1、全体系的alpha-C原子的均方根偏差(RMSD)结果获取及分析 输入如下命令:gmx rms -s cubic_em_hot_sample.tpr -f hot_sample.trr -o rmsd.xvg RMSD值可以反应出模拟过程中体系的稳定情况,将rmsd.xvg导入EXCEL表,绘折线图,由图可知动力学模拟逐渐达到平衡。 全体系的alpha-C原子的均方根涨落(RMSF)结果获取...
else RMSDbetween two protein molecules (ATOM entries) is calculated.hydrogen (bool): If True, hydrogen atoms will be included in theRMSD calculation.atoms (string) [all/c/no_h/ca]: "all" includes all atoms in the RMSD calculation,"c"...
RMSD of the C-alpha carbon atoms of MMP-2 (PDB code: 1HOV) for the equilibration trajectories.Ilenia GiangrecoGianluca LattanziOrazio NicolottiMarco CattoAntonio LaghezzaFrancesco LeonettiAngela StefanachiAngelo Carotti
Those conformational families with the lowest average free energies also contained the best C(alpha) RMSD structures (1.4 A for S15 and HP-36 core) and the lowest average C(alpha) RMSDs (1.8 A for S15, 2.1 A for HP-36 core). For comparison, control simulations starting with the two ...
2.1 and 1.8 angstrom Average C[sub alpha] RMSD Structure Predictions on Two Small Proteins...Presents several model predictions on the 36-mer villin headpiece domain (HP-36) and the 65-mer structured region of ribosomal protein (S15). Approach of the Rosetta protein folding algorithm; Simulation...