DFT Geometry Optimizations of Phosphorylated Amino Acid Analogs (Ethylphosphate (ep)) with Different Counterions in Water

Phosphorylated amino acid analogs cut off at the C alpha, solved in CHARMM TIP3p and either methylammonium, sodium, or guanidinium, were simulated in CHARMM using the CHARMM36m force field. The phosphate groups bear the charges 0, -1, and -2. From these simulations, 50 conformations were picked using clustering. From each of the 50 conformations, smaller water boxes were sliced which were then used in the geometry optimizaions. The water was restrained during the optimization to preserve force field compatibility. Optmizations were run in cp2k using TZV2P-MOLOPT-PBE-GTH, PBE, and DFTD3.本数据集针对在Cα位截断的磷酸化氨基酸类似物开展模拟研究：将此类化合物溶剂化于采用CHARMM力场的TIP3P水模型，且分别添加甲胺、钠离子或胍离子作为共存阳离子的体系中，随后使用CHARMM36m力场在CHARMM程序中完成分子动力学模拟。模拟体系内的磷酸基团分别带有0、-1和-2三种电荷态。通过聚类分析从上述模拟轨迹中选取50个代表性构象。从这50个构象中分别切取出小型水盒体系，将其用于后续几何优化。优化过程中对水分子施加约束，以保证与所用力场的兼容性。几何优化在CP2K程序中完成，采用的计算参数包括TZV2P-MOLOPT-PBE-GTH基组/赝势组合、PBE泛函以及DFTD3色散校正方法。