SIRAH-CoV2 initiative: S1 Receptor Binding Domain in complex with human antibody CR3022 (PDBid: 6W41) (Q6704830)

This dataset contains the trajectory of a 12 microseconds-long coarse-grained molecular dynamics simulation of SARS-CoV-2 receptor binding domain in complex with a human antibody CR3022 (PDB id: 6W41).Simulations have been performed using the SIRAH force field running with the Amber18 package at the Uruguayan National Center for Supercomputing (ClusterUY) under the conditions reported inMachado et al. JCTC 2019, adding 150 mM NaCl according toMachado Pantano JCTC 2020. Glycans have been removed from the structures. The file6W41_SIRAHcg_rawdata.tar contains all the raw information required to visualize (on VMD), analyze,backmap, and eventually continue the simulations using Amber18 or higher. Step-By-Step tutorials for running, visualizing, and analyzingCG trajectories usingSirahToolscan be found at www.sirahff.com. Additionally, thefile6W41_SIRAHcg_12us_prot.tarcontains only the protein coordinates, while6W41_SIRAHcg_12us_prot_skip10ns.tar contains one frame every 10ns. To take a quick look at the trajectory: 1- Untarthe file6W41_SIRAHcg_12us_prot_skip10ns.tar 2- Open the trajectory on VMD using the command line: vmd 6w41_SIRAHcg_prot.prmtop 6w41_SIRAHcg_prot.ncrst 6w41_SIRAHcg_prot_12us_skip10ns.nc -e sirah_vmdtk.tcl Note that you can use normal VMD drawing methods as vdw, licorice, etc.,and coloring byrestype, element, name, etc. This dataset is part of the SIRAH-CoV2initiative. For further details, please contact Martn Soora (msonora@pasteur.edu.uy) or Sergio Pantano (spantano@pasteur.edu.uy).