OptLigandInDU

Overview

OptLigandInDU is an application to optimize a ligand or a series of ligands in a rigid protein active site. This is suitable for screening of a large amount of docked ligands into a protein receptor.

Example Commands

Ligand Optimization in a protein active site

Optimizes the Ligand(s) in a protein active site using FF14SB-Parsley Force Field.

Input files

  • 1H1Q_AB_receptor.oedu : OEDU file containing the protein active site.

  • 1H1Q_AB_fred_docked.oeb : OEB file containing the ligand to optimize.

Command line

prompt> optligandindu 1H1Q_AB_receptor.oedu 1H1Q_AB_fred_docked.oeb 1H1Q_AB_fred_docked_opt.oeb

Output files

  • 1H1Q_AB_fred_docked_opt.oeb : OEB file containing optimized ligands.

Optimize a Ligand pose in a rigid protein

Performs a constrained optimization of the ligand in the rigid protein active site, using FF14SB-Parsley Force Field.

Input files

  • 1H1Q_AB_receptor.oedu : OEDU file containing the protein active site.

  • 1H1Q_AB_fred_docked.oeb : OEB file containing the ligand to optimize.

Command line

prompt> optligandindu -du 2IKO.oedu -in 1H1Q_AB_fred_docked.oeb -out 1H1Q_AB_fred_docked_opt.oeb -optimize poseCartesian

Output files

  • 1H1Q_AB_fred_docked_opt.oeb : OEB file containing optimized ligand.

Command Line Help

A description of the command line interface can be obtained by executing OptLigandInDU with the –help option.

> optligandindu --help

will generate the following output:

Help functions:
  optligandindu --help simple      : Get a list of simple parameters
  optligandindu --help all         : Get a complete list of parameters
  optligandindu --help defaults    : List the defaults for all parameters
  optligandindu --help <parameter> : Get detailed help on a parameter
  optligandindu --help html        : Create an html help file for this program
  optligandindu --help versions    : List the toolkits and versions used in the application

Required Parameters

-du <filename>

An OEDU file with a design unit, containing the protein active site. If the file contains multiple design units, only the first one is used.

[keyless parameter 1]

-in <filename>

Molecular input file name containing 3D coordinates in any format supported by OEChem.

[keyless parameter 1]

Acceptable molecule file formats are:

SZYBKI file format support

File extension

Description

mol

MDL Mol File

mmd, mmod

Macromodel

mol2

Tripos Sybyl mol2 file

oeb

New Style OEBinary

sd, sdf

MDL SD File

xyz

XMol XYZ format

Optional Parameters

File Options

-log

The argument for this flag specifies the name of the log file. The level of detail for logfile information can be altered using the -verbose flag. Generation of an output log may be disabled by providing nul as a argument in Windows and /dev/null as an argument on Linux and macOS. [default = prefix _log.txt]

-prefix

The argument for this flag defines the prefix to be used for various information and data files generated. Most important among these is the ‘prefix_parm.txt’ file which includes a copy of all the parameters used in the run. The prefix is also used to generate a default log file name if not explicitly specified with the -log flag. [default = <app_name>].

-verbose

This is a boolean flag that controls the level of detail written to the log file. By default only minimal information is written to the log file. Verbose logging will cause more information to be written to the log file in order to follow behavior during program execution. [default = false]

-molNames

This parameter takes a text file containing a list of molecule names (one name per line in the file). If this parameter is set then only molecules in the input file(s) (see parameter -in) with names that match those in the text files will be read in.

The general purpose of this flag is to provide an easy mechanism for reading a few specific molecule(s) that are contained in a large file, without having to extract those molecules by hand from the input molecules file. [default = NONE].

-progress

Show progress on screen. Options are ‘none’, ‘dots’, ‘log’ and ‘percent’. The ‘dots’ options will displays dots on screen to show molecules completed. The ‘log’ option will duplicate the log file on screen. The ‘percent’ option will track progress through the input file. [default = none]

Input Options

-proteinMask

Design unit components mask defining the subset of design unit components to be used as protein during optimization. Multiple components can also be combined as a comma separated string to create the input.

Possible values = cofactors, counter_ions, excipients, lipids, metals, nucleic, other_cofactors, other_ligands, other_nucleics, other_proteins, packing_residues, polymers, post_translational, protein, solvent, sugars.

Predefined multi-component values:

  • targetComplex = protein,nucleic,cofactors,solvent,metals,counter_ions,lipids,other_proteins, other_nucleics,other_ligands,other_cofactors.

  • targetComplexNoSolvent = protein,nucleic,cofactors,metals,lipids,other_proteins, other_nucleics,other_ligands,other_cofactors.

  • macroMolComponents = protein,nucleic,other_proteins,other_nucleics.

    [default = targetComplex]

Output Options

-out <filename>

Output file name, in any format supported by OEChem, for an optimized ligand.

[keyless parameter 2]

Optimization Options

-optimize    [Default: cartesian]

Optimization type. Choices: [0] cartesian: Performs a full cartesian optimization [1] poseCartesian: Performs a constrained cartesian optimization, ensuring to hold the ligand pose

-ff    [Default: ff14sb_sage]

The force field to use for optimization. A predefined force field can be used by choosing one from the list of choices. A different Smirnoff/OpenFF formatted small molecule force field can be used with ff14sb by just passing in the small molecule force field OFFXML file as the argument. Choices: mmff94, mmff94s, mmff_amber, mmffs_amber, ff14sb_parsley, ff14sb_sage

-ligandCharge    [Default: current]

Charges to be assigned for the ligand. The default value of current refers to using the existing charges on the ligand. Choices: [0] current [1] am1bcc [2] am1bccelf10 [3] mmff

-gradTol    [Default: 1.0e-6]

Root mean squared (RMS) gradient tolerance for convergence and termination of optimization.

-maxIter    [Default: 1000]

Maximum number of iterations for termination of optimization. Optimization is terminated if either the gradient tolerance gradTol or the maximum iterations limit, whichever occurs first, is reached.

-solventModel    [Default: vacuum]

Solvent model to be used during optimization. Choices: [0] vacuum [1] sheffield [2] pb