GROMACS version:
GROMACS modification: Yes/No
Hi, i have successfully completed my Membrane Protein ligand simulation but i have a thought that ligand will behave as a ligand (chemical nature) as it was very hard to me to figure it out how to run it because i have a ligand that interact with lipid membrane so i saved protein ligand complex and uploaded it on charmm gui and selected ligand as HET atom and made a member protein system and it is successful completed but did charmm gui added chemical forcefield to ligand and will it behave as a ligand can anyone please clarify my confusion.
Can anyone guild me on this
The way you asked the question isn’t very clear. What do you mean by “will a ligand behave as a ligand”? You also haven’t attached any files or snippets so it’s hard to guess what CHARMM-GUI did in your case.
i have first created a protein memb. system then i docked the lig in memb because i want to see the drug will bind to protein or memb and then i aligned docked structure with original pdb that i downloaded from the charm-gui and deleted memb and saved a protein-lig complex and again run the charmgui on this new pdb so that lig (binding to memb) remains in the memb and i selected lig as the het. atom of protein when preparing second file so after selecting lig as het atom will it behave as a true chemical nature or not.
I still don’t understand the “true chemical nature” bit. A model is a model, it will probably reproduce certain properties (like partition coefficients) well and others (like polarization effects) less so. Are you asking about the quality of the parameters, or some specific property you’re trying to predict? Should the ligand bind to the binding site in the protein (very unlikely) or just the membrane (quite likely but not too interesting)?
i want to know will lig behave like as a chemical compound or will it behave as a protein part. I don’t know much about gromacs but i when we run protein-lig simulation we make ligand parameter but i didn’t build it in this so will it affect the ligand traj. or simuation
It can behave like a chemical compound as a part (non-covalent) of the protein, there’s no opposition between these two. If you initially place it in a correct ligand-binding site in the protein, it will probably stay there; if you place it elsewhere, it might take a long time (even months in terms of computation) to find its preferred spot. The complexity can range from trivial to near-infinitely complicated, depending on your case.
And Gromacs will not let you run the simulation without some parameters for the ligand. The question is, where you got the parameters from, how reliable are they, and do you need to put extra effort into parameterization.
Right now you could use talking to someone with experience in simulations (worst-case, an AI chatbot) to refine your understanding of the problem so that you know what the question is that you want answered, or that you can convey your doubt in a way that will let us address it.