The SIRAH-CoV2 Initiative

A free database for coarse-grained simulations of SARS-CoV2 proteins

The Group of Biomolecular Simulations at Institut Pasteur de Montevideo offers to the biocomputing community simulations performed at the Uruguayan National Supercomputing Center (Cluster-UY) using the SIRAH force field running on Amber18. We aim to provide CG trajectories for all SARS-CoV2 reported in the PDB. The list of simulated proteins will be updated as soon as they are completed, but feel free to contact us if you are interested in a particular system.

The following systems in their APO form are currently available: 6LU7, 6YVO, 6W01, 6M3M, 6W4B, 6W02, 6W9C, 6W4H, 6W41, 6YHU, 6W37, 6WIQ, 6W17, 7BTF.

Tar files related to each simulation contain all the information required to visualize (on VMD), analyze, and eventually, continue the simulations. The force field package, referred as SIRAH 2.2 available at http://www.sirahff.com/.

CG simulations are conducted under the conditions reported in the article The SIRAH 2.0 Force Field: Altius, Fortius, Citius.(DOI: 10.1021/acs.jctc.9b00006), adding 150 mM of NaCl according to the SPLIT recipe (DOI: 10.1021/acs.jctc.9b00953).