Re: amber-developers: please proofread and update the Amber 10 documentation

From: Gustavo Seabra <>
Date: Wed, 6 Feb 2008 09:54:06 -0500

Hi Dave,

I looked at the manual, changed some DFTB-related stuff, added some
new DFTB keywords that were missing and a reference about the CM3

I also noticed that, at least in the version that I can see, the QM/MM
equations all seem to have lost formatting, and LyX cannot find a
number of figures. Since my LyX is missing some packages and unable to
create output, I'm not sure this is a real problem or not. I'm now
trying to get the missing packages and will try it again; meanwhile,
could you just verify if you can notice that with your version of LyX
as well? (I'm running LyX under Cygwin, but I believe it did not
install all the packages correctly).

As soon as I get my LyX working well, I can correct the equations
(assuming you confirm that they are really bad). I can try with the
figures as well, but I'm not sure I'll be able to get them all right,
since I didn't write that part and I am not sure what they should be.

I am attaching here my modified amber10 manual and the bib file with
the extra reference.


On Feb 3, 2008 12:27 AM, David A. Case <> wrote:
> Hi everyone:
> Amber serves a big community of users, not the least of which are new people
> that come into our labs with no detailed background in Amber. So it helps us
> and everyone to have good documentation, and it needs to be prepared as
> carefully as the code itself.
> Please, please, take some time an examine the following:
> amber10/doc/AmberTools.{lyx,pdf} and amber10/doc/Amber10.{lyx,pdf}
> a. check for correctness and completeness; remove obsolete material; add
> examples whereever anything might be ambiguous. Add references
> to the appropriate test cases if that would help show how things are done.
> [Because of the move to LyX/latex, there may be real glitches and
> conversion errors that need to be corrected. But view this as an
> opportunity for general updates as well.]
> b. Update the literature references! Many of these are to *your* work, and
> the Amber manual is one way that people will find your papers and take
> advantage of them. Yet most references are still unchanged from Amber 9,
> and hence are at least two years old.
> You will see that the manuals have been extensively reorganized recently. I
> hope this all make sense, but I welcome suggestions or contributions that are
> "big" changes (i.e. more than just proofreading corrections.) How can we best
> aid both experts and relatively new people?
> Please remember that there is a lead time to get manuals run off and bound:
> updates to the manuals need to be made a soon as possible.
> I've put in lots of hours to get us as far as we are now, and am feeling
> grumpy that I haven't had more help. (Some of you have been good about this,
> and I appreciate this.) Consider assigning each person in your group 10 pages
> or so, and ask them to do a careful reading, with a one-week deadline for
> getting back to you. Or an updating party with beer and pizza. Or whatever
> makes sense, but let's try to spread the work out and get as many people as
> possible to contribute.
> ...thx...dac

Received on Sun Feb 10 2008 - 06:07:06 PST
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