AMBER Archive (2008)

Subject: Re: libpdb, ptraj, and nab Was: Re: AMBER: suggestion for next amberTools 1.1

From: David A. Case (
Date: Wed Jun 18 2008 - 19:32:36 CDT

On Wed, Jun 18, 2008, M. L. Dodson wrote:
> This seems like a really good idea. A related question: ptraj uses
> libpdb which seems to trace back to the midas people (or, possibly,
> other people even before that). Would not a better refactoring be to
> fix libpdb to adhere to the wwPDB standard, then fix nab to use libnab
> instead of its built in routines? Then everybody will be capable of
> reading/writing the same formats. I'm not familiar with the code at
> that level, so I may be all wet on this.

It is true that ptraj and NAB have somewhat duplicative code for reading &
writing pdb files, but it's not easy for me to grok the data structures in
libpdb, nor to figure out how they could be integrated into NAB.

On the other hand, I've put the new wwPDB (aka pdb version 3) support into
NAB, since I understand that code. It will be part of the 1.1 release of
AmberTools, due out "soon".

At some point, we should revise all of the Amber libraries to match the new
wwPDB standard. We mostly do already, but there are a few diffs, such as
deoxyribose having H2'1 and H2'2 atoms, where wwPDB has H2' and H2''. We can
handle that using the addPdbAtomMap facility in LEaP (for reading) and the
new putpdb() routines in NAB and ambpdb (for writing), but it would be better
if Amber's internal names matched the new standards. But I'm still trying to
figure out how much this will hurt backwards compatibility (the basic protein
and nucleic acid libraries haven't been changed in 14 years), and hence, when
to really do it.


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