Thank you rmoretti. After removing the “#” and changing the names of all atoms according to the standard GDP.params. Now the program recognizes GDP. However, an error “segmentation fault” happens when I put it in the same chain of the receptor numbered after the C terminal. When I put it in a single chain different from the peptide and the receptor, another error “ERROR: unknown atom_name: GDP CA”. Any idea?
Now it works, after putting the GDP as a single chain following the peptide chain.