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
[EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se
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