glide_sif.py Command Help
Command: $SCHRODINGER/run glide_sif.py
usage: /opt/schrodinger/suites2026-1/mmshare-v7.3/python/common/glide_sif.py [options] <jobname>
Takes command line options and creates a Glide simplified input file (SIF).
The SIF can be used to run Glide jobs using $SCHRODINGER/glide. This can aid
in automating Glide workflows.
For argument values that begin with a hyphen-minus, such as negative numbers,
it is recommended to use "-option=value" instead of "-option value".
Copyright Schrodinger, LLC. All rights reserved.
positional arguments:
jobname Job name; used as basename to create <jobname>.in
options:
-v, -version Show the program's version and exit.
-h, -help Show this help message and exit.
-delimiter DELIMITER, -d DELIMITER
Delimiter used for lists passed as command-line
arguments (default ','). This only affects subsequent
arguments, and can be used more than once.
-amide_mode penal|fixed|free|trans|generalized
amide bond rotation behavior: "fixed", "free",
"penal", "trans", "gen[eralized]" [docking]
-amide_trans_all yes|no
include "nonstandard" amides in trans enforcement
[docking]
-amide_transtol <float>
trans amide tolerance (in degrees) [docking]
-asl_res_interaction <string>
If present, use it; else, use
"radius_res_interaction." [docking]
-aslstrings <string>[,<string>]...
ASL strings for receptor scaling [gridgen]
-calc_input_rms yes|no
report RMS deviation against input geometry of each
ligand [docking]
-canonicalize yes|no docking initiated from a canonical conformation per
input ligand (false by default for HTVS precision)
[docking]
-compress_csv yes|no compress file written when using WRITE_CSV [docking]
-compress_poses yes|no
generate compressed maestro pose and _raw files
[docking]
-core_atoms <int>[,<int>]...
index into reference ligand for each atom in core
[docking]
-core_definition all|allheavy|smarts|mcssmarts|atomlist
is core "all" atoms in molecule, "allheavy" (default),
"smarts" pattern, "mcssmarts" (generate SMARTS from
maximum common substructure), "mcssmarts2" (generate
SMARTS w/2 disconnected cores from MCS) or "atomlist"
[docking]
-core_filter yes|no skip ligands that do not contain the core [docking,
gridgen]
-core_pos_max_rmsd <float>
maximum RMSD of core atom positions [docking]
-core_restrain yes|no
restrain core atoms [docking]
-core_restrain_v <float>
strength of core restraining potential [docking]
-core_smarts <string>
SMARTS pattern to match for core RMSD
calculation/restraint [docking]
-core_snap yes|no When using core constraints ("CORE_RESTRAIN yes"): if
"yes", use "snapping" core constraints algorithm. If
"no", use filtering algorithm. If not set, choose
automatically based on CORE_POS_MAX_RMSD ("yes" if <
0.75; "no" otherwise) [docking]
-corecons_fallback yes|no
if a ligand fails to dock with CORE_SNAP retry it
without [docking]
-csv_props_file <string>
file containing names of m2io properties to be added
to csvfile [docking]
-cv_cutoff <float> Coulomb-van der Waals energy cutoff used for final
filtering [docking, gridgen]
-docking_method confgen|rigid|inplace|mininplace
docking method: confgen=flexible docking; rigid=rigid
docking; mininplace=refine (do not dock);
inplace=score in place (do not dock) [docking]
-dointra yes|no relax bad intramolecular contacts [docking]
-dointra_scale <float>
scaling factor for intramolecular pose relaxation
[docking]
-dscore_cutoff <float>
Docking score cutoff [docking]
-epik_penalties yes|no
include ligand Epik state penalties in the Glide
DockingScore scoring function [docking]
-expanded_sampling yes|no
bypass elimination of poses in rough scoring stage
(useful for fragment docking) [docking]
-flexasl <string> ASL defining flexible receptor atoms [gridgen]
-forcefield <string> force field [docking, gridgen]
-forceplanar yes|no trigger MMFFLD planarity options [docking]
-glide_confgen_efcut <float(min=0)>
energy cutoff during ligand conformer generation
[docking]
-glide_cons_finalonly yes|no
only check for constraint satisfaction after docking
is complete [docking]
-glide_dielco <float(min=0,max=9999.9)>
dielectric constant []
-glide_exvol_penal_num <float>[,<float>]...
