Autodock Vina in Knime, w/o Ligandscout

Hi,

I am trying to replicate a successful KNIME workflow that uses Flare and other nodes to trim down chemical libraries and dock them.

While I do appreciate Ligandscout does provide a Vina node, I am trying to avoid subscriptions/licenses to run opensource.

At the moment the issue seems to be with the pdbqt format that Vina needs.

The workflow generates sdf and pdb that I then convert to pdbqt via the OpenBabel node.

So far so good.

The challenge is to perform the conversion of multiple molecules contained in the same sd file to then generate x number of pdbqt files for Vina to dock.

I believe Vina is not really geared to virtual screen mode but it can be forced to dock each one in a batch mode but have no experience of this.

While I could try to do this via the CLI, the aim is to deploy it in a Knime workflow.

have you come across a similar issue?

Thanks,

O.