Would you mind elaborating about the differences between atom types and atom names? I thought they were essential one in the same; looking at a generic mol2 file, it seems like every atom name has a unique atom type. What differentiates them? Thanks! Nikolay Rodionov| MBA Candidate & B.S. Bioengineering 2015 Martin J. Whitman School of Management & L.C. Smith College of Engineering at Syracuse University Syracuse, New York 13244 Phone: 281.301.9401| Email: Nirodion@syr.edu On 10/24/12 6:00 PM, "Elaine Meng" <meng@cgl.ucsf.edu> wrote:
Sorry, there is no option in Chimera to rename your atoms with Amber names. Looks like the PDB2PQR server might be able to do it:
<http://nbcr-222.ucsd.edu/pdb2pqr_1.8/>
I haven't tried it, though. If it works, you could read the resulting PQR into Chimera and then write Mol2. Elaine