[gmx-developers] tdb files for nucleic acids

[David van der Spoel]

On Thu, 2002-12-05 at 16:37, 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).

The pdb2gmx code could indeed be improved considerably. As you say
hardcoding is not good, so if something is to be done to the code the
hardcoding should move out, and e.g. the modification of termini (or
other chemical groups) should be described in a database of some sort. I
have tried describing things in XML, but have not had time to implement
things really...
Anyway, putting more information about DNA in the code seems not to be a
good idea, because it will make cleanups later even more difficult.


-- 
Groeten, David.
________________________________________________________________________
Dr. David van der Spoel, 	Biomedical center, Dept. of Biochemistry
Husargatan 3, Box 576,  	75123 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
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