Author: Myllykoski, Matti; Kursula, Petri
Title: Structural aspects of nucleotide ligand binding by a bacterial 2H phosphoesterase Document date: 2017_1_31
ID: 0a3okta0_48
Snippet: The complex of LigT with the bound product 2'-AMP was subjected to MD simulations with the program YASARA [50] , version 16.2.21. The structure was placed in a cubic box filled with water, the pH was kept at 7.4, and NaCl was added to keep the salt concentration at the physiological 0.9% (w/w). After initial energy minimization, an MD run of 260 ns was carried out at 298 K. The default YASARA settings were used, saving snapshots every 250 ps, and.....
Document: The complex of LigT with the bound product 2'-AMP was subjected to MD simulations with the program YASARA [50] , version 16.2.21. The structure was placed in a cubic box filled with water, the pH was kept at 7.4, and NaCl was added to keep the salt concentration at the physiological 0.9% (w/w). After initial energy minimization, an MD run of 260 ns was carried out at 298 K. The default YASARA settings were used, saving snapshots every 250 ps, and employing the AMBER14 force field. YASARA scripts were further used for simulation data analysis.
Search related documents:
Co phrase search for related documents- cubic box and force field: 1, 2, 3, 4, 5
- cubic box and MD simulation: 1, 2, 3
- cubic box and salt concentration: 1
- energy minimization and force field: 1, 2, 3, 4, 5, 6, 7, 8
- energy minimization and initial energy minimization: 1, 2, 3, 4
- energy minimization and LigT complex: 1
- energy minimization and MD simulation: 1, 2, 3
- energy minimization and salt concentration: 1
- force field and initial energy minimization: 1
- force field and MD simulation: 1, 2, 3, 4, 5, 6, 7, 8, 9
- force field and salt concentration: 1, 2, 3
- MD run and MD simulation: 1, 2, 3, 4, 5
Co phrase search for related documents, hyperlinks ordered by date