Maninder Singh

3 Questions 12 Answers 0 Followers

Questions related from Maninder Singh

How to calculate Ligand-active site distance in a ligand-protein complex from MD simulation?

I have run a MD simulation of a ligand-protein complex in GROMACS using CHARMM forcefield. Reviewer has asked me to calculate Ligand-activesite distance and binding free energy of ligand with...

28 February 2021 5,015 1 View

How to remove mirror effect in membrane simulation?

Dear all, I performed 200ns MD simulations (gromacs 5.0.7) of peptide and lipid bilayer. Placed 6 copies of the peptide(12 aminoacids long) over the surface of the lipid bilayer(128 lipids, 64...

15 October 2018 8,352 1 View

How to calculate hydrogen bond occupancy in peptide-membrane simulation using gromacs hbond tool?

Dear all, I performed MD simulations (gromacs 5.0.7) of peptide and mixed lipid bilayer (POPS:POPC). Initially placed 6 copies of the peptide parallely over the surface of the lipid bilayer...

15 October 2018 7,270 4 View