Hi,
Fixed.
(sff does not need mm_options.l).
Scott
On Wed, 14 Jan 2009, Wei Zhang wrote:
> it seems the file "mm_options.l" is missing from CVS, which causes sff does
> not compile.
>
> Sincerely,
>
> Wei
>
>
>
> 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
> >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
> >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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>
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Received on Fri Jan 16 2009 - 01:13:34 PST
