Auto3D on Google Colab

[Jameel9]

I tried to run Auto3D on Colab (with GPU) but it return nothing and I couldn't find where was the problem. It gives me a log file that reads

         _              _             _____   ____  
        / \     _   _  | |_    ___   |___ /  |  _ \ 
       / _ \   | | | | | __|  / _ \    |_ \  | | | |
      / ___ \  | |_| | | |_  | (_) |  ___) | | |_| |
     /_/   \_\  \__,_|  \__|  \___/  |____/  |____/  2.1.0
            // Automatic generation of the low-energy 3D structures                                      

================================================================================ INPUT PARAMETERS

path: ligands/smiles.smi k: 1 window: False verbose: False job_name: 20230917-083135-620261 enumerate_tautomer: False tauto_engine: rdkit pKaNorm: True isomer_engine: rdkit enumerate_isomer: True mode_oe: classic mpi_np: 4 max_confs: None use_gpu: True capacity: 42 gpu_idx: 0 optimizing_engine: AIMNET patience: 1000 opt_steps: 5000 convergence_threshold: 0.003 threshold: 0.3 memory: None batchsize_atoms: 1024 input_format: smi

                           RUNNING PROCESS

================================================================================ Checking input file... '''

---

        / \     _   _  | |_    ___   |___ /  |  _ \ 
       / _ \   | | | | | __|  / _ \    |_ \  | | | |
      / ___ \  | |_| | | |_  | (_) |  ___) | | |_| |
     /_/   \_\  \__,_|  \__|  \___/  |____/  |____/  2.1.0
            // Automatic generation of the low-energy 3D structures                                      

================================================================================ INPUT PARAMETERS

path: ligands/smiles.smi k: 1 window: False verbose: False job_name: 20230917-083138-867542 enumerate_tautomer: False tauto_engine: rdkit pKaNorm: True isomer_engine: rdkit enumerate_isomer: True mode_oe: classic mpi_np: 4 max_confs: None use_gpu: True capacity: 42 gpu_idx: 0 optimizing_engine: AIMNET patience: 1000 opt_steps: 5000 convergence_threshold: 0.003 threshold: 0.3 memory: None batchsize_atoms: 1024 input_format: smi

                           RUNNING PROCESS

================================================================================ Checking input file...

---

and the cell finishes running after few seconds as everything was completed as normal. I could not find any _3d.sdf file in the working directory.

[LiuCMU]

Hello @Jameel9, was this issue sovled?

If not, could you attach the log file and the cell output so that I could look into this issue? Thanks!

[Jameel9]

Yes. It worked when I add a name for each smiles string.

Thank you for willing to help.

[LiuCMU]

Cool! Please let us know if you have feedback in the future.

We are planning several updates to Auto3D, too, stay tuned :)