structurebased_adme amphiphilic Command Help

Command: $SCHRODINGER/structurebased_adme amphiphilic

usage: 
$SCHRODINGER/structurebased_adme amphiphilic [<options>] <struct_file>
Calculates the amphiphilic moment of cationic molecules

positional arguments:
  struct_file           Input ligands in maestro format

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

Amphiphilic Moment:
  -multi_state          Use Epik to determine possible protonation states
  -basic_pka            basic pka
  -protocol {HT,standard,macromodel,fast}
                        Sampling algorithm to use. Choices are standard
                        (default) with sampling and a high throughput mode
                        (HT) without sampling
  -lipophilic_predictor {Informatics,Physics}
                        Method of calculating the lipophilicity of each atom.
                        Choices are Informatics-based 'Informatics' or
                        Physics-based 'Physics'. (Default is 'Informatics')
  -use_solvent_form     Use the solvent form of the molecule for calculating
                        the moment of each molecule
  -force_field FORCE_FIELD
                        Set the force field to use for 'Physics'-based
                        predictor: Default is S-OPLS
  -conformation_search_option PLOP_CONF_SAMPLE_OPTIONS
                        Add a keyword-value pair to pass to Prime
                        Conformational sampling stage in the format
                        <keyword>=<value>. See the "Refining Protein
                        Structures" chapter in the Prime User Manual for a
                        description of available options.
  -membrane_score_option PLOP_MEMB_SCORE_OPTIONS
                        Add a keyword-value pair to pass to Prime Low
                        Dielectric scoring stage in the format
                        <keyword>=<value>. See the "Refining Protein
                        Structures" chapter in the Prime User Manual for a
                        description of available options.
  -solvent_score_option PLOP_SOLV_SCORE_OPTIONS
                        Add a keyword-value pair to pass to Prime High
                        Dielectric scoring stage in the format
                        <keyword>=<value>. See the "Refining Protein
                        Structures" chapter in the Prime User Manual for a
                        description of available options.
  -mmod_csearch_option MMOD_CSEARCH_OPTIONS
                        Add a keyword-value pair to pass to Macromodel
                        sampling in the format <keyword>=<value>. See the
                        "Running Macromodel with the Simplified Input File"
                        chapter in the Macromodel Reference Manual for a
                        description of available options.

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