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Hi. I am trying to reproduce your test results about generating antibody CDRs (sequence-structure co-design) using the DiffAb model.
Using the `design_testset.py` script, index 10 (pdb `7bwj_H_L_E`)…
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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…
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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, 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, 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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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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**Description**
I'm trying to create a fresh conda env and run bespokenfit
The env is created with the command
`mamba create -n bespokefit -c conda-forge -c openeye openff-bespokefit openeye-t…
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I found difficulty to install the tutorial T010 because It seems the MDAnalysis package is not installed properly or numpy package is with an issue. Please, see the error message below:
```
ValueE…
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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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@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…