[gmx-users] augustus 1, 2007: remediated pdb format

pim schravendijk pimlists at googlemail.com
Mon Jul 23 14:16:41 CEST 2007

Hi all,

I don't know if this is already known, but I just read that starting
august 1, 2007, the entries in the standard pdb archives will be in
pdb format 3.1.

check the news from july 19 for more details: http://www.wwpdb.org/news.html
Or: http://remediation.wwpdb.org/

The general overview of how to test if the software can handle the new
format correctly is mentioned here:


latest documents on version 3.1 are here:


Most changes are in the 'REMARKS' sections, but also the nomenclature
changed a bit:
For example:

"Deoxy- and ribose nucleotides now have separate chemical definitions with the
DNA forms relabeled as DA, DC, DG, DT, DI and DU. Modified nucleotides
formerly identified as using the "plus-nucleotide" syntax (e.g. +C,
+G) have been
relabeled with the particular 3-letter code corresponding to the full chemical
description of the modified nucleotide."

PDB files using the new markups of amino acids, nucleic bases, and
virus data are here:


It is probably a good idea to check if Gromacs can handle the changes
in the format.

Greetings, Pim

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