You can have a look at the following link:

http://rashmikumari.github.io/g_mmpbsa/

Software uses trajectory created from gromacs.

This reference may also help:

http://pubs.acs.org/doi/abs/10.1021/ci500020m

Dear Hiqmet, 

Thank you..

The MM/PBSA and MM/GBSA methods to estimate ligand-binding affinities

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4487606/

http://www.sciencedirect.com/science/article/pii/S0010465514003154

Dear Anu, 

Thank you.

I would recommend you to first try with files (.mdp) in tutorial. This will minimize errors

Dear Kumar, can you attach the .mdp file or link the tutorial so that I can access...

Dear Shadrack

Find it here http://rashmikumari.github.io/g_mmpbsa/Tutorial.html

All the best