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Dear developers of strucmotif-search,
I'm a bioinformatician working with PDB structures and have been playing with strucmotif-search for past couples of weeks.
It works nicely, but I would like t…
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Hi, When I run the inference, There exists a kill error, No other explanations is offered. So I do not know where to debug.Thank you for your time. Here is my log file.
`~/my_prj/diffdock/DiffDock$ p…
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Hi,
Do you know how I can fix the below error?
ttclust -f trajectory.xtc -t reference.pdb -sa none -cc 0.6 -sr all
```
....
AVERAGE RSMD BETWEEN CLUSTERS : 4.90
Traceback (most recent call…
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Hi,
I want to cluster the five docking poses of a ligand based on the RMSD of only heavy atoms of the ligand. What should I select for `-sr`?
Please note that it should calculate the RMSDs for on…
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### Describe the solution you'd like
Hi @malmans2,
we received the revisions from the ECMWF experts panel regarding the climatology/bias and trend notebooks for CMIP6 and CORDEX.
We would n…
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Dear authors,
first of all let me congratulate you on the great work!
I would like to ask you about the use of the ligand hydrogens - in the paper, you say the final model does not use hydrogens…
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Hi all,
I've been using MD for some time now on proteins only, but now I'm trying to run it with a ligand. I'm trying to use the GAFF force field to simulate the binding of HAP-18, a virus capsid m…
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With AlphaFold, when pLDDT is say above 70, you can gain some trust in the prediction. For DiffDock, what is a range where you would "trust" the results?
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$python -m inference --protein_ligand_csv data/protein_ligand_example_csv.csv --out_dir results/user_predictions_small --inference_steps 20 --samples_per_complex 40 --batch_size 10 --actual_steps 18 -…
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**Describe the bug**
The installation of atomium seems to succeed but is reported to fail. Then MolecularNodes won't accept to do anything :-)
**To Reproduce**
Steps to reproduce the behavior:
1…