[AMBER] New empirical force field tools: Release of R.E.D. Server Dev./R.E.D. Python

From: FyD <fyd.q4md-forcefieldtools.org>
Date: Fri, 22 Nov 2013 11:22:40 +0100

Dear Amber users,

I am pleased to announce the release of a new q4md-forcefieldtools
service: R.E.D. Python interfaced by R.E.D. Server Development at

R.E.D. Server Development is the Internet service, that provides the
hardware and software for charge derivation, force field library
building and force field parameter generation; see

R.E.D. Python is the program, that performs charge derivation, force
field library building and force field parameter generation. R.E.D.
Python gives researchers the means to rigorously generate molecular
electrostatic potential-based empirical force fields for new molecules
allowing their direct validation and/or use in molecular dynamics
simulations. In the current release the additive AMBER and GLYCAM
force field models are fully handled by R.E.D. Python, although
features related to the non-additive model are already implemented.
Charge models designed for the OPLS force field and used by CHARMM are
also available. R.E.D. Python handles force field generation for a
large ensemble of new molecules and molecular fragments. The approach
is particularly suited for polymer modeling (biopolymers such as
proteins, nucleic acids, glyco-conjugates and their bioinorganic
complexes, as well as functionalized and non-functionalized cabon
nanotubes). All the elements of the periodic table are handled by the
service. More generally, the full list of tasks performed by R.E.D.
Server Development/R.E.D. Python is reported at

A demonstration is available from the “Demo” service at the R.E.D.
Server Development home page; see
the data of this demonstration correspond to the R.E.DD.B. project
available at http://q4md-forcefieldtools.org/REDDB/projects/W-46/.

A new version (version 2.4) of the RESP program is executed, and new
charge models are proposed based on chemical equivalencing, chemical
averaging with or without hyperbolic or quadratic restraints; see
RESP 2.4 can be downloaded at http://q4md-forcefieldtools.org/RED/resp/.

A direct application of the use of R.E.D. Python is the generation of
the Sanders et al. force field for the peptide nucleic acid
biopolymer; See http://pubs.acs.org/doi/abs/10.1021/jp4064966 and the
corresponding project in R.E.DD.B.

The persons involved in this project are:
   F. Wang: (1) PhD student & developer of R.E.D. Python
   J.-P. Becker: (1) Developer of the version 2.4 of RESP
   P. Cieplak: (2) co-Principal Investigator
   F.-Y. Dupradeau: (1) co-Principal Investigator
(1) Universite de Picardie Jules Verne, Amiens, France
(2) Sanford | Burnham Medical Research Institute, La Jolla, CA, USA.

The q4md-forcefieldtools project is developed in the context of a
joined french-USA collaboration between the Universite de Picardie -
Jules Verne and the Sanford | Burnham Medical Research Institute, and
is funded by the Conseil Regional de Picardie and the European
Regional Development Fund.

regards, Francois

           F.-Y. Dupradeau

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Received on Fri Nov 22 2013 - 03:00:02 PST
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