PMC:7643666 / 8450-9434 JSONTXT

{"target":"https://pubannotation.org/docs/sourcedb/PMC/sourceid/7643666","sourcedb":"PMC","sourceid":"7643666","source_url":"https://www.ncbi.nlm.nih.gov/pmc/7643666","text":"2.3 Molecular dynamics\nThe structures resulting from molecular docking simulation were subjected to 1 ns molecular dynamic (MD) simulations using GROMACS [29, 30], (Gromos96 53a6 force field) [31]. The structure was immersed in explicit water using the SPC model [32]. The protein was solvated; the system was neutralized by adding Na+ ions, energy minimized, and equilibrated using NVT and NPT runs. The temperature and pressure were kept constant at 300 K and 1.01325 bar using the Berendsen weak coupling-method [33]. The results were used for an MD simulation using Particle Mesh Ewald for long-range electrostatics under NPT conditions. Coordinates were saved every 100 ps. Trajectory files containing the structural coordinates of receptor-ligand complex sampled every 100 ps were fitted in the box and converted in PDB coordinates using the trjconv tool of GROMACS Package. The structures were visualized with Maestro by Schrödinger [34] (see Supplementary Figures S1 and S7).","divisions":[{"label":"label","span":{"begin":0,"end":3}},{"label":"title","span":{"begin":5,"end":23}}],"tracks":[]}