Thomas Graham

reproduction of paper results and ligand/protein prep

1

Hi -- Thanks for the fantastic effort. I would like to reproduce the results you got for the structures found in figure 14, but the PDB ID's are not available...

I have reviewed some previous issues and it appears that the problem I have run into is that our cluster is set up such that we cannot modify the GPU...

Hi, In the paper Santos-Martins2019 a protocol was described whereby crystallographic waters were dealt with by defining them as: Crystallographic waters "For some submissions of Stage 1b, we kept the...

ifps with large number of protein/lig pairs

2

Hi -- I use a docking approach that results in the minimization of a large number of ligands (800k-1M) in a single protein and the protein is also minimized. The...

quickstart fail ingest error during install

10

Hi, I have tried a few things and feel I have configured my machine in a way that reflects what is specified in the quickstart guide, but I am running...

Cannot use csh with micromamba

2

### Troubleshooting docs - [X] My problem is not solved in the Troubleshooting docs ### Anaconda default channels - [X] I do NOT use the Anaconda default channels (pkgs/* etc.)...

azure responses gpt-5-codex 400 The encrypted content for item rs_68dxxx could not be verified

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### What version of Codex is running? 0.41.0 ### Which model were you using? got-5-codex ### What platform is your computer? Linux 4.18.0-553.el8_10.x86_64 x86_64 x86_64 ### What steps can reproduce...