Hi everyone:
I understand that many people hate long emails, but I would really appreciate
it if those people closely involved in Amber 10 development could find the
time to actually read this email, all the way to the end....thx!
It turns out that it is somewhat easier than I expected to move a lot of the
troff code for the Amber manual into LyX/LateX -- tables are really the big
headache still.
Hence, I have finished moving all of the material for AmberTools into
amber10/doc/AmberTools.{lyx,pdf}. This includes newly converted "Force Field"
and "ptraj" chapters, as well as previously-converted NAB, antechamber and
tleap/sleap chapters. There is still work to do on these to bring them up to
the Amber10 release, but changes should now be much easier to make, and the
new output looks nicer and should be easier to maintain.
In brief: to contribute to needed updates, go to www.lyx.org and get a copy of
LyX (versions are available for Linux, Windows and Mac; if you use cygwin on
Windows, get the cygwin version from ftp.lyx.org/pub/lyx/bin/1.5.3). Then
fire up lyx and open AmberTools.lyx. This will more or less look like any
graphical word processor like OpenOffice or Word, so you should be able to
start editing with hardly any learning curve, at least for simple edits.
A few points to note: every paragraph has a style, chosen from a list at the
upper left. Code snippets or commands are in "LyX-Code" style; in addition to
the "standard" style, there are fairly obvious(!?!) choices for "itemize",
"enumerate" and "description" (just apply them to a single paragraph to see
what they do). There are also section headings "Chapter", "Section",
"subsection", etc. (If you are whiz at Fortran, but somehow can't figure this
out, just leave what you add in "standard" format, and I will clean it up.)
If you have things already in latex, you can use the "import" command to
convert them to LyX, and then use copy and paste from there to put into the
AmberTools.lyx file.
Or, if you have things already in Word, send the Word document to me. I have
a copy of word2tex, which allows me to convert it easily to latex, and thence
to LyX. Or (subooptimal:) if you can't get LyX to work, use create a .doc
file in Word or Open Office, and send to me. Use minimal formatting if you
go this way.
[For the curious: it did the troff -> LyX conversion this way:
a. use groff -Thtml to convert to html
b. use MS Word to load the html, then convert to tex
c. use LyX itself to inport the tex]
I'm thinking there will continue to be two manuals for Amber 10: one for
AmberTools (which anyone can get for free), and one for Amber itself
(which will only go to those to license Amber and pay the fee). I haven't yet
bitten the bullet to convert the Amber manual to LyX, but will probably do
that soon (during some boring bowl game, maybe). So, for changes to sander,
please continue for now to update sander.me. I'll send out another email
when/if I make the next conversion steps.
WE STILL NEED TO GET YOUR INPUT ON AMBER10 DOCUMENTATION! In particular:
1. ptraj updates
2. The force field consortium people need to update (i.e. extenively revise)
the force field chapter
3. Obsolete things in sander need to be removed; new functionality needs to
be added.
4. We have nothing on glycom06 yet
5. Lots of detailed fixups: formatting that got screwed up on the conversion;
more examples(!); better explanations of things that tend to confuse new
users, etc.
...happy new year!....dave
Received on Wed Jan 02 2008 - 06:07:19 PST
