[gmx-users] Protein Ligand simulation

[Alex Mathew]

Greetings to all !

i have completed Protein Ligand simulation as per the tutorial,my aim

 to proof that ligand A inhibit Ligand B -what are the  possible analysis i
can perform
i have done the following

RMSD - to see the stability of protein with ligands
RMSF-root mean square deviation of individual residues
hbond-hydrogen bonds between the ligand and protein
energy-VdW and Coulomiv energy
dssp-Secondary structure analysis
pairdist-mean distance betn the ligand and protein in all time
gyrate-radius of gyration whether any structural changed happen in MD

how to find other interactions such as hydrophobic pi-pi etc


Is is possible to do any competitive inhibition study using gromacs?

kindly share some useful articles


best
Alex!!