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Hello, it's relly a wonderful work!
I tried your scipts and checkpoint in the README as follows:
1. I downloaded the checkpoint in [binding_pose_ckpt](https://unimol.dp.tech/ckp/bindind_pose/bindi…
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I have been trying to get DiffDock installed on a Windows server so I can test it with our structures and ligands of interest.
I have been running into difficulties. After getting everything instal…
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**Describe the bug**
SN2 test calculation fails after F– optimization after complete update of autodE and conda
**To Reproduce**
input
```python
import autode as ade
#Runs by default on 4 pr…
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# To-Do
- [x] catalogue all the DUs that ended up with the ligand outside the binding site
- [x] identify potential solutions
- [x] add solutions
# List of unresolved issues:
- [x] docked molec…
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I am trying to run encodermap. The input file has dihedral agles and RMSD, Rg. I am getting this error.
Nan in summary histogram for: encoder/dense_1_biases/histogram
[[node encoder/dense_1_bias…
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Hi everyone,
Recently I have been looking into how one can minimize systems containing frozen particles. In the past, I have attempted to set the mass to zero for the particles that are to be froze…
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I have interpreted `dataset` to refer to functions which pertain to loading, saving, parsing, etc, data from a particular kind of dataset (PDB, Fragalysis, CDD, etc).
Whereas, `data` refers to func…
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I imported the CSV data containing RMSD into Python Idle, but the graphs generated through the Skill_Metrics Python package show individual model RMSD values that are different from the RMSD values o…
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Hi,
US-align is unable to read pdb files from https://esmatlas.com/ . An example is attached. I keep getting "ERROR! Too few residues: 0 residues (
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I used `pd2_ca2main` to generate a PDB file.
I am trying to compare the new file with the old one, but I can't.
```
user_name@server_name:~/bbq_spatial$ python3 calculate_rmsd.py ./bbq_input_pdb…