maximum penalties in kcal/mol for each Glide excluded
volume violation [docking]
-glide_exvol_penal_strength low|small|medium|high|large
penalty specification for (all) Glide excluded
volumes. [docking]
-glide_numexvol <int(min=0)>
number of receptor excluded-volume regions [docking,
gridgen]
-glide_numusexvol <int(min=0)>
number of excluded-volume regions to use [docking,
gridgen]
-glide_output_usehtor yes|no
use rotation of polar hydrogens as pose-distinguishing
criterion [docking]
-glide_recep_aslscale yes|no
for Glide gridgen jobs, take per-atom charge and
radius scaling factors from ASL specification
[gridgen]
-glide_recep_maescale yes|no
for Glide gridgen jobs, take per-atom charge and
radius scaling factors from properties written by
Maestro to the receptor file [gridgen]
-glide_reflig_format maestro|sd|mol2
Glide reference ligand file format [docking]
-glide_rexvol <float>[,<float>]...
sphere radii of Glide excluded volumes [gridgen]
-glide_rexvolin <float>[,<float>]...
inner sphere (max penalty) radii of Glide excluded
volumes [gridgen]
-glide_xexvol <float>[,<float>]...
X-coordinates of centers of Glide excluded volumes
[gridgen]
-glide_yexvol <float>[,<float>]...
Y-coordinates of centers of Glide excluded volumes
[gridgen]
-glide_zexvol <float>[,<float>]...
Z-coordinates of centers of Glide excluded volumes
[gridgen]
-glideconsusemet yes|no
use element-based metal radii for Glide constraints
[docking]
-glidereceptorscalecharges <float>[,<float>]...
per-atom scale factors for receptor charges [gridgen]
-glidereceptorscaleradii <float>[,<float>]...
per-atom scale factors for receptor radii [gridgen]
-glidescorusemet yes|no
use element-based metal radii in Glide scoring
[docking]
-glideuseallexvol yes|no
use all excluded volumes in file (as opposed to
selected ones) [docking]
-glideusexvol yes|no use excluded volumes [docking]
-glideusexvolnames <string>[,<string>]...
excluded-volume labels to use in docking job [docking]
-glidexvolnames <string>[,<string>]...
excluded-volume label list [docking, gridgen]
-grid_center <float>[,<float>]...
coordinates of the grid center [gridgen]
-grid_center_asl <string>
ASL expression defining the grid center [gridgen]
-gridfile <string> path to grid (.grd or .zip) file [docking, gridgen]
-gscore_cutoff <float>
GlideScore cutoff [docking]
-hbond_accep_halo yes|no
include halogens as possible H-bond acceptors in
scoring [docking, gridgen]
-hbond_constraints <string>[,<string>]...
HBOND_CONSTRAINTS "hbond1 47", "hbond2 55" [gridgen]
-hbond_cutoff <float>
H-bond cutoff used for final filtering [docking]
-hbond_donor_aromh yes|no
include aromatic H as a possible H-bond donor in
scoring [docking, gridgen]
-hbond_donor_aromh_charge <float>
count aromatic H as a donor if its partial charge
exceeds this value [docking, gridgen]
-hbond_donor_halo yes|no
include halogens as possible H-bond donors in scoring
[docking, gridgen]
-include_input_conf yes|no
include input conformation in confgen output [docking]
-include_input_rings yes|no
include input ring structures in confgen [docking]
-innerbox <int>[,<int>]...
size of the box bounding the possible placements for
the ligand centroid [gridgen]
-keep_input_csv_fields yes|no
Keep the fields from the input ligand file when using
WRITE_CSV [docking]
-keep_subjob_poses yes|no
keep <jobname>_subjob.poses.zip at the end of a
distributed docking job [docking]
-keepraw yes|no do not delete the unsorted/unfiltered ("raw") pose
file, <jobname>_raw.mae[gz] [docking]
-keepskipped yes|no save skipped ligands to <jobname>_skipped.mae[gz]
[docking]
-lig_ccut <float(min=0)>
charge cutoff to determine whether to use vdW scaling
of ligand atoms [docking]
-lig_maecharges yes|no
use charges from ligand Maestro file instead of those
from the force field [docking]
-lig_vscale <float(min=0)>
ligand vdW scaling (see also LIG_CCUT) [docking]
-ligand_end <int(min=0)>
end ligand [docking]
-ligand_index <int(min=1)>
index of the ligand entry to use for computing default
GRID_CENTER and OUTERBOX [gridgen]
-ligand_molecule <int(min=1)>
index of the ligand molecule to be removed [gridgen]
-ligand_start <int(min=1)>
start ligand [docking]
-ligandfile <string> Glide docking ligands file name [docking]
-ligandfiles <string>[,<string>]...
