[gmx-users] Discussion about DNA naming

[Andrey V. Golovin]

Dear Maik
Actually it's good point, but we tried to do all this in gromacs style, in
order to keep dna/rna names the same in all gromacs forcefields.
About * and ` it's becouse hdb problem, look
in RNA:
C2* and we can add  H2*1 and H2*2 , but exists
O2* and .... we can not add H2*1 becouse it's used, so we change name to O2`
and now we can add H2`1
The solution of this problem is playing around with pbd2gmx code or like we did.
Would be nice to hear some new ideas =)
Goodluck, Andrey

> 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 (').

----
Best regards, Andrey
----------------------------------------------------------------
Andrey V. Golovin
Ph.D,Professor assistant    tel: +7 (095) 939-5305  
Bioengineering and
Bioinformatics Department              
Moscow State University     fax: +7 (095) 939-3181
119899 Moscow            E-mail: golovin at genebee.msu.su
Russia                      web: http://rnp-group.genebee.msu.su
-----------------------------------------------------------------


---------- Original Message -----------
From: Maik Goette <mgoette at mpi-bpc.mpg.de>
To: GMX-mailinglist <gmx-users at gromacs.org>
Sent: Thu, 24 Feb 2005 13:04:58 +0100
Subject: [gmx-users] Discussion about DNA naming

> 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/
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------- End of Original Message -------