Error in Preparing the ligand for hydrated docking tutorial example

[romanchemist]

When I do mk_prepare_ligand.py -i 1uw6_ligand.sdf -o 1uw6_ligand.pdbqt --pH 7.4 -w
I get -> RuntimeError: Cannot place water molecules on atom 7 of type NA with 4 neighbors.
It's error in code and if to add this key 4: (1, 3) in self._hb_config for key 'NA', it also have some problems (adding one extra water, for example: 5 water for protonated ammonia where 2 molecules of water have equal coordinates). For nicotine it's the same.
If it's possible, please check and fix it. Thanks!

[diogomart]

Thank you for reporting this. I can reproduce on my end, will post here when fixed.

[diogomart]

Nitrogens with a +1 formal charge were incorrectly assigned the "NA" atom type. The correct type is "N". It's fixed now in commit 2ae097d. You can get the fixed version by following the instruction to install from source.

Thanks again for reporting this.

[jasonlse]

Hi, I had the same issue. But when I install the fixed version from source I get the following error instead:

Traceback (most recent call last):
File "/opt/miniconda3/envs/vina/bin/mk_prepare_ligand.py", line 173, in
ligand_prepared = preparator.write_pdbqt_string()
File "/opt/miniconda3/envs/vina/lib/python3.9/site-packages/meeko/preparation.py", line 208, in write_pdbqt_string
return self._writer.write_string(self.setup, remove_index_map, remove_smiles)
File "/opt/miniconda3/envs/vina/lib/python3.9/site-packages/meeko/writer.py", line 142, in write_string
self._walk_graph_recursive(root, first=True)
File "/opt/miniconda3/envs/vina/lib/python3.9/site-packages/meeko/writer.py", line 82, in _walk_graph_recursive
self._pdbqt_buffer.append(self._make_pdbqt_line(member))
File "/opt/miniconda3/envs/vina/lib/python3.9/site-packages/meeko/writer.py", line 54, in _make_pdbqt_line
atom_symbol = mini_periodic_table[atomic_num]
KeyError: 0

Is there still an error in the code or am I doing something wrong?

[diogomart]

Fixed in forlilab/Meeko@7e25748
Thanks for finding it and posting here :)

[jasonlse]

Yup, seems to work now. Cheers.