Subject: Future status of the Amber molecular modeling programs

From: David Case <[email-masked]>
Date: Thu, 13 Sep 2001 09:20:14 -0700 (PDT)

The following comments are a general reply to many questions I have been
asked about the future status of the Amber molecular modeling programs.
We were all saddened by Peter Kollman's untimely death, but we definitely
plan to keep the Amber program alive (as Peter certainly wanted).  Here is
some information:

  For several years, David Case (at The Scripps Research Institute in San
Diego) has been in charge of preparing releases, overseeing details of the
code tree, test suites, and documentation.  This will continue.
Contributions to Amber come from many places, including UCSF, and have not
been dependent on any one person or research group.

  Amber has been released on a "two-year" cycle for some time.  Amber6 was
released in January, 2000, and plans are well along for a release of Amber7,
with a target date of January, 2002.  Some of the features we plan for
Amber7 are listed below; all of these were well in the "pipeline" when Peter
Kollman died.

  (1) New force fields for proteins and nucleic acids, including
polarizabilities on atoms, and off-center ("lone-pair") charges to better
handle the orientation dependence of hydrogen bonds.  This is an area that
Peter Kollman was working very hard on, and continued development and
testing is being led by senior collaborators Piotr Cieplak and Jim Caldwell.

  (2) Codes and force fields to automatically treat (almost) any organic
molecule.  This "general organic" Amber force field and corresponding
computer codes for generating atom types and Amber-compatible input files,
should greatly facilitate the incorporation of co-factors and ligands into
Amber-based simulations. The principal developer here is Junmei Wang.

  (3) A "second generation" of generalized Born and other continuum solvent
models, for problems where full explicit solvent simulations are not
practical.  These will include support for free energy simulations, and
advanced methods of handling titratable residues.

  (4) Continued general improvements in the core simulation technologies:
better parallel performance; new QM/MM models (in the Roar package from
Ken Merz' group at Penn State); improved free energy techniques (especially
with PME); updates to the preparation and analysis programs; and so on.

Please note that we cannot yet guarantee either the release date or the
specific set of features that will be included in Amber7, but the
development team is committed to continuing to provide the best program
suite we can put together.  Other features that are in development may also
be ready in time to be included in the Amber7 release.

  Questions can be addressed to me, using the contact information below.

-- 

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David A. Case                     |  e-mail:      [email-masked]
Dept. of Molecular Biology, TPC15 |  fax:          +1-858-784-8896
The Scripps Research Institute    |  phone:        +1-858-784-9768
10550 N. Torrey Pines Rd.         |  home page:                   
La Jolla CA 92037  USA            |    http://www.scripps.edu/case
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