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I believe this to be a bug with Vina 1.2
Environment Information
Vina: 1.2.3
OS: Centos 7.6
Data set: https://github.com/gkxiao/very-negative-vina-score
Expected Behavior
pose_1.pdbqt is a dock…
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Hello,
I am trying to find out the residence time and the binding and unbinding pathways of the protein-ligand complex system. I have amber (netcdf) trajectories in which ligand bind and unbind seve…
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**Describe the bug**
I'm trying to run the [docking score example from the documentation](https://tdcommons.ai/functions/oracles/#docking-scores)
```python
from tdc import Oracle
# 1. One can sp…
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Dear authors,
I just start working with your instrument, I installed cpu-version (conda env create -f environment_cpuonly.yml) and successfully run it. I used 5tgz psb structure as a target. And dock…
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### Bug summary
For the protein RNA membrane system I simulated, I want to calculate the binding energy between protein and RNA, but when I refer to the Multicomponent Systems tutorial, ligand's mol2…
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If the mode is misspelled or an invalid choice, an excpetion occurs:
```
$ python main.py --run_num=1 --mode='fulldock' --aptamerSeq='GCGCGCGCGATATATAT' --ligand='my_ligand.pdb' --ligandType='othe…
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Hi,
If I include an off-the-shelf implicit solvent model in a protein-ligand binding simulation, would the effects of the implicit solvent model extend to the ligand as well? Eg. in this example:
…
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Is this a good place to always post-compose?
http://www.ebi.ac.uk/QuickGO/searchterms/activity%20involved%20in?ontologyType=GO&aspect=Function
not sustainable......
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Hi, I'm interested in using PointCloud to predict binding affinities for a protein of interest and a list of ligands, but I don't understand how was the file examples/5c2h_11.09 generated. Can you let…
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### Issue summary
Hi,
I successfully used gnina (the CPU version) for docking of ligands to a target - with good results.
However, the binding site contains (at least) one conserved water, and I no…