Hello,

When did you make the protein-ligand complex system, did you place ligand in an appropriate place (docking position)? If not you can do it first.

Or, Run100 ns is not enough if your system was large.

Best Wishes

Dear Iqbal Sir,

My protein was not too big, had only 119 sequence.. I did IFD and QPLD docking..Both docking are pretty accurate I guess

I don't know how did you set up your simulation input file and which simulation software you used?