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forlilab / Meeko

Interfacing RDKit and AutoDock
GNU Lesser General Public License v2.1
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Ligand preparation for covalent docking with mk_prepare_ligand.py #103

Closed lovenicole closed 5 months ago

lovenicole commented 5 months ago

Hi, I want to prepare ligand for covalent docking.

However, when I open the help message with the "mk_prepare_ligand.py --help" command, the message of the Covalent docking part is like below. image

I tried preparing one ligand with the command below. mk_prepare_ligand.py -i $id.mol2 -o $id.pdbqt --receptor 8x6r_A_1.pdb --rec_residue "A:CYS:12" --tether_smarts "CCSCC(=O)N" --tether_smarts_indices 1 2

But I got the error.

Covalent docking requires Prody which is not available

I installed Meeko 0.5.0 with pip install meeko.

How can I solve it?

rwxayheee commented 5 months ago

Hi @lovenicole Please try pip install prody to install prody (2.4.1 at the moment)

lovenicole commented 5 months ago

Hi @lovenicole Please try pip install prody to install prody (2.4.1 at the moment)

Thank you very much! The problem is solved.