Hi,
I have simulated protein-GTP complex using Gromacs-2020 and CHARMM36 FF for 250ns. I analyzed binding energy between protein and GTP using g_mmpbsa tool. As we know that GTP binds very strongly to proteins (binding energy should be in high negatives). However, I am getting positive binding energy between protein and GTP for unknown reasons. when I checked the summary file, as shown below, it seems polar solvation energy is the reason behind positive binding energy. Here I am also attaching input files I used for your perusal. Thanks.
SUMMARY
===============
van der Waal energy = -189.277 +/- 20.435 kJ/mol
Electrostatic energy = -184.267 +/- 93.292 kJ/mol
Polar solvation energy = 1234.921 +/- 63.714 kJ/mol
SASA energy = -19.393 +/- 0.848 kJ/mol
SAV energy = 0.000 +/- 0.000 kJ/mol
WCA energy = 0.000 +/- 0.000 kJ/mol
Binding energy = 841.983 +/- 55.707 kJ/mol
===============
END
===============
Venkat Reddy Chirasani check gmx_MMPBSA, a new tool aid to perform end-state free energy calculations with GROMACS files. Things you can do with gmx_MMPBSA:
-binding free energy with different solvation models (PB, GB, or MM/3D-RISM)
-stability
-alanine scanning
-entropy corrections
-binding free energy decomposition
gmx_MMPBSA has been written in Python3.8 and is entirely based on AMBER’s MMPBSA.py, a widely used tool for streamlining end-state free energy calculations. The program is freely available (test files and tutorials included) at https://github.com/Valdes-Tresanco-MS/gmx_MMPBSA
hth!
Increase Solute dielectric constant (pdie=4) in pbsa.mdp file and rerun.
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