[gmx-users] Gromacs tools mistakenly change the name of atoms in coordinate files

[David van der Spoel]

Robert Johnson wrote:
> These are all fine points. However, the question I'm asking is why do
> Gromacs tools change atoms named OXT in PDB files to O2? Of course
> there are always workarounds i.e. just simply change the atom name in
> the coordinate file. However, I was wondering if anyone knew why this
> happened. I suppose I will submit a bugzilla.
> 
you are welcome to submit a bugzilla, but for pdb2gmx this is the 
expected behavior. if you would like to change that you would have to 
edit database files. in principle naming should adhere to IUPAC/IUPAB 
standards (Biochemistry 9, 3471-3479  [1970]), but in practice there are 
at least four different naming schemes around only for hydrogens and 
other atoms (see http://www.bmrb.wisc.edu/ref_info/atom_nom.tbl).
It seems that the GROMACS scheme (which is derived from GROMOS force 
field) is correct for the terminal oxygens.
Almost all programs are wrong as regards hydrogen naming.
-- 
David.
________________________________________________________________________
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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