ryanzr / labodock Goto Github PK

Hi Ryan. Awesome notebooks you got there.

Would like to know if there is also an available for proteins with no native ligands?

Thanks.

Hello Ryan,
Thanks for writing such great notebooks for the community. Google colab is shifted to CUDA 12.2. As a result, the mamba installation script are not getting success.
!mamba install -c conda-forge -c bioconda mgltools=1.5.7 biopython=1.80 openbabel=3.1.1 plip=2.2.2 zlib=1.2.13 xlsxwriter=3.0.3

The installation log generates,

No package can be installed for pin: cudatoolkit 12.2.*

I tried different things, like mentioning cudatoolkit=12.2 in the script, also remove the package version details, so that conda installs the appropriate version by itself. Nothing is working.
Will you be able to update the code?
Thanks

In the 'virtual_screening.ipynb' in the step 'Parameterise ligands with Gasteiger charges'
the following command
!mk_prepare_ligand.py -i {LIG_sdf_lFile} -o {LIG_pdbqt_dFFile}

causes this error:

Traceback (most recent call last):
  File "/usr/local/bin/mk_prepare_ligand.py", line 14, in <module>
    from meeko import MoleculePreparation
  File "/usr/local/lib/python3.10/site-packages/meeko/__init__.py", line 36, in <module>
    from . import analysis
  File "/usr/local/lib/python3.10/site-packages/meeko/analysis/__init__.py", line 7, in <module>
    from .fingerprint_interactions import FingerprintInteractions
  File "/usr/local/lib/python3.10/site-packages/meeko/analysis/fingerprint_interactions.py", line 10, in <module>
    import pandas as pd
ModuleNotFoundError: No module named 'pandas'

I noticed a typo in the notebook 'virtual_screening.ipynb', which causes an error

in "Generate ligand SD files"

    !obabel -:{'"'+LIG_SMI+'"'} -O {LIG_sdf_lFile} --title {LIG_ID} --gen3d \
    --best --minimize --ff {Force_field} --steps {Maximum_steps} \
    --crit {Convergence_criteria} --log 2>> {CMPLIB_obmin_log_lfile}

should probably be:

    !obabel -:{'"'+LIG_SMI+'"'} -O {LIG_sdf_lFile} --title {LIG_ID} --gen3d \
    --best --minimize --ff {Force_field} --steps {Maximum_steps} \
    --crit {Convergence_criteria} --log &>> {CMPLIB_obmin_log_lfile}

Hi Ryan.
First of all, what a delightful piece of work you got here! It's so didactic that I'm planning to use it with my students.
Unfortunately, after a careful reading of your instructions, I am unable to move forward beyond 04 preparing the ligand step, despite I separetely ran the first cell of software installation. However, the issue is particular to the Parameterise ligand with Gasteiger charges, where the pdbqt cannot be found, hence, no docking calculation can be performed.
I attach the error:
"
FileNotFoundError Traceback (most recent call last)
in <cell line: 19>()
17 os.makedirs(LIG_dFLD, exist_ok=True)
18 get_ipython().system('mk_prepare_ligand.py -i {LIG_sdf_lFile} -o {LIG_pdbqt_dFFile} > /dev/null 2>&1')
---> 19 pdbqt_add_chid(LIG_pdbqt_dFFile)
20
21 print(f'+ Parameterisation: {LIG_sdf} > {LIG_pdbqt}')

in pdbqt_add_chid(inpt_file)
5
6 def pdbqt_add_chid(inpt_file: str) -> None:
----> 7 with open(inpt_file, 'r') as inpt:
8 data = inpt.read()
9 new_data = data.replace(' UNL ', ' UNL A')

FileNotFoundError: [Errno 2] No such file or directory: '/content/7KBS_/DOCKING/RLXF/RLXF.pdbqt'
"

I hope you can help me.
Again, such a great work and thanks for sharing,

Abe