I have performed MD simulations of a protein using Gromacs 5.0. Now I want to compute the solvation/hydration energy of protein.Is there a suitable way to calculate deltaG? I have followed free energy calculation tutorial of a small molecule by Dr. Justin Lemkul..But I am not sure if it is applicable to proteins as well.
Please help.
Thank you very much STN.
I was not sure actually about MM-PBSA because in all the papers I have studied, researchers have applied 3D-RISM theory using AMBER package to calculate solvation free energy. I am not sure if MM-PBSA would serve the purpose because in it, the free energy of solvation is the energy required to transfer a solute from vacuum into the solvent. In the MM-PBSA approach, it is calculated using an implicit solvent model. In my case, I am treating explicit water as four point model.
Hi,
It's possible to use Justin's method for proteins. As he himself described it here :
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/free_energy/08_advanced.html
Just keep in mind to set "couple-intramol' = no", If simulation crashes with "couple-intramol=no" then you have to do 2 calculations, first with "couple-intramol=yes" in water/solvent (DeltaG1) and second in protein in vacuum (DeltaG2) with "couple-intramol=yes" then subtract (DeltaG1 - DeltaG2) to obtain correct solvation energy.
Essentially, idea with "couple intramol= no" is that you don't want to decouple intramolecular bonds of protein. We are just interested in obtaining deltaG of protein and water interaction.
Sorry to bump an old thread but how is it possible to simulate DeltaG2 in vaccum.
I get the box collapsing if I use NPT and using a different ensemble for G2 (i.e NVT) feels inconsistent?
Any help would be much appreciated
- Badges
- Science topic
- Similar topics
- Biological Science
- Molecular Biology
- Biomolecules
- Proteins