[gmx-users] Updated atom name nomenclature table, pre-release available

David Mathog mathog at caltech.edu
Tue Feb 21 20:46:22 CET 2006

I've been working on automatic translation into and out of Gromacs.
The into part has worked out pretty well with just a small amount
of logic, but the export part, currently being wired into trjconv,
has proven to be a lot more challenging due to the variations in
atom naming.  I looked all over gromacs for a simple conversion
table and found "atom_noms.tbl" but it was pretty out of date. 
So a search of the web was conducted, a more recent version of
this file located, and that has been modified somewhat to
include Amber, Gromacs and nucleotide names. 

This is a prerelease version - DO NOT USE IT FOR ANYTHING YOU CARE
ABOUT! If you are interested in using the final release version
of this file please take a few minutes to review my changes (see
the Notes) and let me know where the mistakes are.  

Items that need to be checked in particular are:

1. It wasn't at all clear to me how to assign HB1 vs HB2,
HD1 vs HD2 and so forth for Amber.  Or if it even mattered if those
were reversed.

2. From spelunking the gromacs code it seems that Gromacs uses "O"
for both "O" and "OXT" at the C terminus.  So the two "O" entries
in that section of this file are NOT a typo.  Conversely, this
part of Gromacs really, really, really should be changed since having
two different atoms with the exact same name is bad form.

3. The entries for start/end of both protein and nucleic acids
are currently broken out into separate entries that bear no names.
That's easy enough to read but messy to parse.  I'm strongly
leaning towards merging these into the residue records.  That
is, for instance, all amino acids would have OXT in addition to O,
even though obviously all residues in a chain would not have all of
these atoms.  That way a simple translation scheme need only look
up ResName/AtomName in one column to determine the
corresponding AtomName in another column.  Comments pro and con?

4. There was no copyright on any versions of the file I started with
so I assumed it was ok to build onto it.  If anybody knows differently
please let me know ASAP.

The prerelease file is here:



David Mathog
mathog at caltech.edu
Manager, Sequence Analysis Facility, Biology Division, Caltech

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