croshong

Thanks for your reply I have successfully setup your code and alphafold library, several other library from deepmind I'm now running above finetunning command, but it seems to take really...

attached files are log file for finetuning which is still currently running. it's still in training epoch 0 and I could find the finetuned parameter as you mentioned. but for...

 I forgot the attachment

I think model_2_ptm means the file in params/parmas_model2_2_ptm.npz then what is the model_2_ptm_ft ? maybe should it be produced by finetuning?

I could run the prediction with finetuning paramter with following command line python run_prediction.py --targets examples/pmhc_hcv_polg_10mers/targets.tsv \ --outfile_prefix polg_test2 --model_names model_2_ptm_ft \ --model_params_files datasets_alphafold_finetune/params/mixed_mhc_pae_run6_af_mhc_params_20640.pkl \ --ignore_identities and I got the...

Yes but I want to try to install gnina from source to be optimized for my server . to install from source how can I solve the above error?

Thanks for your reply I could find the model detail in https://github.com/gnina/models Now I'm trying to make a simple 3D-cnn script with model in https://github.com/gnina/models in Keras/tensorflow I can modify...

No there is no problem in running example code but I think there is only training data and training process in the example code so to include validation/test process for...

If that's the case, I think training with default2018.model also should fail, but it works well, so I guess there can be other reasson

When I use the data included in https://github.com/gnina/models/tree/master/data/PDBBind2016/General_types/fixed_gen_uff_completeset_*, I got the same error in dense model. Is there something that I should modify ?