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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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11 changes: 6 additions & 5 deletions installation-linux/README.md
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Original file line number Diff line number Diff line change
Expand Up @@ -35,6 +35,7 @@ micromamba install python=3.11 -y
micromamba install pymol-open-source -y
micromamba install rdkit numpy scipy -y
micromamba install chemicalite matplotlib=3.7 pandas -y
micromamba install importlib_resources gemmi -y
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this couple of packages are missing

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will be fixed in release meeko v0.6

```

Several packages are being installed in a single line.
Expand All @@ -53,14 +54,14 @@ 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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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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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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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 -h
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Without the -h it will return an error (help message still visible but we may want to just remove the error message)

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Good point, just opened forlilab/Ringtail#57

```

A new release of Meeko will be available soon.
Expand Down Expand Up @@ -126,12 +127,12 @@ 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
rt_process_vs read -i results.db -e -2 -sdf passing_sdf
```

A file "phenol.sdf" should have been added to "passing\_sdf".