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

Maik Goette mgoette at mpi-bpc.mpg.de
Mon Mar 27 10:39:50 CEST 2006

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.


Maik Goette, Dipl. Biol.
Max Planck Institute for Biophysical Chemistry
Theoretical & computational biophysics department
Am Fassberg 11
37077 Goettingen
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/

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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