Vina: Difference between revisions
Jump to navigation
Jump to search
PedroLacerda (talk | contribs) (Created page with "= Vina (vs.py) = This plugin enables small scale virtual screening with the AutoDock Vina software stack. It uses Meeko and Scrubber to prepare molecular ligands, and PLIP to analyze the results. It was tested on PyMOL 3.0 with Python 3.10. Currently supports only Linux and probably Mac. == Input == Multi-smi SMILES file (e.g. ''mols.smi''). Cc1c(Cl)cccc1Nc1ncccc1C(=O)OC[C@H](O)CO ZINC000000000171 CN(C)CC[C@@H]1c2ccc(Cl)cc2CCc2cccnc21 ZINC000000000179...") |
PedroLacerda (talk | contribs) No edit summary |
||
| Line 19: | Line 19: | ||
[[File:Screenshot from 2025-01-17 17-21-36.png|thumb|right|The preparation step.[[Colosseum]] in Rome]] | [[File:Screenshot from 2025-01-17 17-21-36.png|thumb|right|The preparation step.[[Colosseum]] in Rome]] | ||
While on the preparation step, should fill the '''target receptor''' and '''box center''' selections like presented on picture. Shold also fill the the '''input file''' and '''output folder''. The '''flexible''' selection is optional. | While on the preparation step, should fill the '''target receptor''' and '''box center''' selections like presented on picture. Shold also fill the the '''input file''' and '''output folder'''. The '''flexible''' selection is optional. | ||
=== Running step === | === Running step === | ||
Follow the graphical interface. | Follow the graphical interface. | ||
Revision as of 17:03, 17 January 2025
Vina (vs.py)
This plugin enables small scale virtual screening with the AutoDock Vina software stack. It uses Meeko and Scrubber to prepare molecular ligands, and PLIP to analyze the results.
It was tested on PyMOL 3.0 with Python 3.10. Currently supports only Linux and probably Mac.
Input
Multi-smi SMILES file (e.g. mols.smi).
Cc1c(Cl)cccc1Nc1ncccc1C(=O)OC[C@H](O)CO ZINC000000000171 CN(C)CC[C@@H]1c2ccc(Cl)cc2CCc2cccnc21 ZINC000000000179 CC(C)NC[C@H]1CCc2cc(CO)c([N+](=O)[O-])cc2N1 ZINC000000000570 Cc1nc(NCc2ccccc2)c2cc[nH]c2n1 ZINC000000002036
Guided interface
Preparation step
The preparation step.Colosseum in Rome
While on the preparation step, should fill the target receptor and box center selections like presented on picture. Shold also fill the the input file and output folder. The flexible selection is optional.
Running step
Follow the graphical interface.