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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
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[Question]: how can I get ΔTOTAL and ΔG binding in the output file? #452

Closed niloufar1993 closed 8 months ago

niloufar1993 commented 8 months ago

Hello, my output file just has complex total energy without ligand and receptor and so, without any delta calculations. Would you please tell me what the problem is, and how can I get ΔTOTAL and ΔG binding? The command I entered: mpirun -np 30 gmx_MMPBSA -O -i mmpbsa.in -cs md_0_1.tpr -ct md_0_1_noPBC.xtc -ci index.ndx -cg 15 16 -cp topol.top -o FINAL_RESULTS_MMPBSA.dat -eo FINAL_RESULTS_MMPBSA.csv -do Final_decomp_mmpbsa.dat -deo Final_decomp_mmpbsa.csv --stability

marioernestovaldes commented 8 months ago

you are calculating stability which is only the energy terms for the complex. If you want to calculate binding free energies, follow these tutorials

https://valdes-tresanco-ms.github.io/gmx_MMPBSA/dev/examples/#analysis

niloufar1993 commented 8 months ago

you are calculating stability which is only the energy terms for the complex. If you want to calculate binding free energies, follow these tutorials

https://valdes-tresanco-ms.github.io/gmx_MMPBSA/dev/examples/#analysis

Thank you so much. So, if I omit --stability from the command line, I will get the binding free energy.