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

From: David A. Case <>
Date: Wed, 6 Feb 2008 09:12:01 -0800

On Wed, Feb 06, 2008, Gustavo Seabra wrote:

> 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
> charges.

Thanks for doing that.

> 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).

It's probably easiest for me to fix up the equations (I know they are still
broken in places). The "figures" are mostly just Greek letters and symbols...
I'll work on that.

You are using LyX 1.4.5, which has a different file format than LyX 1.5.x,
which I am using. The program is supposed to go back and forth OK, but it
actually messes up index entries. I can copy and paste what you changed into
my version, but if you actually want to work further on equations and stuff,
please get LyX 1.5.3 (available as a binary on LyX ftp site). This is a bit
of a downer, since I didn't realize there would be this problem.


David A. Case                     |  e-mail:
Dept. of Molecular Biology, TPC15 |  fax:          +1-858-784-8896
The Scripps Research Institute    |  phone:        +1-858-784-9768
10550 N. Torrey Pines Rd.         |  skype:                 dacase
La Jolla CA 92037  USA            |
Received on Sun Feb 10 2008 - 06:07:09 PST
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