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

David van der Spoel spoel at xray.bmc.uu.se
Wed Feb 22 14:25:27 CET 2006

David Mathog wrote:
> 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 table and found "atom_noms.tbl" but it was pretty out of date.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.
It does matter in case it is used for e.g. NMR refinement and they are 
different (e.g. not on ALA but everywhere else for the HB*).

> 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.
But in general these are renamed to O1 and O2, aren't they?

> 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?
I presume you only intend to do that in this file? How about giving 
every amino-acid residue also an H1 H2 and H3 in addition to H?
As long as it is for name translation only I don't see a problem with it.

> 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.
I don't think there is, but it is important that you list the changes 
you made (as you have done).

Do I understand correctly that you are implementing code that translates 
one naming scheme into another? That might actually be most useful in 
editconf in that case, although the logic could be use in trjconv as 
well. How about some heuristic code that derives from a complete pdb 
file what is the most likely source? How about pdb files that use 
multiple standards? Not meaning to discourage you...

David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se

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