Hello to all. I'm new to simulations. I am using Amber20. Basically I used the Flare software for a two nanosecond simulation. The results of the dynamics I then exported them as a pdb file taking a single frame. To this pdb file I also manually added the membrane and I removed the water (always manually) since I will then solvaterò with Amber. Then I make a separate file with just the ligand to put it on Antechamber and thus generate my topologies that I will use for tleap where I join together the file containing protein and membrane.pdb and the ligand.mol2 generator with antechamber. It is the right way to proceed. Because I have made many attempts and have had different errors each time. Among the most common "atom is not a type" or "duplicate atom etc". Do you think I'm wrong at the beginning when I manually generate the pdb file? Are we sure that the pdb file that I take from the dynamic performed with Flare takes me only one frame and that ligand can be read correctly on tleap and antechamber?

Other times it manages to generate pdb and prmtop but fails when it has to generate the .inpcrd file