Project ID: plumID:21.037
Name: Molecular Dynamics simulations of RBD/hACE2 complexes
Archive: https://github.com/maxbonomi/bat-MD/archive/main.zip (browse)
Category: bio
Keywords: SARS-CoV-2, COVID-19, MD, human-ACE2, spike, receptor-binding domain
PLUMED version: 2.7
Contributor: Max Bonomi
Submitted on: 04 Sep 2021
Last revised: 17 Sep 2021
Publication: S. Temmam, K. Vongphayloth, E. Baquero, S. Munier, M. Bonomi, B. Regnault, B. Douangboubpha, Y. Karami, D. Chrétien, D. Sanamxay, V. Xayaphet, P. Paphaphanh, V. Lacoste, S. Somlor, K. Lakeomany, N. Phommavanh, P. Pérot, O. Dehan, F. Amara, F. Donati, T. Bigot, M. Nilges, F. A. Rey, S. van der Werf, P. T. Brey, M. Eloit, Bat coronaviruses related to SARS-CoV-2 and infectious for human cells. Nature. 604, 330–336 (2022)

PLUMED input files

File Compatible with
…ANAL-236-CoV.1/3-ANALYSIS/PLUMED/plumed_driver.dat tested on v2.8 tested on master
…ANAL-236-CoV.2/3-ANALYSIS/PLUMED/plumed_driver.dat tested on v2.8 tested on master
…ANAL-236-CoV.3/3-ANALYSIS/PLUMED/plumed_driver.dat tested on v2.8 tested on master
…L-52-103-CoV.1/3-ANALYSIS/PLUMED/plumed_driver.dat tested on v2.8 tested on master
…L-52-103-CoV.2/3-ANALYSIS/PLUMED/plumed_driver.dat tested on v2.8 tested on master
…L-52-103-CoV.3/3-ANALYSIS/PLUMED/plumed_driver.dat tested on v2.8 tested on master
…2/SARS-CoV-2.1/3-ANALYSIS/PLUMED/plumed_driver.dat tested on v2.8 tested on master
…2/SARS-CoV-2.2/3-ANALYSIS/PLUMED/plumed_driver.dat tested on v2.8 tested on master
…2/SARS-CoV-2.3/3-ANALYSIS/PLUMED/plumed_driver.dat tested on v2.8 tested on master

Last tested: 19 Nov 2022, 10:53:24

Project description and instructions
This egg contains the GROMACS topology and input files as well as the PLUMED/python analysis scripts needed to reproduce the Molecular Dynamics simulations of 3 different spike-RBD/human-ACE2 complexes reported here. See README.md for more information and detailed instructions.

Submission history
[v1] 04 Sep 2021: original submission
[v2] 17 Sep 2021: updated DOI

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plumeDnest:21.037