[gmx-users] Discussion about DNA naming

[Maik Goette]

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 
into GROMACS.

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 
dash (').

What do you think ?

Regards

-- 
Maik Goette, Dipl. Biol.
Max Planck Institute for Biophysical Chemistry
Theoretical & computational biophysics department
Am Fassberg 11
37077 Goettingen
Germany
Tel.  : ++49 551 201 2310
Fax   : ++49 551 201 2302
Email : mgoette[at]mpi-bpc.mpg.de
         mgoette2[at]gwdg.de
WWW   : http://www.mpibpc.gwdg.de/groups/grubmueller/