Remove all unnecessary solvent molecules.

Have you taken the protein conformation at the end time point (ns)???

I agree with Martin Klvana as the file size is large.

or else you might have all the conformations in that file.

I agree with Jobin Thomas.

I guess you have converted all the conformations into a single pdb. That's why your file size is too big. Traceback error in the autodock vina is because autodock vina recognizes only a single conformation for the receptor protein.

Select the desired snapshot from the .xtc file, convert that specific frame into pdb and proceed with the docking.

I hope this will help you!

Sometimes the error is because there are broken bonds in the protein. Open any visualizer and check if thats the case.

you need to clean your file preferably extracting the protein chain only. which should be within 1 MB.. You might be having solvent and membrane in your pdb.

If the problem still persists your peptide backbone could have an issue but that is unlikely as it's already accepted and simulated.. Which simulation software do you use?

how should I exactly select only one conformation? How will I know that this is best for my work?

Yash Gupta - Sir I used gromacs for silmulatios

Great! That means you will have a .xtc file which you can open in VMD (University of Illinois). Load trajectory and export last frame as PDB. You will have the final protein structure. In my experience last frame is not always a stable structure. If you analyze the trajectory you should see a steady decrease in RMSD/RMSF from the original structure. Please confirm nothing erratic started happening at the later time points.

I understand. Xtc file come after salvation and ions and then neutralosation. During all step proteins have change kindly analyse in protein viewer and kindly sort all point before docking. It's typical protein prepration step in backward direction.