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Updated linux vina tutorial #3

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Updated linux vina tutorial #3

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daacdba
Updated linux vina tutorial
DaniDelHoyo Nov 5, 2024
d69d54b
Imports needed
DaniDelHoyo Nov 5, 2024
b28f980
remove importlib_resources
rwxayheee Nov 6, 2024
52a826f
ligand box fix
DaniDelHoyo Nov 7, 2024
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8 changes: 4 additions & 4 deletions installation-linux/README.md
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Expand Up @@ -53,14 +53,14 @@ Running the following commands will install meeko and ringtail in
the currently active micromamba environment.

```
pip install meeko==0.6.0a3
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@DaniDelHoyo DaniDelHoyo Nov 5, 2024

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seems like ringtail install a previous version of meeko, so we should probably install the right version after (or update it from ringtail release).
Also, now this would still not work until the Meeko release from develop

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@rwxayheee rwxayheee Nov 6, 2024

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ringtail does not install meeko (?). It seems like the current ringtail works with meeko develop. Maybe you already talked to someone in the lab, but I can help with specific things that didn't work for you

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@DaniDelHoyo DaniDelHoyo Nov 6, 2024

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my bad, seems like it does install meeko 0.5.1 but when installing it with micromamba, not with pip. We can remove this change then

pip install ringtail
pip install meeko==0.6.0a3
```

Running the following commands should display help messages:
```
mk_prepare_ligand.py
rt_process_vs.py
rt_process_vs
```

A new release of Meeko will be available soon.
Expand Down Expand Up @@ -126,10 +126,10 @@ Copy the files in [toy-example-data](../toy-example-data) to the working dir and
```
scrub.py "Oc1ccccc1" -o phenol.sdf
mk_prepare_ligand.py -i phenol.sdf -o phenol.pdbqt
mk_prepare_receptor.py --pdb pocket.pdb --ligand pocket.pdb --padding 5 -o receptor
mk_prepare_receptor.py --read_pdb pocket.pdb --box_enveloping pocket.pdb --padding 5 -o receptor -p -j -v
mkdir results
./vina_1.2.5_linux_x86_64 --receptor receptor.pdbqt --config receptor.box.txt --ligand phenol.pdbqt --out results/phenol.pdbqt
rt_process_vs.py write -o results.db -fp results -m vina -ai -rf receptor.pdbqt
rt_process_vs write -o results.db -fp results -m vina -ai -rf receptor.pdbqt -sr
mkdir passing_sdf
rt_process_vs.py read -i results.db -e -2 -sdf passing_sdf
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@DaniDelHoyo DaniDelHoyo Nov 5, 2024

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Here there seems to be a bug with the "-sdf", Diogo is aware of it

```
Expand Down