Shuo-Lin Weng

3 Questions 4 Answers 0 Followers

Questions related from Shuo-Lin Weng

How to modify the Amber code to save the trajectory of solute only?

Dear Amber user, I want to study the interactions between protein and ions. I am running a simulation with protein, ions and water and I want to save the trajectories of protein and ions. I know...

27 March 2023 5,779 2 View

How to make Zn move along with Zn-binding domain?

Dear all Gromacs user, I am using Gromacs to run NVT and NVT equilibrium. Before the equilibrium, my input gro file shows all atoms (proteins, Zn, Na and Cl ions, and waters) stayed in the box...

18 February 2023 4,724 1 View

How to add a zinc ion to a protein pdb file?

Dear all, I am running MD simulation of a protein containing a zinc finger (ZnF) domain. I got its all-atom pdb file and I know there are 4 sulfur atoms in 4 cycteins of ZnF domain interacting...

11 January 2023 8,669 4 View