array of filenames to dock. Can be used instead of
LIGANDFILE [docking]
-ligprep yes|no run input ligands through LigPrep on the fly [docking]
-ligprep_args <string>
command-line options to pass to LigPrep [docking]
-macrocycle yes|no generate macrocycle ring templates on the fly using
Prime [docking]
-macrocycle_options <string>
options string to pass to Prime's macrocycle conformer
generator [docking]
-max_iterations <int(min=0)>
maximum number of iterations during docking
minimization [docking]
-maxatoms <int(min=1,max=500)>
maximum number of ligand atoms; larger ligands will be
skipped [docking]
-maxkeep <int(min=1)>
maximum number of poses to keep after the rough
scoring stage [docking]
-maxref <int(min=1)> maximum number of poses to refine [docking]
-maxrotbonds <int(min=0,max=100)>
maximum number of rotatable bonds. Ligands exceeding
this limit will be skipped [docking]
-metal_constraints <string>[,<string>]...
METAL_CONSTRAINTS "metal1 64", ... [gridgen]
-metal_cutoff <float>
metal bond cutoff used for final filtering [docking]
-metcoord_constraints <string>[,<string>]...
METCOORD_CONSTRAINTS "label <ncoordsites>", ...
[gridgen]
-metcoord_sites <string>[,<string>]...
METCOORD_SITES "<x1> <y1> <z1> <r1>", "<x2> <y2> <z2>
<r2>", ...; Note that the list of "<x> <y> <z> <r>"
tuples in a single METCOORD_SITES specification covers
*all* of the specified METCOORD_CONSTRAINTS. Thus the
number of such tuples is equal to the *sum* of all the
<ncoordsites> specifications. [gridgen]
-nenhanced_sampling <int(min=1,max=4)>
expand size of the Glide funnel by N times to process
poses from N confgen runs with minor perturbations to
the input ligand coordinates [docking]
-nmaxrmssym <int(min=0)>
max number of poses to compare taking symmetry into
account [docking]
-noe_constraints <string>[,<string>]...
NOE_CONSTRAINTS "<label> <x> <y> <z> <rmin> <rmax>",
... [gridgen]
-nosort yes|no don't sort poses from "_raw.mae" file into
"_[lib|pv].mae" [docking]
-nreport <int(min=0)>
maximum number of poses to report at the end of the
job (zero means "unlimited") [docking]
-nrequired_cons <string>
number of constraints that need to be satisfied (must
be an integer or "all") [docking]
-nucleic_acid_mode yes|no
Set to the docking mode optimized for nucleic acids
[docking]
-outerbox <float>[,<float>]...
outer (grid) box size in Angstroms [gridgen]
-peptide yes|no use grid and sampling settings optimized for
polypeptides [docking, gridgen]
-phase_db <string> Absolute path to Phase database to use as source of
ligands to dock [docking]
-phase_nconfs <int(min=1)>
Number of confs per ligand to read from Phase DB
[docking]
-phase_subset <string>
Subset file listing the IDs of the ligands to dock
from a Phase database [docking]
-pose_displacement <float(min=0)>
minimum heavy-atom "max displacement" for counting two
poses as distinct [docking]
-pose_htorsion <float(min=0,max=60)>
minimum deviation (degrees) in polar H torsion for
counting two poses as distinct [docking]
-pose_outtype poseviewer|ligandlib|poseviewer_sd|ligandlib_sd|phase_subset|none
format for file containing docked poses: "poseviewer"
for _pv.mae output; "ligandlib" for _lib.mae;
similarly "poseviewer_sd" and "ligandlib_sd" for sdf
output; "phase_subset" for bypassing _lib or _pv in
favor of a Phase subset file. [docking]
-pose_rmsd <float(min=0)>
minimum heavy-atom rmsd for counting two poses as
distinct [docking]
-poses_per_lig <int(min=1)>
maximum number of poses to report per each input
ligand [docking]
-posit_constraints <string>[,<string>]...
POSIT_CONSTRAINTS "<label> <x> <y> <z> <r>", ...
