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

From: Jason Swails <>
Date: Mon, 24 Oct 2011 20:26:36 -0400

On Mon, Oct 24, 2011 at 8:08 PM, B. Lachele Foley <> wrote:

> Since Jason didn't say this explicitly: If you're gonna bother with
> fortran-style formatting, using the FLAG and FORMAT specs is important and
> should not be ignored, no matter what anyone else does (even if they -are-
> Jason's elders and he should be more respectful... ;-).

:). No disrespect, just stating, in unix terms,

grep -e "FLAG" -e "FORMAT" || echo "Old!"

And everyone knows that computers age faster than people (heck, they age
faster than bananas)

 You cannot assume there will be white space in this style of formatting, so
> it is really important to let parsers know how the line will be divided.

What I meant was that you can ignore prmtop files that do NOT have the
%FORMAT and %FLAG since those haven't been created by any leap version in
years, certainly not that %FORMAT and %FLAG can be ignored. It's not
unreasonable not to support topology files older than Amber 7 format since
even GB simulations in Amber don't anymore.

I have a prmtop reader, too! In fact, we have two from our group. We
> should all get together and form a club. Or a committee. Or at least sit
> around and drink. Oh, yeah... we do that at the annual meeting....

It's amazing what you can avoid doing in code if you just know how to screw
with the topology file correctly :).

> We really need to update the docs. Ross's offer of a drink obviously
> hasn't been enough to entice me to do it. Maybe in my spare time (ha...).
> Jason, did I interpret your comments as meaning you're doing that? If so,
> then yay!

Some of the docs do need to be updated. 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? For the former, I haven't done that yet, and may or may not get
around to it before I graduate -- it's about dead last on my priority list.
 For the latter, I've already updated it a little while ago, so it should be
up-to-date. I added the %FORMAT and %FLAG descriptors, updated the
currently-used FORMATs (not including the weird formats that chamber
employs). I also added the SCEE/SCNB sections, so I don't think I'm missing
too much if anything (I didn't add anything about various additions for
other programs, like HCP or LES or anything). I kept notes in about
deprecated sections, like the perturbed sections of yesteryear, just for
completeness sake, but there are notes about how they're unused (I even
mentioned gibbs, which is a program I've never even actually seen).

There's even a document about OFF files now :) (now that's an ugly format),
but for the foreseeable future the only stuff I'll be documenting is what
I've actually coded.

All the best,

Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
AMBER-Developers mailing list
Received on Mon Oct 24 2011 - 17:30:03 PDT
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