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 MMPBSA.py/mm_pbsa.pl 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 MMPBSA.py/mm_pbsa.pl, 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:
extractFrcmod.py / top2ff : extractFrcmod.py 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,
Jason
On Mon, Jun 13, 2011 at 8:16 PM, case <case.biomaps.rutgers.edu> 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 <jason.swails.gmail.com> -----
>
> Date: Mon, 13 Jun 2011 14:53:59 -0600
> Subject: redundant redundancies
> From: Jason Swails <jason.swails.gmail.com>
>
> 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:
>
> extractFrcmod.py 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 -----
>
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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 Jun 13 2011 - 22:30:03 PDT
