AMBER Archive (2008)

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

From: M. L. Dodson (
Date: Wed Jun 18 2008 - 10:43:44 CDT

David A. Case wrote:
> On Tue, Jun 17, 2008, Alan wrote:
>> I see now that 'rdparm' comes with amberTools 1.0. So, why not having
>> 'ambpdb' too?
> Ambpdb requires an F95 fortran compiler, which is a natural requirement for
> Amber itself, but not required for any other parts of AmberTools. Adding
> ambpdb to AmberTools would add a lot to the configuration requirements. Plus,
> without Amber10, the only use I can see for ambpdb would be to work with
> restart files created by NAB. But NAB already has a putpdb() command, which
> mostly serves the same purpose.
> One possibility (volunteers welcome!) would be to update NAB's putpdb()
> function to include the new wwPDB (aka "version 3") formats, and a few other
> things that ambpdb has. Then, one could write a new "ambpdb" as a simple
> driver program in NAB [essentially doing getpdb() followed by putpdb().]
> We could then retire the original ambpdb; if you've looked at that code, you
> can see that this could be a real win.
> ....dac

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.

I just remember at some distant time in the past, I wanted to generate
a pdb file of some flavor and only one of ambpdb, ptraj, and nab would
do it. (No I don't remember the details and cannot rule out pilot

Bud Dodson

M. L. Dodson
Business Email: activesitedynamics-at-comcast-dot-net
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