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pablo-arantes / making-it-rain

Cloud-based molecular simulations for everyone
MIT License
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Provide the necessary input files (cannot work) #92

Closed Salahalmulla closed 9 months ago

Salahalmulla commented 9 months ago

Hi sir Provide the necessary input files (cannot work) and the followings are appeared:

[08:37:22] Explicit valence for atom # 1 O, 3, is greater than permitted

ArgumentError Traceback (most recent call last) in <cell line: 122>() 187 out.close() 188 hmol = Chem.MolFromMolFile('temp.mol', removeHs=False) --> 189 charge_mol = Chem.rdPartialCharges.ComputeGasteigerCharges(hmol) 190 charge = Chem.GetFormalCharge(hmol) 191 print("Charge = " + str(charge))

ArgumentError: Python argument types in rdkit.Chem.rdPartialCharges.ComputeGasteigerCharges(NoneType) did not match C++ signature: ComputeGasteigerCharges(RDKit::ROMol mol, int nIter=12, bool throwOnParamFailure=False) Best regards

pablo-arantes commented 9 months ago

Hello,

It appears there is a problem during the 'preparation of the PDB file for the ligand' step. RDkit seems unable to properly interpret your ligand's structure. Could you take a moment to review your ligand PDB file for accuracy? For reference, you might find it helpful to compare your file with the example PDBs provided in our GitHub repository, specifically for the protein-ligand notebook.

Best regards, Pablo

Salahalmulla commented 9 months ago

Thank you pablo Best regards

Salahalmulla commented 9 months ago

Hi pablo Since the error that occurred in the Independence install, and the problem in: ["kilojoule/mole" is not compatible with Unit "kilojoule/(nanometer*mole)" Since then I haven't been able to run: Provide the necessary input files Note that the same files were working perfectly before these problems, and I ran them at different times, different nanoseconds It seems that there was confusion in this section after the above two problems were fixed The attached files for protein and ligand were used Regards

‫في الجمعة، 15 ديسمبر 2023 في 10:06 م تمت كتابة ما يلي بواسطة ‪Pablo Ricardo Arantes‬‏ @.***‬‏>:‬

Closed #92 https://github.com/pablo-arantes/making-it-rain/issues/92 as completed.

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