Hi Francesco, According to the AMBER mailing list, there is a program that comes with AMBER that changes hydrogen names from standard PDB to "AMBER PDB." See these links: http://amber.ch.ic.ac.uk/archive/200704/0377.html http://amber.scripps.edu/doc6/html/AMBER-sh-17.3.html I do not know if it changes the names of non-hydrogen atoms or works with version 3.0. You may want to ask the AMBER people about this, or if there are any newer versions of this programs or similar scripts. You may also want to take a look at Simulaid (free for academics): http://atlas.physbio.mssm.edu/~mezei/simulaid/ It performs many simulation-related tasks including conversions of residue and atom names between various conventions including PDB and AMBER. Again, I have not tried it myself. Best, Elaine