[gmx-users] Discussion about DNA naming
mgoette at mpi-bpc.mpg.de
Thu Feb 24 13:04:58 CET 2005
Dear Gromacs users
I would like to start a discussion about the naming of residues and
atoms of DNA in GROMACS.
For there will be better implementation of DNA parameters in the future,
in fact the implementaion of DNA into OPLS and the implementation of the
AMBER FF (which includes DNA parameters), it makes sense (in my
opinion), to choose a unity naming of DNA as residues (bases) and of
their different atoms, too.
I don't know, if there is a unique naming of DNA in the PDB files, but I
don't think so. This and the different naming of DNA in AMBER or
elsewhere is quite annoying to work with and I think it may be a good
idea to make rules for that before everything is implemented finally
I would like to suggest, that base-naming is either DGUA (DXXX) and
DXX5, DXX3 for terminals, or DG (DX) and DX5, DX3 for terminals.
I would also suggest to name the ribose atoms by asterisk (*) not by
What do you think ?
Maik Goette, Dipl. Biol.
Max Planck Institute for Biophysical Chemistry
Theoretical & computational biophysics department
Am Fassberg 11
Tel. : ++49 551 201 2310
Fax : ++49 551 201 2302
Email : mgoette[at]mpi-bpc.mpg.de
WWW : http://www.mpibpc.gwdg.de/groups/grubmueller/
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