Closed Jameel9 closed 12 months ago
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!
Yes. It worked when I add a name for each smiles string.
Thank you for willing to help.
Cool! Please let us know if you have feedback in the future.
We are planning several updates to Auto3D, too, stay tuned :)
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
================================================================================ 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
================================================================================ Checking input file... '''
================================================================================ 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
================================================================================ 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.