prime_mmgbsa Command Help
Command: $SCHRODINGER/prime_mmgbsa
usage:
$SCHRODINGER/prime_mmgbsa [<options>] <struct_file>
Any option can be placed in an input file for ease of use. The input
structure should be specified on a line using "STRUCT_FILE <input mae file>".
All other options should be placed one-per-line with the preceding dash
removed. For example, the following two calculations are equivalent:
> prime_mmgbsa file_pv.mae -job_type ENERGY -lcons SMARTS.C
or
> prime_mmgbsa input.inp
where the contents of input.inp are:
STRUCT_FILE file_pv.mae
JOB_TYPE ENERGY
LCONS SMARTS.C
Note that HOST, SUBHOST and NICE flags must be set via the commandline.
All atoms in the ligand will have the i_psp_Prime_MMGBSA_Ligand property
set to 1, so that asl expressions can then be used for specifying parts of
the structure relative to the ligand. For example,
"fillres within 5 (atom.i_psp_Prime_MMGBSA_Ligand 1)"
selects all residues within 5 Angstroms of the ligand.
SMARTS expressions can be included in all asl expressions. The command
-lcons SMARTS.C will apply constraints to all aliphatic carbons in the ligand.
run $SCHRODINGER/prime_mmgbsa -h for a complete listing of all options.
positional arguments:
struct_file For most situations, this should be a Maestro file
with the receptor as the first entry, followed by the
ligand poses (e.g. a Glide pose viewer file). If the
-ligand option is specified, then the input should
instead be a Maestro file with each entry containing a
protein-ligand complex.
options:
-h, --help show this help message and exit
-report_prime_log REPORT_PRIME_LOG
(yes/no) Return an output file with the extension
.Prime.log with the Prime logfiles of all component
jobs. By default this in included if less than 100
ligands are used
-csv_output CSV_OUTPUT
(yes/no) Return a csv format output file -out.csv with
the calculated energies.
-report_top REPORT_TOP
Report the specified number of top-scoring ligands in
the log file. All ligands are reported in the CSV and
structure output files.
-v show program's version number and exit
-jobname JOBNAME, -JOBNAME JOBNAME, -j JOBNAME
Set the base name of outputs
Input:
-ligand LIGAND_ASL Specify the ligand with an asl expression (required
for trajectory processing). If this option is present
then the input should be a maestro input file with
each entry containing both the ligand and the
receptor. The asl expression provided here will be
used to determine which part of the complex structure
is the ligand.
Output:
-out_type {PV,COMPLEX,LIGAND,FLEXIBLE,COMPLETE}
The type of Maestro file to output. Choices are PV,
COMPLEX, LIGAND, FLEXIBLE and COMPLETE . LIGAND
produces a ligand-only file. PV will produce a
combination of the input receptor and the optimized
ligand positions. COMPLEX will return the optimized
ligand and receptor conformations. FLEXIBLE outputs
the optimized conformations of the flexible portions.
Please note that this is not a full protein structure
and cannot be used for any subsequent calculations. Of
these, only COMPLEX will return the full optimized
receptor conformation. PV files are default if
inputting a PV file, COMPLEX files are the default if
inputting a series of complexes. COMPLETE includes the
optimized free receptor and ligand structures to the a
complex output file
Molecular Mechanics (PRIME):
-receptor_region RSEL_ASL, -rsel RSEL_ASL
Designate a region of the receptor as flexible using
an asl expression. Expressions can refer to atoms in
the ligand or the receptor and the selected region is
the union of all the regions for each ligand-receptor
pair in the input PV file. By default the entire
receptor is frozen.
-rflexdist FLEXDIST, -flexdist FLEXDIST
Treat all residues within this distance of the ligand
as flexible. By default the entire receptor is frozen.
(overwrites -receptor_region flag)
-rflexgroup {residue,side,polarh}
Select a portion of the region defined with rflexdist
flag to be flexible. residue: Choose the entire
residue. side: Choose the sidechain of each residue.
polarh: Choose the polar hydrogens on each residue.
-target_flexibility Run a two-stage MMGBSA calculation where the second
stage runs with the subset of flexible protein
residues identified by the first
-target_flexibility_cutoff TARGET_FLEXIBILITY_CUTOFF
Cutoff for determining movement for target flexibility
in Angstroms
-ligand_region LSEL_ASL, -lsel LSEL_ASL
Choose a section of the ligand to be treated as
flexible. By default the entire ligand is flexible.
-job_type {ENERGY,REAL_MIN,SIDE_PRED,SIDE_COMBI,SITE_OPT,PGL}
Prime jobtype to use to sample flexible regions.
Setting this option multiple times will result in
multiple sampling algorithms being used. Options are:
REAL_MIN (default): Local minimization. ENERGY: No
sampling, just calculate a single-point energy.
SIDE_PRED: Optimize sidechains using Prime sidechain
prediction. SIDE_COMBI: Optimize sidechain using
Combinatorial Sidechain Prediction. (Limited to <5
sidechains). SITE_OPT: Run a binding-site optimization
consiting of prime sidechain predictions and
minimziations designed specifically for predicting
induced fit effects. PGL: Run a Prime PGL Binding-Site
Optimization on all flexible regions. See the manual
for more details on this protocol.
-rigid_body Minimize the ligand as a rigid body
-num_output_struct NUM_OUTPUT_STRUCT
The maximum number of poses to return per compound.
This will only be relevant if mulitple job types are
selected or job types that return multiple outputs are
used.
-lcons LCONS Select a portion of the ligand to harmonically
constrain with an ASL expression. By default no
constraints are used.
-rcons RCONS Select a portion of the receptor to harmonically
constrainwith an ASL expression. By default no
constraints are used.
-str_cons STR_CONS Strength of Receptor and Ligand Constraints in
kcals/mol/A^2. The default value is 1.0 kcal/mol/A^2
-fbw_cons FBW_CONS Width of flat bottom potential for constraints in A.
The default value is 0.0A
-prime_opt PRIME_OPTIONS
Pass any keyword value pair to the Prime Refinement
stage in the form <keyword>=<value>. See the "Refining
Protein Structures" chapter in the Prime User Manual
for a description of available options. If you would
like to change the force field from it's default value
( S-OPLS if the proper license is present ) use
-prime_opt OPLS_VERSION=OPLS_2005
-use_ligand_charges Use the partial charges in the input ligand file.
-frozen Do not treat any part of the ligand or receptor as
flexible. This overwrites the -ligand_region and
-receptor_region flags.
-membrane Use Prime implicit membrane model (must be set up in
receptor file through Maestro)
Watermap:
-watermap WATERMAP_FN, -WATERMAP WATERMAP_FN
Score ligands against this watermap. Input should be a
ct file containing the watermap generated with the
current version of the Schrodinger suite.
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