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:
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¶
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]
-
-molnames
¶
This parameter specifies 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 database, without having to extract those molecules by hand from the database.
Output Options¶
-
-out
<filename>
¶ Output file name, in any format supported by OEChem, for an optimized ligand.
[keyless parameter 2]
-
-prefix
¶
Prefix used to name output files.
-
-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]
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_parsley]
¶ 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: [0] mmff94 [1] mmff94s [2] mmff_amber [3] mmffs_amber [4] ff14sb_parsley
-
-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