
ConfGen and Macromodel. The first stage involves a quick presampling with ConfGen to generate
an ensemble of conformations. These conformations are then used by Macromodel to perform an
additional round of conformation-sampling. In 'global' mode, the strain results are often input
dependent due to undersampling. To reduce this dependency, the 'global_enhanced' option is
recommended. In 'local' mode, the free state is generated by local minimization only of the input
ligand. The force field used for the local minimization is defined by the 'score_method'.
The lowest energy free and bound states are then further optimized using either Macromodel,
Prime or Jaguar (QM). In the case of the bound ligand, this optimization is restrained to
only sample around the input conformation. The energy of the free state is then compared to the
energy of the bound state to determine the strain energy. The strain properties are stored as
structure-level properties in the final Maestro file.
positional arguments:
struct_file Input Maestro file; must contain the ligands of interest
options:
-h, --help show this help message and exit
-v show program's version number and exit
-jobname JOBNAME, -JOBNAME JOBNAME, -j JOBNAME
Set the base name of outputs
Ligand Strain:
-skip_larger_than SKIP_LARGER_THAN
Only calculate strain values for ligands with fewer than this cutoff number of atoms; default = '250'
-nconf NCONF Number of ligand conformers to generate and use for scoring of the free state; default = 200 when 'score_method' is 'Macromodel' or 'Prime'; if the 'score_method' is 'Jaguar'then the default = 5
-force_field FORCE_FIELD
Specify the force field used for the 'Macromodel' scoring method and conformation sampling in 'global' and 'global_enhanced' search methods; default = 'S-OPLS'
-score_method {Macromodel,Jaguar,Prime}
Method used for scoring the ligand conformations: Macromodel, Prime or Jaguar (QM); default = 'Macromodel'
-out_type {simple,all}
Specify the type of output Maestro file to generate:
'simple' (default): Contains just the input ligand with its strain properties stored as structure-level properties
'all': Contains the input ligand as above, but also includes the determined
"global and local reference minimum structures
-search_method {local,global,global_enhanced}
Method for ligand conformational search:
'global' (default): Perform a conformational search using Macromodel
'global_enhanced': Perform a two-stage conformational search using Macromodel. The first stage is a quick presampling to generate an ensemble of conformations to be used as an input for the main conformation-sampling stage. When using 'global' search, the strain results are often input dependent due to undersampling. To reduce this dependency, the 'global_enhanced' option is recommended. This option can significantly increase the run time.
'local': Use local minimization to generate the 'free' ligand conformation. The force field used for the local minimization is defined by the 'score_method'.
-mmod_csearch_option MMOD_CSEARCH_OPTIONS
Specify keyword-value pairs to pass to Macromodel during conformational sampling, in the form <keyword>=<value>; see the "Running Macromodel with the Simplified Input File" chapter in the Macromodel Documentation for a description of the available options.
-mmod_minimize_option MMOD_OPTIONS
Specify keyword-value pairs to pass to Macromodel during optimization, in the form <keyword>=<value>; see the "Running Macromodel with the Simplified Input File" chapter in the Macromodel Documentation for a description of the available options.
-prime_minimize_option PRIME_OPTIONS
Specify keyword-value pairs to pass to Prime during optimization, in the form <keyword>=<value>; see the "Refining Protein Structures" chapter in the Prime Documentation for a description of available options.
-qm_optimize_option QM_OPT_OPTIONS
Specify keyword-value pairs to pass to Jaguar (QM) during optimization, in the form <keyword>=<value>; these pairs are placed in the '&gen' section of the Jaguar input file, as described in theJaguar Documentation chapter "The Jaguar Input File"
-qm_score_option QM_SCORE_OPTIONS
Specify keyword-value pairs to pass to Jaguar (QM) during scoring, in the form <keyword>=<value>; these pairs are placed in the '&gen' section of the Jaguar input file, as described in theJaguar Documentation chapter "The Jaguar Input File"
Job Control Options:
-HOST <hostname> Run job remotely on the indicated host entry.
-WAIT Do not return a prompt until the job completes.
-D, -DEBUG Show details of Job Control operation.
-NOJOBID Run the job directly, without Job Control layer.
Standard Options:
-NJOBS NJOBS Divide the overall job into NJOBS subjobs.
-RETRIES RETRIES If a subjob fails for any reason, it will be retried RETRIES times. (Default: 2)
-NOLAUNCH Set up subjob inputs, but don't run the jobs.
Restart Options:
-restart_file RESTART_FILES
Output of a partially completed subjob; keyword may be used multiple times, once per partial subjob
-RESTART Run 'restart_file' automatically by guessing the names of the files to use
Examples:
To calculate the strain energy of a ligand with the default settings, use the
following command:
$SCHRODINGER/ligand_strain input.mae
To calculate the strain energy of a ligand with the OPLS4 force field, use the following
command:
$SCHRODINGER/ligand_strain input.mae -force_field S-OPLS
To calculate ligand strain without performing a conformational search and only using
local minimization to determine the free state, use the following command:
$SCHRODINGER/ligand_strain input.mae -search_method local