[gmx-developers] tdb files for nucleic acids

[K.A. Feenstra]

Luke Czapla wrote:
 > 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).

Only the DNA residue names are hard-coded, I think. Furthermore there
is a hard-coded list of AA-residues names that should be translated.
The thing to do here, I think, is to have a translation list for
residue names, like the xlate.dat for atom names.

Otherwise, the current implementation for termini, which Erik L. has
made optionally residue-specific, is probably sufficient to do what
you need.


-- 
Groetjes,

Anton
  ________ ___________________________________________________________
|        | Anton Feenstra                                            |
| .      | Dept. of Pharmacochemistry - Vrije Universiteit Amsterdam |
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