You may use "lie" command in cpptraj to calculate VdW and Elec energies.

I have no clue how to calculate hydrophobic interaction, since all the papers just present the hydrophobic surface without quantitative analysis.

I don't know the direct method to calculate salt bridge. But you may use "mask" command to find the atom around your salt and use BASH or PYTHON to deal with the output file and get the number of salt bridges for each frame.

Thanks. Can you please share a sample input file?

Edit: I tried using Lie command in cpptraj. I have a question on the credibility of the result. In successive frames, I observe huge difference in EELEC and EVDW values. How is that possible? Am I missing out on something?

You can observe electrostatic interactions using application APBS:

http://sourceforge.net/projects/apbs/

Also check out application VMD, It is widely used for visualization and analysis of trajectories, supports many external plugins and can be scripted:

http://www.ks.uiuc.edu/Research/vmd/

http://ambermd.org/tutorials/advanced/tutorial24/

I am already doing MMGBSA and LIE analysis. What extra information can I expect from FEW?

Apart from salt bridges, hydrophobic interactions and formation of direct H-bond between protein and inhibitor, there could be possibility of formation of solvent mediated H-bonds.

If you can export in PDB format, you can use the Protein-Ligand Interaction Profiler (PLIP), which detects hydrophobic contacts, (solvent mediated) hydrogen bonds, salt bridges, halogen bonds, pi-stacking, and pi-cation interactions. The PLIP output files are in XML format and thus parseable. In your case, you could generate a list for all snapshots and compare the interactions on atom level. There's also the option to do visual comparison with PyMOL session output files.

https://github.com/ssalentin/plip

I know this a little late to answer, but for anyone else coming here looking for answers. VMD has an awesome tool to analyze salt bridges. Go to "Extensions -> Analysis -> Salt Bridges"

It dumps out all the salt bridges as individual files to a directory, making it easy to parse and analyze in R or Python.