Re: [AMBER-Developers] Ideas about a reorganization of the Amber manuals

From: Gustavo Seabra <>
Date: Sun, 26 Jan 2014 17:54:49 -0200

Hi all,

I, for one, am glad to see the sqm part back with sander.

About the manual, I don't know what was discussed in the Amber Meeting but,
just in case it wasn't discussed, I'd like to suggest adding an online
version (wiki maybe?). My guess is that it will be far more used than any
print or pdf version.

Gustavo Seabra.
Em 26/01/2014 15:48, "David A Case" <> escreveu:

> Hi everyone: I want to expand here on some ideas about documentation that
> came up at the recent Amber Developers' Meeting.
> The current Amber manuals (Amber12.pdf and AmberTools13.pdf) are divided
> that
> way to reflect licensing distinctions between the two parts of the code.
> This never really made a lot of sense, and will be less important now that
> we are changing the licensing of sander.
> In my own thinking, I decided start over, hypothetically merging everything
> into one manual. We can decide later how it might be divided, e.g. for
> printing or other purposes. Below is a tentative table of contents for
> this
> merged Manual.
> [NOTE: we won't be actually doing anything to files in the git repo for a
> while; please continue to proofread and update the Manual files as you have
> been doing.]
> Amber 14 Manual
> Part I. Introduction, installation and testing
> combines chap. 1 of AmberTools and Chapter 1 of Amber
> Part II. Amber force fields
> Molecular mechanics force fields (expanded from Chap 2 of AmberTools;
> add Amoeba material from Amber manual)
> Implicit solvent models (to contain the relevant parts of Chap 3 from
> the Amber manual (for GB) , plus Chap. 10 (PBSA) and Chap. 11 (RISM)
> from AmberTools
> QM/MM (Chaps 3.6 to 3.8 of current Amber manual, plus Chap 7 on sqm
> from
> AmberTools)
> EVB (Chap. 3.4 of Amber manual)
> GAFF and antechamber (Chap. 5.1 to 5.5 from AmberTools)
> MCPB (Chap. 5.6 from AmberTools)
> Part III. System preparation
> Chaps 3 and 4 of AmberTools (LEaP and parmed, etc.)
> Part IV. Running simulations
> Chapters 2,4,5,6,7,8 from current Amber manual;
> Chapter 13 on mdgx from AmberTools
> Chapters 15-20 on NAB from current AmberTools manual;
> Part V. Analysis
> cpptraj (Chap 8 from AmberTools)
> (Chap. 12 from AmberTools)
> MMPBSA/FEW (Adapted/expanded from Appendix D of Amber manual)
> AmberLite (Chap. 6 of AmberTools)
> Crystal analysis (mostly new)
> etc.
> Appendices, etc.
> As discussed at the meeting, it might make good sense to split out Part II
> above (on force fields) into a separate document, and add to it info about
> using the Amber force field in other programs. If we do go back to
> physically
> printing and binding the Manuals, a spiral-bound book (which is the only
> kind
> that really works) has a maximum of about 400 pages.
> Comments/suggestions are welcome; please send these to the amber-developers
> list.
> ...thx...dac
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Received on Sun Jan 26 2014 - 12:00:02 PST
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