On Mon, Oct 24, 2011 at 9:55 PM, B. Lachele Foley <lfoley.uga.edu> wrote:
> > I'm not quite sure what you're asking here -- are you asking
> > if I was going to update the prmtop specification for chamber
> > topologies, or if I was just going to update it in general?
>
> I was thinking of the online file specifications. Last time I looked,
> there were a number of little things that could be said more clearly or
> completely or that obviously corresponded to an earlier version of the file
> spec. There might be other places I should be thinking of, but that's were
> I usually go for docs. I haven't yet had cause to investigate chamber tops
> enough to know whether the docs are good or not. This is also pretty low on
> my priority list, so I understand your viewpoint. I don't think it's an
> exceptionally urgent thing, but it's nice to have docs be right.
>
Yea, the online docs were the ones I updated --
http://ambermd.org/formats.html. The topology file section should be pretty
accurate. I kept archaic sections around with a deprecation note in the
off-chance that tleap still makes them (it still supports nbona != mbona
even though sander and pmemd complain).
That documentation doesn't match chamber-prmtops in general, though. The
FORMATs are different (which can make parsing them in anything other than
Fortran a pain), and chamber obviously has a lot of extra FLAGs
(urey-bradley terms, cmap, alternate 1-4 A/BCOEF arrays, etc.) which aren't
included in the documentation.
All the best,
Jason
> :-) Lachele
>
> Dr. B. Lachele Foley
> Complex Carbohydrate Research Center
> The University of Georgia
> Athens, GA USA
> lfoley.uga.edu
> http://glycam.ccrc.uga.edu
>
>
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>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Mon Oct 24 2011 - 20:30:04 PDT
