epik Command Help
Command: $SCHRODINGER/epik
/opt/schrodinger/suites2026-1/epik-v7.5/bin/Darwin-x86_64/epik_app -h
SCHRODINGER: /opt/schrodinger/suites2026-1
Running Epik Classic version 7.5135
Epik. Copyright Schrodinger, LLC. All rights reserved.
Current invocation:
epik -h
Syntax: epik <options> -imae input_file.mae -omae output_file.mae
Options:
-a Estimate pKas for acids only.
-b Estimate pKas for bases only.
-best_neutral Provide the most populated neutral tautomer.
-best_neutral_zwit Provide the most populated neutral tautomer and optionally
a low energy neutral zwitterion if one is identified.
-charging_scale_factor <number> Sets the scaling factor for the
r_epik_ionization_penalty_charging contribution to the
r_epik_charging_adjusted_penalty property.
-HELP Print this message.
-h Print this message.
-help Print this message.
-cg <rdiff> <rms> Use geometry as well as connectivity when identifying
unique structures. Normally only connectivity is used.
Structures are distinct if:
rdiff > 0.0 and any position differs by more than rdiff
rms > 0.0 and the rms difference in positions is larger than rms
-cyp | CYP Perform CYP reactivity calculations.
-es <file_name> File name for the epik solvation model file.
-inp <file_name> Keyword value file name for the calculation.
-highest_pka <number> Set the highest pKa to estimate when sequentially
ionizing to <number>.
-lowest_pka <number> Set the lowest pKa to estimate when sequentially
ionizing to <number>.
-ma <number> Structures containing more than <number> atoms will not
be adjusted.
Default: 150
-mapka <number> pKa values for structures containing more than <number> atoms
will not be calculated.
Default: 500
-mbs <file_name> File name for describing metal binding adjustments to pKa values.
-metal_binding Also generate states appropriate for interacting with metal
ions in protein binding pockets.
-ms <number> Maximum number of generated structures per
input structure.
Default: 16
-nt Do not tautomerize
-p <number> The minimum probability for generated states. (Default: 0.01
-ph <number> The target pH.
-pht <number> pH tolerance for generated structures.
pHt = -log_10( p )
Default: 2.
-pKa_atom Report pKa for specific atoms as a ct level property.
-retain_i Ensure that the ionization and tautomerization state
of the input structure is retained in the output.
-retain_i_lab Like retain_i except that only labeled input structures
are retained.
-retain_t Ensure that the tautomeric state of the labeled input
structure is retained in the output.
-retain_t_lab Like retain_t except that only labeled input structures
are retained.
-s <solvent_name> The name for the solvent to use.
It must be one of "water" or "DMSO"
Default: water
-scan Sequentially ionize up and down starting from the optimum
structure for pH 7.0 or the value given with the -ph option.
-skip_prob_fragment <number>
Controls whether to check for problematic fragments when
adjusting structures.
<number> = 0 do not check. Default: 1 check
-tn <number> maximum number of tautomers.
Default 8.
-tp <number> minimum probability for tautomers.
Default: 0.1 X the minimum probability for generated states.
-ts <file_name> The name for the tautomer database file to use.
-v Print the version number.
-verb # controls MMERR level of reporting.
0: MMERR_FATAL - only report errors
1: MMERR_WARNING - only report errors and warnings
2: MMERR_INFO - report errors, warnings, and processing
information.
3: MMERR_DEBUG - report errors, warnings, processing
information, and debugging information
Unless -ph is specified pKas are estimated using the input structure.
When -ph is specified then variations on the input structure
are generated and the pKas for each of those calculated.
If no structure meets the criteria for output the most probable
structure is kept so that at least one structure is always produced
for each input structure.
Notes on retention behavior
Structures forcibly retained are selected for inclusion in the output ahead
of any more probable structures.
-retain_i forces the retention of the exact combination of the input
tautomerization and ionization state.
-retain_t will force retention of the various ionized forms of the
input tautomerization state based upon their ionization probabilities
At a minimum the most probable ionization state of the input tautomeric
form is retained.
specifying: -retain_i and -retain_t uses a combination of the behaviors given
above. Specifically, forcibly retain a copy of the exact combination of
the input tautomerization and ionization state plus probable ionization
states of the input tautomer.
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Job Level Options
-DEBUG Show details of operation of the toplevel scripts.
-HOST <hostname> or
-HOST <hostname:nproc> or
-NO_JOBCONTROL Do not use job control but print Epik Classic messages to
<jobname>.log
-NOJOBID Do not use job control and print Epik Classic messages to the
screen.
-PROJ <name> Assign job to a Maestro project <name>.
-TMPDIR <directory>
The name of the directory used to store files temporarily
during a job.
-WAIT Do not return a prompt until the job completes.
-RESTART Restart the previously failed parent job.
This facility works only for local jobs.
** Distributed job options:
-SUBHOST <hostname> or
-SUBHOST <hostname:nproc> or
-SUBHOST "hostname1:nproc1 hostname2:nproc2 ... hostnameN:nprocN"
Run the subjobs on the specified hosts.
The driver is run on the host specified with -HOST.
-NJOBS <number> Number of subjobs to create.
If this option is omitted, -NJOBS will be set to the number
of cpus requested with -SUBHOST option.
-JOBCTS <number> Ensure that each subjob has no more than this many
structures to process. Defaults to 10000.
-STRICT_END Terminate if any of the subjobs dies.
-MAX_RETRIES Number of allowed retries per subjob.
-first First structure to process.
-last Last structure to process.
-OUTPUT_ORG <option>
Produce more than one output structure file.
If option is BY_SUBJOB produce one output file for each
subjob. Otherwise create a new directory called: option
and create separate output files for each input ligand
within this new directory.
-NC or -nc Do not clean up by removing intermediate files.
By default many intermediate job files are removed.
-nx Do not run jobs, but create specified subjob directories and
input structures.
-j <range_values> Only run specified subjobs.
For example of range values;
10 job number 10
1:15 job numbers 1 to 15
"1, 5, 10" job numbers 1, 5, and 10
"1:15, 18" job numbers 1 to 15 and 18
"1:5, 15:20" job numbers 1 to 15 and 15 to 20