Updated linux vina tutorial #3
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| @@ -53,14 +53,14 @@ Running the following commands will install meeko and ringtail in | |||
| the currently active micromamba environment. | |||
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| ``` | |||
| 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
installation-linux/README.md
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| 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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Here there seems to be a bug with the "-sdf", Diogo is aware of it
installation-linux/README.md
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| @@ -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
| ``` | ||
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| 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
| @@ -35,7 +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 | |||
| micromamba install gemmi -y | |||
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Removed backport because forlilab/Meeko#225
Updated version of the linux vina tutorial