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Hi, is it possible to release a code of benchmark? I am having trouble reproducing the reported RMSD. I got a little bit higher results using SCWRL4. I repacked the whole protein backbone (multiple ch…
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I installed pytorch according to the instructions in the readme, but it still reports errors during the run, as follows.
how can I fix the issues up? thanks,
`C:\\Docking_Lab\DiffDock>python` -m …
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Currently, it is not straightforward to run inference on an arbitrary, user-defined protein-ligand complex. [The old repository](https://github.com/jaechanglim/DTI_PDBbind) is helpful in this regard, …
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Add `symmetry {"CD1", "CD2"}` or something like that to `ResidueType` which can be used for rmsd, alignment, etc. This could be called for each symmetrical substructure.
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# Task Overview
- [x] Download and align MERS structures from the PDB
- [x] Create design units for every MERS structure (`Structure_Source`) and fragalysis compound (`Compound_ID`)
- [x] Run docki…
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Hello developers:
I am new to `gmxapi`, I hope to control the operation of MD through the conformation generated during the MD run. For example, I have a reference configuration **ref.gro** and an …
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@kaminow can you add here what you've done to calculate RMSD, what's worked, what hasn't?
# Methods
## 1) Basic OpenEye
`oechem.OERMSD(ref, mobile)` where ref and mobile are `OEMolBase` objects…
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**Describe the bug**
Cannot create an instance of Oracle
**To Reproduce**
Steps to reproduce the behavior:
1. Execute
```
from tdc import Oracle
gsk3 = Oracle(name = 'GSK3')
```
2. Error m…
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Hi,
using the module I got geometries which, in my humble opinion, are too far from each other for a very small RMSD calculated. These molecules look similar if I take original geometries.
When the …
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**Error parsing coordinates for updated cartesian syntax in Q-Chem 6.0**
Using Q-Chem 5.3/5.4 with autodE v 1.3.4 works like a charm. However, with the updated LIBOPT3 driver in Q-Chem 6.0, the print…