search

Valdes-Tresanco-MS / gmx_MMPBSA

gmx_MMPBSA is a new tool based on AMBER's MMPBSA.py aiming to perform end-state free energy calculations with GROMACS files.
https://valdes-tresanco-ms.github.io/gmx_MMPBSA/
GNU General Public License v3.0
225 stars 65 forks source link

How to extract per frame energy values #116

Closed ataulislam80 closed 2 years ago

ataulislam80 commented 2 years ago

Describe the issue I am interested to extract protein ligand each frame mmgbsa evergy value. My aim is to prepare a table of 10k frames vs mmgbsa energy in excel. requesting you kindly guide me how to get those values and which file contain those values?

If you will report an error, please complete this form To Reproduce Steps to reproduce the behavior:

  1. Which system type are you running? (Protein-Protein, Protein-Ligand, etc)
  2. The command-line are you using.

Additional context The gmx_MMPBSA.log file

marioernestovaldes commented 2 years ago

check this video in the documentation (44 seconds to be more precise) about gmx_MMPBSA_ana functionalities... you can extract the data in CSV files that can be opened afterward in excel...

hope this helps!

Valdes-Tresanco-MS commented 2 years ago

If you are familiar with Python, you can also use the API to get this information