MD simulation for Protein-Ligand problems in dump

User discussions
1

GROMACS version: 2020.1
GROMACS modification: No

Hello,
I’m running a protein-ligand simulation.
There’s no error when i did NVT/NPT equilibration, and when i’m running a 20ns MD simulations its also complete. But when i did the dump command and analyze the protein-ligand interactions, the ligand didn’t went to the active site of the protein. There’s no problem when docking the ligand, but when the MD simulation the ligand didn’t match.
Any solution or reference with this problem ?

Thank you in advance!

Screenshot (6)
Screenshot (6)1366×768 116 KB

2

Did you create MD simulation movie? How about energy minimization?

3

Hi
I see that you are running the protein-complex tutorial and I have some doubts about this tutorial.
My problem occurss when I run the comand gmx make_ndx -f jz4.gro -o index_jz4.ndx.

So, please, could you send (viea email or whatever) the files that are make in that step so I can figure out where is the error in that??

Thanks in advance