> > Is pdb2gmx recognising the N-terminal residue as PRO? > I think so. However in my case pdb2gmx does not read the entry PRO-NH in the ffG43a1-n.tdb file. Only NH3+,NH2, or None are read. I cheat pdb2gmx by replacing the header [ PRO-NH ] by [ NH2 ] and it works for me now. Phuong