Preparing the Workflow
General
In addition to the general preparation which is required for any VirtualFlow module as describe here, for VFVS the input-files folder needs to be set up as described below.
Preparation of the input-files Folder
input-files FolderFor using VFVS, a set of docking scenarios has to be set up by the user, and it can be any number of them. This is done in the input-files folder, which contains the following items:
Configuration files for the docking programs
Receptor structures
Other files needed by the docking program
Optional: Input ligand collection in ready-to-dock VirtualFlow format (can also be located at another location, which can be specified in the control file)
Docking Scenario Folders
For each docking scenario, a new folder is created within the input-files folder. Choosing descriptive names of the docking scenario which encodes some of its properties is recommended, such as
input-files/qvina_rigid_receptor1
for a docking scenario where qvina is used as the docking program, receptor structure 1 is used, and the receptor is held rigid.
Docking Program Config Files
Each docking scenario folder needs to have a file called config.txt, which is used by the configuration file used by all supported docking programs. For instance, for all the AutoDock Vina-based docking programs, this would be the config file which all these programs required.
Within these config files, also the receptor structure which is used by that docking scenario is specified. All files which are specified in these configuration files have to be relative paths with respect to the tools folder. This is the case because all docking programs are started by VirtualFlow from the tools folder. For instance, if the receptor structure file input-files/qvina_rigid_receptor1/receptor1.pdb is specified in the docking program configuration file input-files/qvina_rigid_receptor/config.txt, then the path to the receptor which needs to be used would be ../input-files/qvina_rigid_receptor1/receptor1.pdb.
AutoDock Vina-based Docking Programs
Within the docking program config files, all desired/required options have to be specified, except
the ligand, since the ligand is variable and VFVS takes care of it
The number of CPU cores (multi threading) in the config file, which can be specified via the option cpu, will be replaced by the option in the VirtualFlow control file option cpus_per_queue. Still, the cpu option needs to be present in the docking program config file, so that VirtualFlow can replace the value by the value of cpus_per_queue.
PLANTS
As always in VirtualFlow, also the config file of the docking program PLANTS is placed in a subfolder in the input-files directory, and needs to contain a file called config.txt. All file paths which are set in the config.txt file need to be relative to the tools folder, as for any other docking program.
As required by PLANTS the receptor has to be in the MOL2 format. More information can be found in the manual of PLANTS:
PLANTS requires ligands to be in the MOL2 format. VirtualFlow can therefore use libraries in the typical VirtualFlow library format where all ligands are stored in the MOL2 format. Alternatively, VirtualFlow Ants can also use ligand libraries in the PDBQT Format, and convert them on the fly to the MOL2 format so that PLANTS can use PDBQT libraries. This library format option can be set in the control file via the parameter ligand_ibrary_format. If the library is in the PDBQT format, then SPORES has to be installed for the on the fly conversion. More details on how to install SPORES and PLANTS can be found here:
https://docs.virtual-flow.org/documentation/-LdE8RH9UN4HKpckqkX3/vfvs/installation/prerequisites
Shared Folder for Receptor Structures
It is recommended to create a separate folder for the receptor structures, such as
input-files/receptors
where all the receptor structures which are used are stored. Different docking scenarios can then make shared used of them. But theoretically, they can be stored also in docking scenario folders.
Ligand Input Database
The ligand database to be used can be stored in any location, and the location can be specified in the control file.
The required ligand input database can be prepared either from scratch with VFLP, or a ready-made database can be used. For virtual screenings, most users would use a ready-made database. For this purpose, we are providing the REAL database from Enamine, which can be downloaded here from the VirtualFlow website:
There, specific subsets of the database can be downloaded, as well as the required collection lengths file which is needed to set up the tools folder as described earlier here (i.e. this file can be used for the central task todo.all list which is used by VirtualFlow).
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