The ligprep Command
To run LigPrep from the command line, use the ligprep command. The syntax of the ligprep command is as follows.
ligprep [options] [ meta-options] {-imae|-isd|-ismi|-icsv} input-file {‑omae|‑osd} output-file
You must specify an input structure file using either ‑imae for input files in Maestro format, ‑isd for input files in SD file format, -ismi for input files in SMILES format as a list of SMILES strings (.smi) or -icsv for input files in CSV format containing a SMILES string with optional title and properties on each line, separated by commas (.csv). The output file is specified with -omae for Maestro format or -osd for SD format. Maestro input and output files can be in uncompressed (.mae) or compressed (.maegz or .mae.gz) form. If it is not otherwise specified, the job name for the LigPrep job is the stem of the output structure file name, formed by removing the file extension, and also -out if present.
The ligprep command has a number of options for controlling the stages of the process. These options can be specified in two ways:
- On the command line. For a complete listing of these options, enter the command
ligprep -long_help. - In an input file. For a complete listing of input file keywords and their correspondence to the command options, enter the command
ligprep -sif_docs. This is a useful way of specifying a set of options that you use commonly, and not have to retype them each time you run a LigPrep job.
You can combine options specified on the command line with options specified in an input file. Options specified on the command line override the settings from the input file.
The standard Job Control options, for selecting the host, defining a scratch directory, and so on, are supported, as are the common -LOCAL and -WAIT options—see Running Jobs From the Command Line for a complete listing. In particular, you should note the syntax of the -HOST option, which is used to specify the list of hosts used for the job. In addition to these options, the ligprep command supports a range of other job options for both the control of the job and for distributing jobs over multiple processors.
The ligprep command also has a number of meta-options, which set a group of options with particular values. You can use options together with meta-options; the options override any values set by the meta-options.
The adjust, vary and expand meta-options control the range of structures generated. You can use all three of these meta-options in the same ligprep command, but c, i and t must not appear more than once. For instance, you could use -adjust_t -vary_c -expand_i, but not -adjust_t -vary_c -expand_it.
The retain meta-option can be used to require that at least one structure produced for each input structure retains the characteristics denoted by the suffix. For instance, -retain_t means that the tautomerization state in the input structure will be present in at least one of the output structures for that molecule. The retain meta-option can be used with any of the adjust, vary and expand meta-options.
LigPrep jobs run in the background under Schrödinger’s Job Control facility. The job output is normally written to a temporary directory and then copied back to the job submission directory when the job finishes. You can direct the temporary files and the output to the job submission directory with the ‑LOCAL option of the ligprep command. The .log file is written to the job submission directory and is updated during the run. For more information on the Job Control facility, see the Job Control Guide — Contents (JOB CONTROL IS DEPRECATED).