Amali Guruge

4 Questions 4 Answers 0 Followers

Questions related from Amali Guruge

How to calculating the pore size of water channels in a polymer-water interface structure?

Hi All, I am simulating a water-polymer interface using GROMACS. I want to calculate the size of (e.g., pore distribution) pores in water channels. Since my system contains both the interface and...

17 March 2024 9,527 0 View

How can I model a hexagonal phase using Packmol?

Dear All, I want to arrange my surfactant molecules in a hexagonal arrangement for my MD simulation. Appreciate, if anyone can guide me to do that. Thank you.

01 July 2018 6,354 2 View

Ligand interactions with DNA

Dear All, I have two receptor-ligand complexes. In one system, the ligand intercalates in DNA and from two hydrogen bonds (one with the enzyme and one with DNA duplex). In other system, the ligand...

22 March 2016 6,862 3 View

How do I identify pi-pi interactions using PyMOL?

Dear all, I want to identify pi-pi base stacking interactions between my ligand and DNA. How can I do this using PyMOL? Can anyone help me? Thank you in advance.

13 November 2015 8,452 6 View