How to prepare todo.all for a single sdf file

VFLP VFLP 1
#1

I want to screen my database which has ~2000 compounds in a single sdf (or mol) file, I don’t know how to prepare the todo.all file, anybody knows how to prepare the todo.all with a single file?

#2

Hello hen_umn and welcome to the forum!

At this time VirtualFlow cannot screen sdf or mol files directly. An option would be to use VFLP and start from SMILES and convert these to .pdbqt format.

However, please keep in mind that

VFLP (VirtualFlow for Ligand Preparation) is dedicated for the curation of libraries containing large numbers of small molecules.

I would suggest that for a library of 2000 compounds, you can most likely screen in a more straightforward fashion, using simple bash scripts to extract docking scores, for example.

Kind regards,

Sorin

#3

Thank you Sorin,
I have one more question, I download part of ZINC15 Library from Index of /bcmp/wagner_lab/virtualflow/zinc15_20180825_pdbqt_tar
I don’t have the collection-length file like the REAL Library, so how can I prepare the todo.all file?, I know with the collection-length file, collection.txt, it’s easy, are there any command/script to get the collection-length file?

Thanks again,

henry

#4

Hi Henry,

There is a collection of scrips for various purposes, under VFTools. A script that might be useful in your case is located here.
Also, we kindly ask you to read the excellent documentation provided by the developers of VirtualFlow.

Happy docking!

Kind regards,

Sorin Draga