[gmx-users] First release, translation supporting PDB<->(AMBER, GROMACS)

[Maik Goette]

Hi David

Hmmm...may it be, that those guys at the pdb took one of my advices?
I would wonder, though...
Anyway...the oxygens are usually named O5*. That is a problem for 
determinig the terminus and a correct protonation.
I would really suggest to use the O5T naming for the DNA. It works in 
GROMACS and IMHO makes sense.

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/


David Mathog wrote:
> Ok, I fixed the bugs that came up in trjconv.  
> 
> As before the download link is:
> 
>   ftp://saf.bio.caltech.edu/pub/software/molbio/gromacs-cit-33.tar.gz
> 
> and this is actually a link to gromacs-cit-33-0.1.2.tar.gz, as this
> version is 0.1.2.
> 
> I do have a PDB terminology question though.  In the PDB
> documentation it indicates that O5T and O3T should be used
> for the terminal oxygens on the ends of nucleic acid strands:
> 
> http://deposit.rcsb.org/adit/docs/pdb_atom_format.html
> 
> This in analogy to the OXT on protein. However O5T and O3T seem
> never to be used in practice - O5* and O3* were found in those
> positions in every PDB file I looked at. 
> 
> Am I misreading this and O5T,O3T refer to some _other_ terminal
> oxygens on a nucleic acid strand???
> 
> Thanks,
> 
> David Mathog
> mathog at caltech.edu
> Manager, Sequence Analysis Facility, Biology Division, Caltech
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