6 Questions 9 Answers 0 Followers
Questions related from Aby Jimson
I have done a 50 nano second protein simulation using Gromacs and obtained an RMSD value greater than 3 nm. is it ok to proceed with it or is the value incorrect?
27 November 2022 4,826 2 View
I have ran a simulation of a protein structure using Gromos force field and obtained the radius of gyration. Is it mandatory to get a linear plot? How does high or low RoG matters? What it implies...
27 November 2022 7,981 2 View
What is the use of energy range in the config file in autodock vina? What is the normal values?
16 January 2022 7,298 1 View
Hi. I am working with ligands containing Se and Te. It is possible to dock them using AutoDock 4.2 since i have added thwir parameters. But can i do the same with vina? Can we add additional atom...
31 December 2021 8,054 2 View
Hi. Is it mandatory to optimise our ligand before docking using Autodock or Autodock vina? I have not received the structure from any database therefore the structure was drawn using Marvin draw...
30 December 2021 5,570 3 View
Importance of RMSD in GROMACS
01 January 1970 4,859 0 View
