The basic idea of molecular dynamics depends on the solution of Newton’s equations of motion for individual particles (atoms, ions, and molecules) [15]. MDS predicts the properties of assemblies of molecules in terms of their structure and the microscopic interactions between them [15, 16]. The downloaded solved structures for SARS-CoV-2 and HCV RdRps (PDB ID: 7BTF and 2XI3, respectively) are prepared using PyMOL software. Water molecules and ions are removed (except the Zn+2 and Mg+2), while any redundant chains are excluded. Additionally, any missed Hydrogen atoms are added using PyMOL. The High-performance computing unit (Bib Alex) of the Bibliotheca Alexandrina, Alexandria, Egypt, is used to perform the MDS study under the project entitled 'Structural demystifying of some Hepatitis C Virus proteins; An in silico study.' Nanoscale Molecular Dynamics (NAMD 2.13) software is used in the MDS. Its viewer software VMD is used to prepare the input files and analyze the trajectories [15, 17]. CHARMM 36 force field is used in NAMD, and the TIP3P water model is employed [15, 18]. The periodic boundary conditions are used in simulating the system while the temperature is raised from 0 K up to 310 K gradually in the equilibration phase. One hundred nanoseconds MDS production runs are performed for both SARS-CoV-2 and HCV RdRps at the NVT ensemble. After docking, 20 ns MDS runs are performed for the protein-sofosbuvir complexes. Cluster analysis is performed utilizing Chimera software's default parameters (UCSF) [19].

Note: The content above has been extracted from a research article, so it may not display correctly.



Q&A
Please log in to submit your questions online.
Your question will be posted on the Bio-101 website. We will send your questions to the authors of this protocol and Bio-protocol community members who are experienced with this method. you will be informed using the email address associated with your Bio-protocol account.



We use cookies on this site to enhance your user experience. By using our website, you are agreeing to allow the storage of cookies on your computer.