Christian Kenneth

2 Questions 2 Answers 0 Followers

Questions related from Christian Kenneth

How to solve high RMSD problem for calculation of Protein-Ligand RMSD?

I ran a MD simulation for 30 ns using Amber99ff ILDN for protein forcefield and GAFF for ligand forcefield for GKRP and F1P (PDB: 4BB9) consecutively. However, the result shows that the RMSD...

18 November 2022 6,245 3 View

Should I directly using DFT-optimized structure for docking or should I rewrite some of its properties?

Based on PubChem calculation, the ligand structure only possess 1 rotational bond (TORSDOF). However, the ligand structure that came out from DFT optimization has been calculated differently by...

13 July 2022 8,960 3 View