Jerkwin
commented
4 weeks ago Hi Vignesh,
The electrostatic contribution is inversely proportional to the dielectric constant (ϵ), as are ΔE(ele) and ΔE(PB). This dependence arises from how the electrostatic energy is calculated: Eele=q_i q_j/(4pi ϵ)
For very large ϵ, the electrostatic contribution to ΔG is quite small. If the proteins in both images are the same, ΔE(SA) values are close to each other, while ΔE(VDW) and ΔE(PB) vary in opposite directions, which may explain your point (3).
Jicun
Respected Sir, Greetings.
I, S.R. Vignesh, am a Research Scholar at the Indian Institute of Technology - Guwahati (IIT-G) working under the guidance of Dr. Priyadarshi Satpati, in computational studies focusing on protein-peptide interactions. I have performed MM-PBSA using your bash script and I have a couple of doubts, regarding that.
Here, I attached two images of MM-PBSA data from multiple trials with varying dielectric constant ϵ. (a) System set-up of Image1: Charge of Protein: Peptide:: +5: +1 Salt Conc: 0.0001 (b) System set-up of Image2: Charge of Protein: Peptide:: +5: -1 Salt Conc: 0.0001
My basic understandings and doubts: (1) Electrostatic contribution (Debye-Huckel term included) to ΔG reduces upon increasing the ϵ. (2) Also, polar solvation energy reduces upon increasing the ϵ. How and Why?
(3) The values of ΔG at higher ϵ, are almost similar to the two cases. How and Why?
I request you, it would be highly helpful if you could explain to me (2) and (3) and kindly share your knowledge.
Thank You for your time and have a nice day.
Best Regards, S.R. Vignesh
