Hyeonsu Na

3 Questions 1 Answers 0 Followers

Questions related from Hyeonsu Na

What do I do when I don't see density in my gromacs energy selection?

I tried to proceed with NPT as usual in protein MD simulation in water and get the density for the whole system. However, I don't see any "density" items in my "gmx energy" selection. The same...

08 February 2024 6,826 0 View

How can I use the phosphorylation-processed PDB file on the gromacs?

I've finished processing phosphorylation on the protein model using the PyTMs plugin in PyMOL. I've tried various methods, but I get the fatal error below on pdb2gmx. Is there a...

21 December 2023 5,370 1 View

How to merge two artificially cut PDB files?

In order to reduce the influence between domains that can cause dimerization in MD simulations through biosensor structures, FL biosensors were isolated, structural prediction was performed with...

21 December 2023 4,575 2 View