Update quick start guide to use psi4-ambertools stack #172
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j-wags
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I was able to install everything (on my second try) and get the "one-off" example and Python API sections to run. I took notes while working through the installation process and quick start guide. They are here, unedited, but the relevant feedback I have to give is:
- The installation guide gave rough benchmark for AmberTools fragmentation but none for OpenEye. This is minor but when reading it I was expecting a number there as well.
- On startup, the CLI printed (
OpenFF Bespoke) - this probably should be something likeOpenFF BespokeFitfor consistency? - It would be nice to have a copy-paste button on the code sections the user is meant to copy. I'm referring to this button elsewhere:
- For the commands that fit one molecule, it would be nice to have an idea of how long each step might take. I have no familiarity with XTB and have no clue if 10+ minute runtime is normal or if I screwed up something during installation. (As a grad student, there's a decent chance I would have killed the task and moved on to something else if a part of a "quick start" guide took this long.)
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| these also as they can speed up certain operations significantly. OpenEye software requires a free-for-academics | ||
| license to run. |
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| these also as they can speed up certain operations significantly. OpenEye software requires a free-for-academics | |
| license to run. | |
| these also as they can speed up certain operations significantly. OpenEye software requires a [free-for-academics | |
| license](https://www.eyesopen.com/academic-licensing) to run. |
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| :::{warning} | ||
| There is an incompatibility between the AmberTools and Psi4 conda packages on Mac, and it is not possible to | ||
| create a working conda environment containing both. | ||
| ::: |
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I don't suggest this be edited here, but if it becomes a common pain point for users we more clearly should document the alternatives, i.e. XTC on macOS or switching over to Linux
This was referenced May 17, 2022
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Description
To resolve a package incompatibility between psi4 and ambertools on mac, this PR updates the quick-start guide to use xTB and AmberTools, and documents the current known incompatibility.
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