[gmx-users] Protein Ligand simulation

Alex Mathew alexmathewmd at gmail.com
Fri May 6 16:45:20 CEST 2016

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


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