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I successfully installed the package and executed it for the protein-ligand complex using the following command on a system equipped with an NVIDIA GeForce RTX 4070 Ti:
python -m rf2aa.run_inferenc…
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Hi, I ran default MSA search by jackhammer for P26341 (uniprot ID) and then when I did the inference, I got an error: 'First MSA sequence is not the {query_sequence=}'. How do I fix this? Shall I rer…
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Hi!
I am quite new in PeptideShaker so I am still not familiar with all the available options and more importantly with methods that the program utilizes to do certain things.
Now I'm struggling w…
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Hi! Sorry to ask, but I find myself hard to find the final paper result of the experiment (novelty, diversity, novelty). In the paper they are measured by scRMSD and TM-score, how can I find the pytho…
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Amber can give different names to histidine amino acid by examining which protons are present : HID, HIE, or HIP instead of HIS.
This raises an issue when featurizing the protein in Diffdock becaus…
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I followed the instruction of using run_docking_inference.py, supplied pdb file from Posebuster dataset, sdf file of ligand from Posebuster dataset, and txt file of smiles converted from ligand. I tes…
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Hi There
I run into this problem. It seems that pro_ema_inference_epoch138_model.pt is not in the workdir file.
Could you please provide it?
Thanks!
python run_single_protein_inference.py…
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Hi,
When trying to run diffdock using the command below, I got this error. Please advice how to fix this:
(diffdock) [root@oric-zCHS3IvgQd:~/DiffDock]# python -m inference --config default_infe…
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I recently used RFAA protein_sm prediction, but it is very slow on our HPC (depend on protein size, the running time can be range from 15~90 minutes). Also, it met GPU OOMs for large protein system.
…
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I wish to perform a docking simulation involving a single ligand and a single protein. And then use this code in 'https://github.com/deepmodeling/Uni-Mol/tree/main/unimol'
`nthreads=20 # Num of th…