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Fast Rigid Exhaustive Docking | ||||
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Fast Rigid Exhaustive Docking | ||||
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fred -dbase my_ligands.oeb.gz -rec my_rec.oeb.gz
FRED will dock the ligands in the file my_ligands.oeb.gz to the receptor my_rec.oeb.gz. No scoring function has been specified so FRED will use its default scoring function Chemgauss3 (see section 4.3.5).
-dbaseThis tells FRED where the ligands it is going to dock are, in this case the file my_ligands.oeb.gz. The ligand file should have multiple conformers of all flexible ligands (see section 5.5 for more detail on preparing the ligand database).
-recThis specifies a receptor file to dock to the ligand into. The receptor file must be created prior to running FRED with this command line. This file can be created by FRED or by the fred_receptor GUI.
setup.txt
receptor.oeb.gz
status.txt
chemgauss3_docked.oeb.gz
chemgauss3_scores.txt
fred -dbase my_ligands.oeb.gz \
-pro my_protein.pdb \
-box bound_ligand.mol2 \
-addbox 4.0
FRED will create a receptor and then dock the ligands in the file my_ligands.oeb.gz to it. No scoring function has been specified so FRED will use its default scoring function Chemgauss3 (see section 4.3.5).
-dbaseThis tells FRED where the ligands it is going to dock are, in this case the file my_ligands.oeb.gz. The ligand file should have multiple conformers of all flexible ligands (see section 5.5 for more detail on preparing the ligand database).
-proThis specifies the protein structure used to create the receptor file. This file should not contain a bound ligand.
-boxThis specifies a box defining the extents of the active site. The format of this file is any supported 3d molecule format. The box will always be aligned along the x,y and z axis. The max and min x,y and z values denoting the sides of the box will the the max and min x,y and z values of any heavy atom on the molecule passed.
This example uses a bound ligand. Without modification the box created around it would be unreasonably small, however we are also using the -addbox flag which increases the size of the box created.
-addboxThis flag tells FRED to extend each side of the box it created with the -box flag by 4 Angstroms. (if the dimensions of the box were initially 12x12x12, the modified box would have dimensions 20x20x20).
setup.txt
receptor.oeb.gz
status.txt
chemgauss3_docked.oeb.gz
chemgauss3_scores.txt
fred -dbase my_ligands.oeb.gz -rec my_rec.oeb.gz -oformat sdf.gz
FRED will dock the ligands in the file my_ligands.oeb.gz to the receptor my_rec.oeb.gz. No scoring function has been specified so FRED will use its default scoring function Chemgauss3 (see section 4.3.5).
The output format of docked structures will be gzipped sdf.
-dbaseThis tells FRED where the ligands it is going to dock are, in this case the file my_ligands.oeb.gz. The ligand file should have multiple conformers of all flexible ligands (see section 5.5 for more detail on preparing the ligand database).
-recThis specifies a receptor file to dock to the ligand too. The receptor file must be created prior to running FRED with this command line. This file can be created by FRED or by the fred_receptor GUI.
-oformatThis flag tells FRED that the docked structures it outputs should be in sdf gzipped format, rather than the default OEB gzipped format. If sdf were specified instead of sdf.gz regular non-gzipped SDF format would be used.
setup.txt
receptor.oeb.gz
status.txt
chemgauss3_docked.sdf.gz
chemgauss3_scores.txt
fred -dbase my_ligands.oeb.gz \
-rec my_rec.oeb.gz \
-prefix myrun \
-output_dir /results/site/FRED
FRED will dock the ligands in the file my_ligands.oeb.gz to the receptor my_rec.oeb.gz. No scoring function has been specified so FRED will use it's default scoring function Chemgauss3 (see section 4.3.5).
All output file will be prefixed with the text "myrun_", and placed in the directory /results/site/FRED (which must exist). Note that it is not necessary to specify both -prefix and -output_dir, you can specify one (or none) if you only want to set the a prefix to the output filenames or an output directory respectively.
-dbaseThis tells FRED where the ligands it is going to dock are, in this case the file my_ligands.oeb.gz. The ligand file should have multiple conformers of all flexible ligands (see section 5.5 for more detail on preparing the ligand database).
-recThis specifies a receptor file to dock to the ligand too. The receptor file must be created prior to running FRED with this command line. This file can be created by FRED or by the fred_receptor GUI.
-prefixThis flag tells FRED to pre-append all output files it writes with the text "myrun_" (the _ is added automatically).
-output_dirThis flag tells FRED that all output files should be written in the directory /results/site/FRED.
These files will all be written to /results/site/FRED, rather than the working directory as they normally would.
myrun_setup.txt
myrun_receptor.oeb.gz
myrun_status.txt
myrun_chemgauss3_docked.sdf.gz
myrun_chemgauss3_scores.txt
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Fast Rigid Exhaustive Docking | ||||
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