# making-it-rain **Repository Path**: irrelevant2021/making-it-rain ## Basic Information - **Project Name**: making-it-rain - **Description**: Cloud-based molecular simulations for everyone - **Primary Language**: Unknown - **License**: MIT - **Default Branch**: main - **Homepage**: None - **GVP Project**: No ## Statistics - **Stars**: 0 - **Forks**: 0 - **Created**: 2022-01-11 - **Last Updated**: 2022-01-11 ## Categories & Tags **Categories**: Uncategorized **Tags**: None ## README # Making-it-rain Cloud-based molecular simulations for everyone ![alt text](https://github.com/pablo-arantes/Making-it-rain/blob/main/GraphAbs.png) ## Hello there! This is a repository where you can find a Jupyter notebook scripts for running Molecular Dynamics (MD) simulations using OpenMM engine and AMBER and CHARMM force fields files on Google Colab. This repository is a supplementary material of the paper "***Making it rain: Cloud-based molecular simulations for everyone***" and we encourage you to read it before using this pipeline. The main goal of this work is to demonstrate how to harness the power of cloud-computing to run microsecond-long MD simulations in a cheap and yet feasible fashion. 1. **AMBER** [![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/pablo-arantes/Making-it-rain/blob/main/Amber.ipynb) - `Using AMBER to generate topology and to build the simulation box` 2. **CHARMM** [![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/pablo-arantes/Making-it-rain/blob/main/CHARMM_GUI.ipynb) - `Using inputs from CHARMM-GUI solution builder` 3. **AlphaFold2+MD** [![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/pablo-arantes/Making-it-rain/blob/main/AlphaFold2%2BMD.ipynb) - `Using AlphaFold2_mmseqs2 to generate protein model + MD simulation using AMBER to generate topology and to build simulation box` **UPDATE (Oct 18 2021)** 4. **Protein-Ligand simulations** [![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/pablo-arantes/making-it-rain/blob/main/Protein_ligand.ipynb) - `Using AMBER to generate topology and to build the simulation box and for the ligand using GAFF2 or OpenFF force fields` 5. **Using AMBER Inputs** [![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/pablo-arantes/making-it-rain/blob/main/Amber_inputs.ipynb) - `Using inputs from AMBER suite of biomolecular simulation program` 6. **Using GROMACS Inputs** [![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/pablo-arantes/making-it-rain/blob/main/Gromacs_inputs.ipynb) - `Using inputs from GROMACS biomolecular simulation package (AMBER, CHARMM and OPLS force fields are compatible)` ![alt text](https://github.com/pablo-arantes/Making-it-rain/blob/main/fluxogram_gh.png) ## Bugs - If you encounter any bugs, please report the issue to https://github.com/pablo-arantes/Making-it-rain/issues ## Acknowledgments - We would like to thank the OpenMM team for developing an excellent and open source engine. - We would like to thank the AlphaFold team for developing an excellent model and open sourcing the software. - We would like to thank the ChemosimLab ([@ChemosimLab](https://twitter.com/ChemosimLab)) team for their incredible [ProLIF](https://prolif.readthedocs.io/en/latest/index.html#) (Protein-Ligand Interaction Fingerprints) tool. - Credit to Sergey Ovchinnikov ([@sokrypton](https://twitter.com/sokrypton)), Milot Mirdita ([@milot_mirdita](https://twitter.com/milot_mirdita)) and Martin Steinegger ([@thesteinegger](https://twitter.com/thesteinegger)) for their fantastic [ColabFold](https://github.com/sokrypton/ColabFold) - A Making it rain by **Pablo R. Arantes** ([@pablitoarantes](https://twitter.com/pablitoarantes)), **Marcelo D. Polêto** ([@mdpoleto](https://twitter.com/mdpoleto)), **Conrado Pedebos** ([@ConradoPedebos](https://twitter.com/ConradoPedebos)) and **Rodrigo Ligabue-Braun** ([@ligabue_braun](https://twitter.com/ligabue_braun)). - Also, credit to [David Koes](https://github.com/dkoes) for his awesome [py3Dmol](https://3dmol.csb.pitt.edu/) plugin. - Finally, we would like to thank Professor [Giulia Palermo](https://palermolab.com/) for her support and thoughtful comments in the development of the present work. ## Do you want to cite this work? Arantes P.R., Depólo Polêto M., Pedebos C., Ligabue-Braun R. Making it rain: cloud-based molecular simulations for everyone. Journal of Chemical Information and Modeling 2021. DOI: [10.1021/acs.jcim.1c00998](https://doi.org/10.1021/acs.jcim.1c00998). [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.5196783.svg)](https://doi.org/10.5281/zenodo.5196783) ## trackgit-views