ligprep -long_help Command Help
Command: $SCHRODINGER/ligprep -long_help
usage: ligprep [options] (-ismi|-icsv|-imae|-isd) infile (-osd|-omae|-osmi|-ocsv) outfile
Examples:
Process SMILES input to generate 3D structures in relevant
protonation states, save results in Maestro format:
ligprep -ismi input.smi -omae output.mae -epik
Process SMILES input from CSV file, sample protonation states,
generate 3D geometries, save results in compressed Maestro format:
ligprep -icsv input.csv -omae output.maegz -epik
Process 2D structures in SD format, sample relevant protonation
states and stereoisomers, build 3D geometries, and store results
in SD format:
ligprep -isd input.sd -osd output.sd -epik
Process compressed 2D SD file to produce Maestro file with
various ionization states, tautomers, and stereoisomers:
ligprep -expand itc -isd input.sd.gz -omae output.mae -epik
Process 3D Maestro file using chiralities from input geometry:
ligprep -g -imae input.mae -omae output.mae
Process compressed 3D Maestro file generating up to 64 stereoisomers
and ignoring input chiralities:
ligprep -ac -s 64 -imae input.maegz -omae output.mae
Meta options: (turn on a number of actual options)
-unt : Only run stereoizer and cgx to untangle structures.
-adjust <itc> : Adjust to a suitable state.
-vary <itc> : Generate different states.
-expand <itc> : Aggressively generate different states.
-retain <itc> : Retain characteristics of the input structures
(specifying 'i' also turns on retention of tautomers).
<itc> specify one or more of:
c chiralities
i ionization and neutralization
t tautomerization
General:
-h, -help Print brief help message.
-long_help Print exhaustive help message.
-v, -version Print product version.
-inp <filename> Read arguments from the supplied input file.
-ma <number> Skip some processing steps for the structures that
contain more than specified number atoms (Default:
200).
-u <string>, -variant_root <string>
Name of the CT-level property whose value is to be
used to derive variant names stored in the
s_lp_Variant CT-level property (Default: s_m_title).
-sif_docs List supported simplified input file format (SIF)
keywords.
-R <string> Run only one of the stages of ligand preparation:
htreat - h, desalter - d, filter - f, neutralizer - n,
tautomerizer - t, epik - e, stereoizer - s, guard - g,
force-field based geometry optimization - c.
-W <string> Options for various stages of ligand preparation.
<string> consists of comma separated designators:
first designator specifies what program the options
are to be passed to and must be one of the: ci -
sdconvert on input structures, co - sdconvert on
output structures, f - filter, e - epik, ex - epikx, s
- stereoizer. Remaining designators are passed to the
program in the order specified with the commas
removed.
-m <number>, -max_stereo <number>
Maximum number of the low-energy stereoisomers to
keep. A value of zero disables the filtering.
-a, -align Keep atoms close to their original positions.
Desalter:
-nd Disable desalter (Default: enabled).
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.
-es <specfile> Use non-standard Epik Classic pKa file.
-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.
-mbs <specfile> Use non-standard Epik Classic metal binding file.
-no_refine Disable the final refinement in EpikX.
-ph <number> Effective/target pH. (default = 7.0 for Epik Classic,
7.4 for Epik)
-pht <number> pH tolerance for generated structures.
Tautomerization:
-nt Disable tautomerizer (Default: enabled).
-t # Run tautomerizer and set the maximum number of
tautomers to generate to # (Default: 8).
-tp # Run tautomerizer and set the minimum probability for
retaining tautomers to # (Default: 0.01).
-ts <specfile> Use non-standard tautomer patterns specification file.
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.
-ns Do not use the stereoizer.
-s # Generate up to this many (#) stereoisomers per input
structure. (Default: 32).
-strict_v2000_stereo For SD V2000 input, generate enantiomers if the chiral
flag is 0.
Filtering:
-ng Disable filtering out of exotic structures.
-f <filename> Filter structures via LigFilter using specifications
from the file provided. Default: do not filter.
-lp Pass -addprops to LigFilter.
-lab Add an internal tracking label to the processed
structures.
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.
-bvac Set dielectric constant to 1.0 for the final force-
field based geometry optimization.
-cgx_noopt Skip final force-field based geometry optimization.
-no_cm1a Skip CM1A charge assignment for S-OPLS.
-L <path> CGX fragment library path. Overrides default location
in the appdata directory if specified.
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.
-RETRIES RETRIES If a subjob fails for any reason, it will be retried
RETRIES times.
-STRICT Terminate the job if any subjob dies.
-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.
-D, -DEBUG Show details of Job Control operation.
-TMPDIR TMPDIR The name of the directory used to store files
temporarily during a job.
-NICE Run the job at reduced priority.
-SAVE Return zip archive of job directory at job completion.
-NOJOBID Run the job directly, without Job Control layer.