Hello,
I'm running an protein-ligand complex with molecular dynamics simulation on GROMACS. First i'm doing the molecular docking with the protein and ligand, there is no issue regarding the docking. The ligand match with the active site of the protein (enzyme). But when i'm running the molecular dynamics simulations, the ligand didn't match with the protein active site. I wonder if someone facing the same problem with me.
Here i post a picture regarding the condition of the protein-ligand interaction after the MD simulations.
Thank you in advance!
When you removed the PBC, did you choose the ligand for centering? If yes, then change it to protein fir centering and system for output.
I guess you are using Chimera for visualization of your trajectory, but VMD is much more efficient in visualization and shows the solvent molecules in a better way than Chimera. Just watch your trajectory in VMD and see if the ligand suddenly jump out of the active site. If that's the case, then the problem is caused by centering during PBC removing. If the ligand deviates slowly away from the active site, then it's interaction with the receptor was not efficient.
Thank you for your answer Jameel M. Abduljalil , i've already choose the protein to centering and system for output but it still no change. I have no idea why this thing happen, because i've tried using another ligand and same thing happen. Just one ligan out of 4 that succes binding to the protein. Does this case have correlation to the ligand topology by any chance? thank you
What about the quality of your receptor protein model? I had this problem when I was working on a bad quality model.
I did a pH variation to the protein model, so it has more H. But again, it works with specific ligand but not working with another ligand. I think the protein isn't the problem. When i prepare the ligand topology, there is warning about missing line in .itp files. I get rid of that warning but the result of the md is bad. Jameel M. Abduljalil
I faced a problem like that recently, the ligand was showing good scores during docking, and then got out of its place during the MDS. firstly, I thought it was the efficiency of binding, but, it ended up being a problem with the ligand topology, having high penalty scores, so I changed the ligand, as it is a tough process to parameterize a small molecule from scratch.
I attached a file of the ligand.prm maybe you can see the same with your ligand. Ariztha Delivia Putri
Thank you for your answer Ahmed Samir Mohamed , i just look through the .prm file but it's on different format with mine (i attach it below). May i know which charmm version you used to prepare your ligand? And are you prepared the ligand topology using the tutorial based on this website http://www.mdtutorials.com/gmx/complex/index.html or not? Thank you in advance for your help!