have look to this tools:

http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0046902

The analysis can now be performed in gromacs itself..

g_mmpbsa was useful in my case. pls refer to this link:

http://rashmikumari.github.io/g_mmpbsa/Download-and-Installation.html

HTH

In addition, please have look to our new tool GMXPBSA:

http://www.sciencedirect.com/science/article/pii/S0010465514002240

we have also a mailing list: https://groups.google.com/d/forum/gmxpbsa and the tool can be downloaded here http://gdriv.es/gmxpbsa too

Best

is g_mmbbsa run in ubuntu??