Re: [AMBER-Developers] prmtop file format specification/documentation

From: Jason Swails <>
Date: Mon, 24 Oct 2011 23:22:41 -0400

On Mon, Oct 24, 2011 at 9:55 PM, B. Lachele Foley <> 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 -- 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,

> :-) Lachele
> Dr. B. Lachele Foley
> Complex Carbohydrate Research Center
> The University of Georgia
> Athens, GA USA
> _______________________________________________
> AMBER-Developers mailing list

Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
AMBER-Developers mailing list
Received on Mon Oct 24 2011 - 20:30:04 PDT
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