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

[David Mathog]

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