s_mmpbsa: Supernova's tool of binding free energy calculation for Gromacs trajectory, using molecular mechanics Poisson-Boltzmann surface area (MM/PB-SA) method.

The s_mmpbsa program can be freely used for both academic and commerical purposes.

MM/PB-SA method is the most popular method to rapidly calculate binding free energy, especially for biological systems. However, as a widely-used MD program, Gromacs has not officially support MM/PB-SA calculation. Although there have been numerous programs that can calculate binding free energy with GROMACS trajectory, most of them have some limitations at different aspects, for example: (1) Difficult to use and install (2) Lack of support for new version of Gromacs (3) Too slow (4) Not cross-platform. Instead, s_mmpbsa provides a convinent interface (like Multiwfn) to calculate binding free energy for GROMACS trajectory.

• Open source and freely available.
• No need for preparing running environment (e.g., for Python), only needs Gromacs program when running on linux system. (In contrast to other programs such as gmx_MMPBSA.py, s_mmpbsa is developed with Rust).
• Interactive operation, no need to write parameter files. Also, user can write shell script to invoke s_mmpbsa for batch use.
• Very fast. Due to the efficency of rust program.
• Considers electric screening effect, as "CHIN. PHYS. LETT. 2021, 38(1), 018701" describes.

For Ubuntu system, maybe user should run the following commands to avoid cc error.

sudo apt update
sudo apt install build-essential

Currently s_mmpbsa has supported to fix PBC conditions and write trajectory to MMPBSA_[name].xtc. However, it is still better to re-check if the trajectory PBC has been totally fixed by xtc visualization software, such as VMD.

# Firstly, add s_mmpbsa folder to $PATH.
# Start s_mmpbsa, and input as follow (support # comments, but not recommended to input comments)
md.tpr
1 # load xtc file
md_pbc.xtc # if not PBC-fixed, click "return" and use default md.xtc
2 # load ndx file
[return] # default index.ndx
0 # go to next step (Trajectory Parameters)
1 # select receptor group
[protein group number]
2 # select ligand group
[ligand group number]
5 # set time interval, usually analysis per 1 ns
1
0 # go to next step (MM/PB-SA Parameters)
# Usually no need to change. The PB and SA parameters could be modified by 8 and 9
0 # go to next step (start calculation)
[return] # use default system name or input your name
# Wait for calculation finish
1 # view summary
[return] # output energy summary with default file name or input your name
2 # output energy by time
[return]
3 # output energy by residue
1 # write residues within 3 A (also try other options)
[return]
4 # output other infomations
-1 # view pdb file with residue-wised INVERSED binding energy filled in B-factor column
0 # exit s_mmpbsa program

Release file: https://github.com/supernova4869/s_mmpbsa/releases, where "s_mmpbsa.exe" and "s_mmpbsa" are s_mmpbsa executable files on Windows and Linux operation systems, respectively.

The s_mmpbsa program should be properly cited if the work will be published.

Currently, s_mmpbsa is still in-develop. If you want to utilize s_mmpbsa in your work, please cite the program as following:

Jiaxing Zhang, s_mmpbsa, Version [current version], https://github.com/supernova4869/s_mmpbsa (accessed on yy-mm-dd)

After the detailed paper about s_mmpbsa is published (if fortunately), please cite the corresponding paper instead of the web page here.

Dr. Jiaxing Zhang (Contact: [email protected], Tianjin University)

If you encountered any difficulty while using s_mmpbsa, or you found any bugs, or you have any suggestion on improving s_mmpbsa, please E-mail me or join my QQ group 864191465 to describe.

• Add support of other PBSA solvers, e.g., AFMPB, Delphi2, and also built-in LPBE solver
• Add figures: plotting data, 2D interaction plots like Ligplot+, 3D plots scripts with PyMOL
• Multi-threading
• Alanine scanning