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

From: David A Case <case.biomaps.rutgers.edu>
Date: Sun, 26 Jan 2014 13:48:15 -0500

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
   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)
   MMPBSA.py (Chap. 12 from AmberTools)
   MMPBSA/FEW (Adapted/expanded from Appendix D of Amber manual)
   AmberLite (Chap. 6 of AmberTools)
   Crystal analysis (mostly new)

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



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Received on Sun Jan 26 2014 - 11:00:02 PST
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