Amit Roy

@roselightheart thank you! That appears to have solved the problem.

I experience the same issue as well.

I can confirm that changing `h5py` to `h5py=2.10.0` in `environment.yml` makes the error go away.

I encounter the same problem when I run the Google Colab notebook.

These are my results: { "affinity_pred_value": 2.5308895111083984, "affinity_probability_binary": 0.40284594893455505, "affinity_pred_value1": 2.6539573669433594, "affinity_probability_binary1": 0.3593267500400543, "affinity_pred_value2": 2.4078216552734375, "affinity_probability_binary2": 0.4463651478290558 } As the saying goes, close enough for government work.

I want to add that I have managed to make some progress and actually get a full simulation to run. Here are the steps that I took, just in case...

Just to add a quick note: I tried altering the call to `modeller.addSolvent` in `line 94` of `simulateComplex.py` by replacing the `padding` option with `boxSize` as follows: ``` modeller.addSolvent( system_generator.forcefield,...

No, I have not been using `analyse.py`. I could not get that file to run without errors. The image above was taken from PyMol, which opened both the `output_minimised` and...

I just want to add that I have managed to get `analyse.py` and that script appears to have corrected the off-centre image: 

I am unable to find any example of the correct way to specify a template in the YAML file. Would someone please be kind enough to post an example here?