Covalent docking?

[louetme]

I tried covalent docking as available in normal Autodock4 with the atom type "Z" but it seems this atom type is not recognized by the GPU version.

I got: "Error: Ligand includes atom with unknown type: A or Z!" I checked in the file processligand.cpp and indeed there is no atom type "Z".

Do you plan to implement this feature?

Thanks

Maxime

[diogomart]

Hi,

It's not yet supported in the GPU version, but it's likely it will be in the future.

Best,

On Tue, 30 Jun 2020 at 03:41, louetme [email protected] wrote:

I tried covalent docking as available in normal Autodock4 with the atom type "Z" but it seems this atom type is not recognized by the GPU version.

I got: "Error: Ligand includes atom with unknown type: A or Z!" I checked in the file processligand.cpp and indeed there is no atom type "Z".

Do you plan to implement this feature?

Thanks

Maxime

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[WilliamWWolff]

Hello,

I can see that this is still an open issue on GitHub, but was wondering if you had a vague timeline for implementing covalent docking - though I imagine you must have other priorities!

William

[diogomart]

Hi William,

We have been developing a workflow for covalent docking in autodock-gpu, which involves preparing a flexible sidechain with meeko. You'll need to git clone or download the meeko repository and install with pip install ., as opposed to getting it from PyPI, because we haven't created a github/PyPI release with the recent code that handles covalent ligand preparation.

When running the command line tool mk_prepare_ligand.py, the relevant arguments are:

Covalent docking (tethered):
  --receptor RECEPTOR   receptor filename. Supported formats: [pdb/mmcif]
  --rec_residue REC_RESIDUE
                        examples: "A:LYS:204", "A:HIS:", ":LYS:"
  --tether_smarts TETHER_SMARTS
                        SMARTS pattern to define ligand atoms for receptor attachment
  --tether_smarts_indices IDX IDX
                        indices (1-based) of the SMARTS atoms that will be attached (default: 1 2)

the ligand must be modified to include the sidechain and the alpha carbon, but not the other backbone atoms. As an example, consider an acrylamide reacting with a cysteine. The ligand is R-NC(=O)C=C, but what's passed to meeko must be R-NC(=O)C-CSCC, and the SMARTS pattern could be --tether_smarts CCSCC(=O)N --tether_smarts_indices 1 2, as atoms 1 and 2 in the SMARTS are the alpha- and beta-carbons, respectively.