From: Javier Goicochea (
Date: Tue Jan 27 2009 - 03:05:09 CST

Hello All,

I have noticed that most PDB files provide different name to atoms in the
same structure or molecule. These names are set to identify (up to some
extend) their relation with other atoms and connectivity. My questions are:

Is VMD tie in anyway to a particular naming convention?

Which naming convention is used typically in the PDB files?

Where do I find this naming convention (book, publication), if any?

Let mention that I am neither a Chemist nor a Biologist, just a Mechanical
Engineer with little experience in VMD.

Thank you in advance, Javier