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tutorials/0.9.3/sbgrid_seminar.md

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---
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permalink: /tutorials/0.9.2/sbgrid_seminar
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permalink: /tutorials/0.9.3/sbgrid_seminar
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layout: splash
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title: "LightDock SBGrid Seminar"

tutorials/0.9.3/simple_docking/index.md

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permalink: /tutorials/0.9.2/simple_docking
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permalink: /tutorials/0.9.3/simple_docking
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title: "Simple Docking"
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<center><h1 style="margin-top:40px">Simple protein-protein docking example</h1></center><br>
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<center>
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<img src="/tutorials/0.9.2/simple_docking/2uuy.png">
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<img src="/tutorials/0.9.3/simple_docking/2uuy.png">
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</center>
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* table of contents
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[lightdock3_setup] INFO: LightDock setup OK
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```
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**NOTE** For a detailed description of the setup stage, please check the [LightDock basics](https://lightdock.org/tutorials/0.9.2/basics#2-setup-a-simulation)
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**NOTE** For a detailed description of the setup stage, please check the [LightDock basics](https://lightdock.org/tutorials/0.9.3/basics#2-setup-a-simulation)
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{: .notice--warning}
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If the setup is successful, we will find a file called `setup.json`, which includes all the details about this LightDock simulation.
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As you may have noticed, we have instructed LightDock to use only 1 CPU core (`-c 1`). By default, LightDock will look for the total number of available cores. If you want to specify a different number, use the flag `-c`. MPI is also supported by using the `-mpi` flag.
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**NOTE** For more information about the simulation stage, please check the [LightDock basics](https://lightdock.org/tutorials/0.9.2./basics#3-run-a-simulation)
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**NOTE** For more information about the simulation stage, please check the [LightDock basics](https://lightdock.org/tutorials/0.9.3/basics#3-run-a-simulation)
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## 4. LightDock results
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Inside the `swarm_0` folder, we will find 200 new PDB structures corresponding to the 200 glowworm agents used in the current example. Try opening them on PyMOL and have a quick look at them:
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<center>
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<img src="/tutorials/0.9.2/simple_docking/2uuy_swarm_0.png">
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<img src="/tutorials/0.9.3/simple_docking/2uuy_swarm_0.png">
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</center>
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**Congratulations!** You have successfully run your first docking simulation with LightDock!
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{: .notice--success}
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You can find all the simulation data already generated here: [simulation.tgz](/tutorials/0.9.2/simple_docking/data/simulation.tgz)
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You can find all the simulation data already generated here: [simulation.tgz](/tutorials/0.9.3/simple_docking/data/simulation.tgz)
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**Attention!** In this simple example we did not cluster predicted structures for the different swarms (`swarm_0` in this case), but **for realistic simulations it is critical to always cluster intra-swarm structures**.
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{: .notice--danger}

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