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

From: Wei Zhang <>
Date: Wed, 14 Jan 2009 14:01:43 -0600

Hi Dave,

     it seems the file "mm_options.l" is missing from CVS, which
causes sff does not compile.



On Jan 14, 2009, at 1:49 PM, David A. Case wrote:

> 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
> please report any funny results. Note that you need to
> do
> "cvs update -d ...." to get the new sff directory into your working
> area.
> 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
> email.]
> 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!
> ...regards...dac
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Received on Fri Jan 16 2009 - 01:13:08 PST
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