[gridgen]
-postdock yes|no perform post-docking minimization and scoring
[docking]
-postdock_itmax <int(min=1)>
maximum number of iterations for post-docking
minimization [docking]
-postdock_npose <int>
maximum number of best-by-Emodel poses to submit to
post-docking minimization [docking]
-postdock_scitmax <int(min=1)>
maximum number of iterations for post-docking strain
correction [docking]
-postdockcg yes|no use conjugate gradient minimization (instead of
variable metric) in post-docking minimization
[docking]
-postdockligmin yes|no
include minimization in post-docking [docking]
-postdockstrain yes|no
include strain correction in post-docking score
[docking]
-precision SP|HTVS glide docking precision [docking]
-radius_res_interaction <float(min=0)>
use residues within this distance of the grid box
center [docking]
-rec_maecharges yes|no
use charges from receptor Maestro file instead of
those from the force field [gridgen]
-recep_ccut <float(min=0)>
charge cutoff used to determine whether to use vdW
scaling of receptor atoms [gridgen]
-recep_file <string> receptor file name [gridgen]
-recep_index <int> index of the receptor entry in RECEP_FILE to use for
gridgen (-1 means the last structure in the file)
[gridgen]
-recep_vscale <float(min=0)>
vdW scaling for receptor atoms (see also RECEP_CCUT)
[gridgen]
-ref_ligand_file <string>
Glide reference ligand file name [docking, gridgen]
-refindex <int(min=1)>
index of the reference ligand structure [docking]
-report_cpu_time yes|no
Report the CPU time spent on docking each ligand in
the r_glide_cpu_time pose property [docking]
-reward_intra_hbonds yes|no
reward formation of intramolecular hydrogen bonds in
the ligand [docking]
-ringconfcut <float> energy cutoff during ring conformer generation
[docking]
-ringonfly yes|no sample ring conformations if no template found and
store as templates for reuse [docking]
-sample_n_inversions yes|no
include (non-ring) N inversions in confgen [docking]
-sample_rings yes|no sample ring conformations using templates during
confgen [docking]
-schrodinger_ring_template_sources <string>
Ring template file to use. Overrides the environment
variable SCHRODINGER_RING_TEMPLATE_SOURCES [docking]
-score_input_pose yes|no
score and report the input pose in addition to the
docked poses [docking]
-score_minimized_input_pose yes|no
score and report the minimized input pose in addition
to the docked poses [docking]
-scoring_cutoff <float>
rough score cutoff [docking]
-shape_atoms <int>[,<int>]...
atom indexes from reference ligand that define the
reference shape. Default is all heavy atoms plus polar
hydrogens. [docking]
-shape_ref_ligand_file <string>
Reference ligand for shape constraints (takes
precedence over REF_LIGAND_FILE) [docking]
-shape_refindex <int(min=1)>
index of the reference ligand structure for shape
constraints [docking]
-shape_restrain yes|no
apply shape constraints during docking [docking]
-shape_typing ELEMENT|PHASE_QSAR|MACROMODEL|NONE
atom-typing scheme to use for shape constraints
[docking]
-skip_epik_metal_only yes|no
skip ligand ionization/tautomeric states that have
been prepared by Epik or LigPrep specifically to
interact with a metal ion [docking]
-strain_gsfactor <float>
Coefficient of strain-energy correction to Glidescore
[docking]
-strain_gsthresh <float>
Threshold for strain-energy correction to Glidescore
[docking]
-strainelec yes|no include electrostatics in post-docking strain
correction [docking]
-use_cons <string>[,<string>]...
USE_CONS "<name>[:<feature_index>]", ... [docking]
-use_ref_ligand yes|no
use reference ligand for RMSD evaluation or core
constraints specification [docking]
-useflexasl yes|no specify movable atoms by ASL in Glide input file
[gridgen]
-useflexmae yes|no specify movable atoms by property in input .mae file
[gridgen]
-vsdb_max_hits <int> maximum hits stored in the vsdb file. [docking]
-warhead_atoms <int>[,<int>]...
the two warhead atoms in the reference ligand that are
directly attached to the linker; required when using
CORE_DEFINITION mcssmarts2 [docking]
-write_csv yes|no write <jobname>.csv listing results for all ligands
(even ones that didn't report a pose) [docking]
-write_docking_report yes|no
Writes out an HTML report for the docking job
[docking]
-write_res_interaction yes|no
generate per-residue interactions with the ligand for
residues specified by "RADIUS_RES_INTERACTION" or
"ASL_RES_INTERACTION" [docking]
-write_timings_csv yes|no
write a CSV file with CPU times for each subjob, as
well as overall pre- and post-processing [docking]
-write_vsdb yes|no write <jobname>.vsdb listing results for the
vsdb_max_hits poses. [docking]