AMBER Archive (2008)

Subject: Re: AMBER: suggestion for next amberTools 1.1

From: David A. Case (
Date: Tue Jun 17 2008 - 10:42:14 CDT

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.


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