[gmx-developers] tdb files for nucleic acids

[Luke Czapla]

Hi,

  I'd like to make tdb files for the nucleic acids.  I want termini which
are by default missing the 5' end's 5' phosphate and the 3' end's 3'
phosphate (keeping the end oxygen and adding a hydrogen), with options to 
have termini which include the phosphate. 
According to the manual and looking through the source, this is all hard
coded into pdb2gmx, so I was wondering if I should add all the nucleic
acids- I already have code to convert A in a PDB file as a residue to DADE
or ADE depending on the presence of O2*, to the aminoacids.dat and define
new termini types or if there is a better way to make pdb2gmx work
seemlessly with files from the PDB database that include nucleic acids
(which are always separate chains, that may be useful).

-Luke