How can I measure the formation of water mediated hydrogen bonds formed between a ligand and a protein complex during simulation. I'm using gromacs 4.5v. Is there any specific way by which we can calculate the number of hydrogen bonds?
Water mediated hydrogen bonds are very difficult to monitor in a molecular dynamics simulation. 1) They are much less stable (around 4 kcal.mol⁻¹) than protein-protein hydrogen-bonds (~8 kcal.mol⁻¹), and 2) as they are more labile, they break more easily and are rapidly replaced by another water molecule. You have to select a particular residue and all water molecules to find out how many HB are established, but you will not find which specific water molecules (and how many) are involved). If your water molecules are relatively stable and 'trapped' between ligand and protein, maybe you can check them. If not, is more accurate to chech ligand-protein interactions (with LigPlot software) that focus only in water molecules...
For further informations on g_hbond, check: "Van der Spoel, D., Van Maaren, P. J., Larsson, P., & Tîmneanu, N. (2006). Thermodynamics of hydrogen bonding in hydrophilic and hydrophobic media. J Phys Chem B, 110(9), 4393–8. doi:10.1021/jp0572535"
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