Re: [AMBER-Developers] [ redundant redundancies]

From: Jason Swails <>
Date: Mon, 13 Jun 2011 23:05:15 -0600

Hello everyone,

The descriptions for each program are done (but only for AmberTools 1.5,
none introduced since then). It is now Chapter 2 of the AmberTools manual,
and is part of the master branch. Please feel free to improve the (short!)
description for your program(s).

tleap/sleap, cpptraj/ptraj, and are obviously 3 of the
big ones.

For cpptraj/ptraj, I think cpptraj offers something new over ptraj that
makes it worth keeping, but ptraj does too much to discard at this point. I
support keeping both here.

For tleap vs. sleap; I'm not quite sure what the design goal for sleap was
in the first place (as I wasn't around when it was begun), but it appears to
be a bit buggy, and with no GUI version available, people will probably
continue to use tleap/xleap. I don't think we can get rid of tleap (at
least not at this point).

For, I'll obviously support our version, and it does
everything the perl version does as well as MM/3D-RISM and QM/MMGBSA if one
isn't built.

Onto some of the smaller ones, here are the redundancies I found: / top2ff : produces a complete frcmod
along with LJ non-bonded terms.
ambpdb / top2mol2 : ambpdb does what top2mol2 does as well as prints out
other formats (PDB, PQR)
reduce / protonator : based on descriptions I found, reduce does what
protonator does and more
mmE / NAB, sander, pmemd, mdgx : I'm not quite sure what sets mmE apart,
although it may just be an example program using MTK++
sequenceAligner/superimposer : It seems that superimposer just does part of
what sequenceAligner does? Perhaps Martin can clarify here a little?

Some more redundancies: we have Bob's pubfft (?) used in pmemd, as well as 2
versions of fftw (2.1.5 and 3.2.2).

All the best,

On Mon, Jun 13, 2011 at 8:16 PM, case <> wrote:

> I agree with Jason's comments below. I'm happy to let him get started as
> proposed, but I hope everyone will help out in working on simplification.
> There are both types of issues outlined below, plus much bigger issues,
> e.g.:
> tleap vs sleap
> ptraj vs cpptraj
> python vs perl versions of mm-pbsa
> I don't have any magic answers, but cleanup and simplification of both code
> and documentation should be a high priority for the next release.
> [On Jason's specific points, we can probably retire top2mol2, top2ff,
> and maybe some of the other minor antechamber scripts.]
> ...dac
> ----- Forwarded message from Jason Swails <> -----
> Date: Mon, 13 Jun 2011 14:53:59 -0600
> Subject: redundant redundancies
> From: Jason Swails <>
> I'm going through Amber and AmberTools right now and adding a section of
> the
> manual that more or less lists all of the programs that exist in each
> package right now that gives a short (1-sentence) description of its
> functionality and where in the manual you should look for its description.
> In doing so, though, I've found numerous redundancies. For instance:
> and top2ff do the same thing (although the first one
> provides a more complete FF file from a given prmtop). top2mol2 mimics
> ambpdb with the -mol2 flag. I can provide a more complete list after I'm
> done, though I think we should start thinning out the number of provided
> programs; at the very least eliminating redundancies. There are 97 (!)
> programs installed with AmberTools (just serial).
> Thanks!
> Jason
> ----- End forwarded message -----
> _______________________________________________
> AMBER-Developers mailing list

Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
AMBER-Developers mailing list
Received on Mon Jun 13 2011 - 22:30:03 PDT
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