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forlilab / Meeko

Interfacing RDKit and AutoDock
GNU Lesser General Public License v2.1
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rigid ligand docking #102

Closed alfredoq closed 2 months ago

alfredoq commented 2 months ago

Dear Meeko developers,

while preparing a molecule .pdbqt is there a way to indicate that all rotatable bonds should be kept rigid?

many thanks in advance,

Alfredo

diogomart commented 2 months ago

Dear Alfredo,

Yes with

-r "[*][*]" -b 1 2

These options are the short version of

  -r SMARTS, --rigidify_bonds_smarts SMARTS
                        SMARTS patterns to rigidify bonds
  -b i j [i j ...], --rigidify_bonds_indices i j [i j ...]
                        indices of two atoms (in the SMARTS) that define a bond (start at 1)
alfredoq commented 2 months ago

Thank you Diogo for the prompt reply,

and in case of using Meeko through the Python api, this should be indicated as a parameter? (which one?)

Thank you again!

diogomart commented 2 months ago

You are welcome.

It's rigidify_bonds_smarts and rigidify_bonds_indices. For example: https://github.com/forlilab/Meeko/?tab=readme-ov-file#possibly-useful-configurations-of-moleculepreparation

alfredoq commented 2 months ago

great! I will try it,

thanks