Shakeel Jameeluddin Abbassi

3 Questions 1 Answers 0 Followers

Questions related from Shakeel Jameeluddin Abbassi

During analysis of in silico thermal denaturation of a dimeric protein should I calculate RMSD, RMSF, etc of individual monomers or the whole dimer?

Protein is a homodimer. Which approach would be more appropriate?

05 July 2016 587 1 View

How can I calculate binding free energy between protein and ligand during protein+ligand complex (GROMACS) md simulations?

I have done an MD run of a protein with ATP using CHARMM force field. I want to calculate binding free energy, which commands can I use for the above. Any suggestions. Thank you.

04 March 2015 3,259 6 View

In protein ligand simulation using gromacs, how to extract both protein and ligand together to visualize the complex in VMD?

I have simulated protein ligand complex but I am unable to extract both the protein and ligand together.

04 June 2014 7,633 2 View