ligprep Command Help
Command: $SCHRODINGER/ligprep
usage: ligprep [options] (-ismi|-icsv|-imae|-isd) infile (-osd|-omae|-osmi|-ocsv) outfile
General:
-h, -help Print brief help message.
-long_help Print exhaustive help message.
-inp <filename> Read arguments from the supplied input file.
-sif_docs List supported simplified input file format (SIF)
keywords.
Ionization:
-epik Use Epik Classic for ionization and tautomerization
(Recommended, overrides -i).
-epikx Use Epik for ionization and tautomerization
(Recommended, overrides -i).
-emb, -epik_metal_binding
Run Epik with the metal_binding option so that states
appropriate for interactions with metal ions in
protein binding pockets are also generated.
-i {0,1} Ionization treatment: 0 - do not neutralize or ionize,
1 - neutralize (Default: 1). Note that -epik option
overrides -i and always implies ionization and
tautomerization.
-ph <number> Effective/target pH. (default = 7.0 for Epik Classic,
7.4 for Epik)
-pht <number> pH tolerance for generated structures.
Stereoisomers:
-ac Do not respect existing chirality properties and do
not respect chiralities from the input geometry.
Generate stereoisomers for all chiral centers up to
the number permitted (specified using the -s option).
This is equivalent to "Generate all combinations" in
the Ligand Preparation user interface. Default
behavior is to respect only explicitly indicated
chiralities.
-g Respect chiralities from input geometry when
generating stereoisomers.
-s # Generate up to this many (#) stereoisomers per input
structure. (Default: 32).
Force-field based geometry optimization:
-bff {14,16} Force-field to be used for the final geometry
optimization. Default: 14 (OPLS_2005). For S-OPLS
specify 16.
Standard and job control options:
-NJOBS NJOBS Divide the overall job into NJOBS subjobs.
-NSTRUCTS NSTRUCTS Divide the overall job into subjobs with no more than
NSTRUCTS structures.
-HOST <hostname> Run job remotely on the indicated host entry.
-WAIT Do not return a prompt until the job completes.
-LOCAL Do not use temporary directory for job files. Keep
files in the current directory.
Typical usage:
Sample protonation states and stereoisomers, optimize geometry
using OPLS force-field, and store results in Maestro format:
ligprep <input> -omae outfile.maegz -epik
where <input> is one of:
-ismi infile.smi
-icsv infile.csv
-isd infile.sd
-imae infile.mae
Help topics for subcommands are listed below: