[Chimera-users] Chimera vs Amber, which one digresses from the average pdb rules?

[Elaine Meng]

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