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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Received on Mon Jun 13 2011 - 19:30:04 PDT
