Please, I’m not experienced in this field and I need help. I want to check the ligand-interaction of 2 molecules, but I’m not able to merge the 2 PDB files correctly, because it’s like the ligand is not in contact with the protein at the right site as it was shown in the literature. There is another problem, I can only find the molecule (that is supposed to be a ligand) as a protein on PDB, there is any way to convert it to a ligand PDB file?
I think there are many things in your post that require clarification if you are expecting meaningful answers, but I will give it a try.
First, PyMol is a visualization program, so it is not really meant for manipulating PDB files in a way you describe.
If you have coordinates of two independent molecules – a receptor (presumably a protein) and a ligand – there is no simple way to put them together. Your choices are: 1) dock the ligand, which is not trivial and most definitely can’t be done in PyMol (unless there is some kind of a recent plugin for that purpose); 2) find a complex of a similar protein and a similar ligand and try superimposing your structures onto that complex. Option #2 is mostly a quick fix for visualization purposes, as you would still have to dock the ligand properly or at least minimize the complex.