Supported docking programs and scoring functions
Last updated
Last updated
VFVS 2.0 supports many docking programs and scoring functions that run on both CPUs and GPUs. For using docking programs and scoring functions on GPUs, please modify the job submission file (/tools/templates/template1.slurm.sh
) to indicate access to GPU nodes for running docking. To use a specific docking program or a scoring function of interest, the following modification may be required:
Properly install the executable binary programs.
Modify the all.ctrl
file located in the tools/templates
directory to specify the format of the ligands to be screened and the name of the docking program to be used.
Create the configuration file (config.txt
) to provide the parameters required by the docking program to dock. Examples of how the config.txt file looks like for each docking program are displayed in .
The AutoDock_GPU executable program (of name 'autodock_gpu') should be placed in the/tools/bin
directory. The corresponding executable program needs to be compiled based on the user’s system using the instructions described .
In all.ctrl
file, set
For an example of theconfig.txt
file, please refer to .
The autodock4 executable program (of name 'autodock_cpu') should be placed in the/tools/bin
directory. The corresponding executable program needs to be compiled based on the user’s system using the instructions described .
In all.ctrl
file, set
For an example of theconfig.txt
file, please refer to .
Installation of the external docking program is not required.
In all.ctrl
file, set
Installation of the external docking program not required.
In all.ctrl
file, set
Installation of the external docking program is not required.
In all.ctrl
file, set
In all.ctrl
file, set
Installation of the external docking program is not required.
In all.ctrl
file, set
Installation of the external docking program is not required.
In all.ctrl
file, set
Installation of the external docking program not required.
In all.ctrl
file, set
Installation of the external docking program is not required.
In all.ctrl
file, set
Installation of the external docking program is not required.
In all.ctrl
file, set
Installation of the external docking program is not required.
In all.ctrl
file, set
Installation of the external docking program is not required.
In all.ctrl
file, set
The FitDock executable program (of name 'FitDock') should be placed in the/tools/bin
directory.
In all.ctrl
file, set
The Gnina executable program (of name 'Gnina') should be placed in the/tools/bin
directory.
In all.ctrl
file, set
The GalaxyDock3 executable program (of name 'GalaxyDock3') should be placed in the/tools/bin
directory.
In all.ctrl
file, set
The GOLD executable program (of name 'gold_auto') should be placed in the/tools/bin
directory.
In all.ctrl
file, set
Installation of the external docking program is not required.
In all.ctrl
file, set
The HDock executable program (of name 'hdock') and the createpl executable program (of name 'createpl') should be placed in the/tools/bin
directory.
In all.ctrl
file, set
Installation of the external docking program is not required.
In all.ctrl
file, set
The iGemDock executable program (of name 'mod_ga') should be placed in the/tools/bin
directory.
In all.ctrl
file, set
Installation of the external docking program is not required.
In all.ctrl
file, set
The LigandFit executable program (of name 'ligandfit') should be placed in the/tools/bin
directory.
In all.ctrl
file, set
Installation of the external docking program is not required.
In all.ctrl
file, set
The MDock executable program (of name 'MDock_linux') should be placed in the/tools/bin
directory.
In all.ctrl
file, set
The MCDock executable program (of name 'mcdock') should be placed in the/tools/bin
directory.
In all.ctrl
file, set
Installation of the external docking program is not required.
In all.ctrl
file, set
Installation of the external docking program is not required.
In all.ctrl
file, set
Installation of the external docking program is not required.
In all.ctrl
file, set
Installation of the external docking program is not required.
In all.ctrl
file, set
Installation of the external docking program is not required.
In all.ctrl
file, set
Installation of the external docking program is not required.
In all.ctrl
file, set
In all.ctrl
file, set
The QuickVina-W-gpu executable program (of name 'qvina_w_gpu') should be placed in the/tools/bin
directory.
In all.ctrl
file, set
In all.ctrl
file, set
Please ensure that obabel is loaded into the environment (module load openbabel for Slurm)
In all.ctrl
file, set
Installation of the external docking program is not required.
In all.ctrl
file, set
The SEED executable program (of name 'seed4') should be placed in the/tools/bin
directory. In addtion, AmberTools needs to be loaded in order to use SEED.
In all.ctrl
file, set
Installation of the external docking program is not required.
In all.ctrl
file, set
Installation of the external docking program is not required.
In all.ctrl
file, set
Installation of the external docking program is not required.
In all.ctrl
file, set
In all.ctrl
file, set
In all.ctrl
file, set
Installation of the external docking program is not required.
In all.ctrl
file, set
The rf-score-vs executable program (of name 'rf-score-vs') should be placed in the/tools/bin
directory.
In all.ctrl
file, set
Installation of the external docking program is not required.
In all.ctrl
file, set
The gnina executable program (of name 'gnina') should be placed in the/tools/bin
directory.
In all.ctrl
file, set
Installation of the external docking program is not required.
In all.ctrl
file, set
Installation of the external docking program is not required.
In all.ctrl
file, set
Installation of the external docking program is not required.
In all.ctrl
file, set
For an example of theconfig.txt
file, please refer to .
For an example of theconfig.txt
file, please refer to .
For an example of theconfig.txt
file, please refer to .
The ADFR executable program (of name adfr) should be placed in the/tools/bin
directory. The corresponding executable program needs to be compiled based on the user’s system using the instructions described .
For an example of theconfig.txt
file, please refer to .
For an example of theconfig.txt
file, please refer to .
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file, please refer to .
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file, please refer to .
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file, please refer to .
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file, please refer to .
The qvina_gpu executable program (of name 'qvina_gpu') should be placed in the/tools/bin
directory. Instructions for compilation can be found .
For an example of theconfig.txt
file, please refer to .
For an example of theconfig.txt
file, please refer to .
The key word 'rbdock' must be able to activate the program (see , or, download with conda: conda install -c bioconda rdock)
For an example of theconfig.txt
file, please refer to .
For an example of theconfig.txt
file, please refer to .
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file, please refer to .
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file, please refer to .
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file, please refer to .
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file, please refer to .
For an example of theconfig.txt
file, please refer to .
The qvina_gpu executable program (of name 'qvina_w_gpu') should be placed in the/tools/bin
directory. Instructions for compilation can be found .
For an example of theconfig.txt
file, please refer to .
The qvina_gpu executable program (of name 'qvina_w_gpu') should be placed in the/tools/bin
directory. Instructions for compilation can be found .
For an example of theconfig.txt
file, please refer to .
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file, please refer to .
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