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pablo-arantes / making-it-rain

Cloud-based molecular simulations for everyone
MIT License
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protein_ligand Colab - Violation occurred on line 240 in file Code/Numerics/Optimizer/BFGSOpt.h #84

Closed dimkorov closed 7 months ago

dimkorov commented 11 months ago

Hello,

I would like to run some protein-ligand simulations with your notebook but always get the error below when I am using any other ligand other than the example (the ligand from pdb: 3HTB):

It stops here ---> 84 ff.Minimize(maxIts=1000)

and the error is

Invariant Violation bad direction in linearSearch Violation occurred on line 240 in file /home/conda/feedstock_root/build_artifacts/rdkit_1692275722171/work/Code/Numerics/Optimizer/BFGSOpt.h Failed Expression: status >= 0

Is there anything I can do to overcome this issue? Any help would be greatly appreciated.

Thank you in advance.

Best regards, Dimitris

pablo-arantes commented 11 months ago

Hi @dimkorov

Thank you for letting me know about the issue. I will take a look and back to you.

Thank you.

Best,

Pablo

Elsword016 commented 10 months ago

I ran into a similar issue, it kind of got fixed when I used the 3D structure of the ligand from PubChem and used the .sdf file rather than converting it into a PDB (cause it triggered another error while generating topology, ligand_gaff.pdb wasn't getting created). Maybe this might solve your issue too. Using .sdf fixed it both while running on colab as well as locally on my PC on vscode.

pablo-arantes commented 9 months ago

Hello everyone,

I have changed the code. Please try running it again and inform me if it functions correctly.

Thank you.

Best regards