binding_pose_metadynamics.py Command Help
Command: $SCHRODINGER/run -FROM psp binding_pose_metadynamics.py
usage:
Metadynamics Analysis of Binding Poses
$SCHRODINGER/run -FROM psp binding_pose_metadynamics.py <input complexes> -HOST <CPU Queue> -SUBHOST <GPU Queue>
This algorithm is designed to rank various binding configurations of a single
ligand in a single binding site.
The metadynamics portion of the dynamics will be returned as well as a plot with
the extension -out.pdf which plots the average value of the collective variable
over the simulation
Output Properties:
r_psp_MetadynamicsBinding_CompScore -- Composite Score linearly combining
the r_psp_MetadynamicsBinding_PoseScore and
r_psp_MetadynamicsBinding_Persistence scores. Lower values equate to
more stable complexes. The equation is PoseScore - 5 * Persistence
r_psp_MetadynamicsBinding_PoseScore -- Expectation of the RMSD of the
pose over the course of the metadynamics. Lower values equate to
more stable complexes.
r_psp_MetadynamicsBinding_Persistence -- Average persistence of contacts
over the course of the metadynamics trajectories. Higher values equate
to more stable complexes
r_psp_MetadynamicsBinding_Persistence_HBond -- Average persistence of
HBonds
r_psp_MetadynamicsBinding_Persistence_Pi -- Average persistence of Pi-Pi
stacking and T-Shaped interactions
r_psp_MetadynamicsBinding_In_RMSD -- Optional RMSD after the relaxation
step. This can help identify cases where the relaxation before the
metadynamics is materially changing the pose
positional arguments:
struct_file Structures to process. These should be Ligand-Receptor
complex mae files or pre-equilibrated CMS files. The most
common source for the complex mae files will be the output
of IFD runs. Equilibrated CMS files are designed to be
used for systems containing membranes, nucleic acids or
any other components that require additional or different
equilibration protocols than the default 'relaxation'
protocol provided by Desmond which has been designed
for soluble proteins.
options:
-h, --help show this help message and exit
-ligand_asl LIGAND_ASL
ASL Expression defining the ligand (required).
example "res.ptype UNK"
-nposes NPOSES Number of poses to re-score.
By default all poses are scored but this can be used
to score only the first N poses in the input file
-selected_poses SELECTED_POSES [SELECTED_POSES ...]
The entries in the input file to run (or rerun).
This value should be 1-indexed. Note that if you
are rerunning a job with the -previous_metadir flag
then this will be pose numbers in the output file of
the previous run.
-ntrial NTRIAL Number of trials per pose (default is 10)
-anchor_region ANCHOR_REGION
ASL expression of the anchor region. This should be
the backbone of 3 to 4 residues in what is thought to be
the rigid core of the protein. This should
only be used in combination with 'ligand' cv
-height HEIGHT Bias potential height in the metadynamics simulation,
unit: kcal/mol, (default is 0.05)
-restrain RESTRAIN Whether to use restraints (yes/no default is yes
-smoothing SMOOTHING Smoothing constant for CV (default:50)
-score_fraction SCORE_FRACTION
Set the fraction of the CV to use as the score for ranking.
0.2 means the last 20 percent will be used. (Default: 0.2)
-label_property LABEL_PROPERTY
CT-level property to use as a label. Otherwise use
the title of the structure
-run_mode {all,prep,rescore,md,mtd}
Modify the mode of binding_pose_metadynamics.
all -- preps runs and scores the subjobs.
prep -- preps the jobs, but does not run them or score the
results.
rescore -- for an already completed job, run or re-run the
scoring.
md -- Runs multisim up to and including the unbiased MD
stage. Does not perform the full workflow.
Does not score jobs.
mtd -- Runs the metadyanmics stage. Meant to be run on a
a previous job run with the 'md' run_mode.
Will also perform scoring. The jobname must match
the jobname used with the 'md' run.
Note rescore MUST be run with the same settings as the original
run.
Default: all
-previous_metadir PREVIOUS_METADIR
Add additional trials to an existing
BindingPoseMetadynamics run.
and with the same settings as the original run. Note that
the output maestro file should be used as the input
-metadir_basename METADIR_BASENAME
Specify the name of the binding pose metadynamics workdir.
If this option is not set, the jobname will be used to set the
name of the workdir
-report_md_equil_rmsd
For each trial, for each pose, will report the RMSD
of the pose immediately after MD equlibration but
before any metadynamic repulsion has been applied.
This will also produce an additional output file,
JOBNAME-mdequil_out.maegz, containing these poses.
The RMSDs will also be printed to the logfile.
-ligand_tail_for_md_equil_rmsd LIGAND_TAIL_FOR_MD_EQUIL_RMSD
For -report_md_equil_rmsd ONLY, skip atoms defined by
the given SMARTS patterns for the purposes of RMSD calculations.
These atoms are considered ligand tails whose positions is not
physically relevant
-no_hmr Do not use hydrogen mass repartitioning as part of MD
Default is to use HMR
-solvate SOLVATE Use solvate pocket as part of the multisim workflow
(yes/no default is no)
-cloud PRE_EMPTIBLE_CPU_HOST
The argument to -cloud is a pre_emptible CPU host used
for the system builder jobs. -SUBHOST will be used
exclusively for GPU subjobs and can be a pre-emptible
GPU host
-v show program's version number and exit
-jobname JOBNAME, -JOBNAME JOBNAME, -j JOBNAME
Set the base name of outputs
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.
-SUBHOST <hostname> or -SUBHOST <hostname:nproc> or -SUBHOST "hostname1:nproc1 ... hostnameN:nprocN"
Run the subjobs on the specified hosts. The driver is run on the host specified with -HOST.
-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.