Dear Friend,

MM-PBSA.py is a module of amber tools. Fortunately amber tools is a free software!

http://ambermd.org/#AmberTools

Best,

Dear Friend,

MM-PBSA.py is a module of amber tools. Fortunately amber tools is a free software!

http://ambermd.org/#AmberTools

Best,

Thank you. But can you suggest me how to prepare input and issue commands as I have maestro output file.

1-extract snapshots from your trajectory as separated PDB files

2- convert each PDB to amber Format (using Leap module)

3-calculate binding free energy using MMPBSA.py module for each snapshot.

http://ambermd.org/tutorials/advanced/tutorial9/

Best,

Thank you

You can try the well known APBS or PDB2PQR

http://www.poissonboltzmann.org/

@melchor can you describe the steps or give me link to calculate MM-PBSA energy using APBS/PDB2PQR

http://ambermd.org/AmberTools.php

You can also use g_mmpbsa if you use GROMACS

https://rashmikumari.github.io/g_mmpbsa/