[gmx-users] Discussion about DNA naming

Maik Goette mgoette at mpi-bpc.mpg.de
Fri Feb 25 10:45:07 CET 2005


Dear Andrey

I see. I didn't thought about that problem, because I never used 
RNA...but nevertheless it has to be solved.
It could be possibly a good idea to rename all hydroxyl-Oxygens in the 
ribose by Ox' or so (how about Ox!). I don't have anything against the 
dash, but against mixing it up in different forcefields.
Here the "standard" of the PDB:

Nucleic Acids

Atom names employed for polynucleotides generally follow the precedent 
set for mononucleotides. The following points should be noted.

* The asterisk (*) is used in place of the prime character (') for 
naming atoms of the sugar group. The prime was avoided historically 
because of non-uniformity of its external representation.

* The ring oxygen of the ribose is denoted O4 rather than O1.

* The extra oxygen atom at the free 5' and 3' termini are designated O5T 
and O3T, respectively.

RESIDUE                                  ABBREVIATION
-----------------------------------------------------------------------
Adenosine                                  A
Modified adenosine                        +A
Cytidine                                   C
Modified cytidine                         +C
Guanosine                                  G
Modified guanosine                        +G
Inosine                                    I
Modified inosine                          +I
Thymidine                                  T
Modified thymidine                        +T
Uridine                                    U
Modified uridine                          +U
Unknown                                  UNK


Probably, the guys from the PDB didn't thought of that 
"hydrogen-problem". So is there anyone in the mailinglist, who has 
"contacts" to the PDB people? We should solve this problem together with 
them, to avoid problems later on.

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/


Andrey V. Golovin wrote:
> 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 -------
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