[gmx-users] pdb atom nomenclature

Mark Abraham Mark.Abraham at anu.edu.au
Wed Jul 8 17:00:39 CEST 2009

Stefano Meliga wrote:
> Hello,
> I used editconf to produce a pdb out of a gro file and I noticed that 
> there are 3 atoms names that do not match with the pdb nomenclature:
> they are O1 and O2 for the last aminoacid of the chain and CD of ILE
> A pdb file has respectively O, OXT in the end of the chain and CD1 for ILE.
> I was wondering if you should consider it for next GROMACS release.

Force field atom nomenclature is highly non-standardized, and is 
specified by the force field in use. Thus, it won't match the PDB 
standard, in general.


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