[AMBER-Developers] change in source-code organization for NAB

From: David A. Case <case.biomaps.rutgers.edu>
Date: Wed, 14 Jan 2009 14:49:19 -0500

Scott and I have committed a significant change to the organization of
the NAB code, splitting it into two directories:

amber11/src/sff (sff=simple force field, although it's not all that
                 simple anymore!) contains energy-based routines that do
                 not depend on the NAB language, or on the NAB
                 MOLECULE_T data structure)

amber11/src/nab everything else.

The Makefiles have been updated, and these changes should be invisible
to current users. We run some tests, but something may have slipped
through...so please report any funny results. Note that you need to do
"cvs update -d ...." to get the new sff directory into your working

What's going on: The sff code creates libsff.a, which has a lot of
routines that can be linked into other codes, without the overhead of
all of NAB. This should soon include mort (gleap) and UCSF-DOCK. We're
hoping that ptraj might also use these routines to carry out energy
analysis. [Wei: I'll send you some thoughts about mort in a separate

Note: to run NAB you need libsff.a (and the Makefile makes sure this
happens). The reverse is not true: libsff is designed to be used in the
absence of the NAB language. Many (including me) have been using the term
"NAB" to mean both parts, and we will have to sharpen our language as we
go forward.

Note also: NAB (the language for molecular manipulation, esp. for nucleic
acids) is also undergoing a renovation. Building on collaborations with
Wilma Olson, we are adding new DNA analysis procedures, and should soon
have some new building routines (e.g. for three- and four-way junctions!),
and so on. Tom will recognize this as a blast from the past!


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Received on Fri Jan 16 2009 - 01:13:01 PST
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