Good afternoon,
I was wondering if Is there a way to work with a database instead of working with separate files in Autodock?
It is computationally expensive to do a process file by file. Since it takes time for the computer to 1)look for the file that is needed for the process 2)Open the file 3) Do the process 4) Close the file.
I have a database that has millions of compounds and it would be very computationally expensive to do the process file by file. I do not have much computational resources.
Therefore, I would like to use one file to perform my docking process without splitting my file into separate files to do separate processes.
I am looking for a way to convert one .mol2 file that has multiple ligands in it to one .pdbqt. file. I would like to convert it so I can use it to do Autodock calculations.
I have read and tried to do it with that MGL Tools. However, it says that the input file should contain only one molecule.
Is there a way to use a single .pdbqt with all the molecules to carry out the docking process?
Is there a way to use single files that contain the information of all ligands in just one?
I really thank you in advance for all the help that can be provided!
Hugs
Stellamaris
Hi Stellamaris,
You can convert a multi-molecule mol2 file to a multi-molecule pdbqt file by OpenBabel (http://open-babel.readthedocs.io/en/latest/Command-line_tools/babel.html).
obabel ligand_multi.mol2 -opdbqt -O ligand_multi.pdbqt
But, I don't think AutoDock can handle a single multi-molecule pdbqt file.
I previously posted shell scripts (vina.sh & energy.sh) for docking many ligands by use of AutoDock Vina, which use separate pdbqt files:
https://www.researchgate.net/post/How_to_do_virtual_screening_of_a_library_of_ligands_through_autodock_Vina/1
You can split a multi-molecule file by OpenBabel with -m option:
obabel ligand_multi.mol2 -opdbqt -O ligand.pdbqt -m
Above mentioned method is feasible for performing VS on a database. But,
more easily you can use Raccoon software to perform docking of a whole database containing all files in .mol2 format.
For autodock ligands must be in separate .pdbqt files. But that is not really a problem. One can easily use openbabel (as Yoshinobu suggested) or write a simple script to split a .mol2 with mutliple ligands into separate .mol2 files with just one ligand, then use a script to convert every .mol2 file to .pdbqt using prepare_ligand4.py and then dock them separately in Autodock (which also can be automated by writing a simple script that will dock the entire directory of .mol2 files).
Dear Colleagues, thank you so much for your help. It has been very useful and I am already running my Autodock calculations. I really appreciate the help that has been given to me.
Hugs
Stellamaris
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