In the context of a joined French-USA research project between the Universit� de Picardie - Jules Verne and the Sanford | Burnham Medical Research Institute empirical force field features related to the Amber additive and non-additive force field models were implemented in a new version of the R.E.D. program. An object oriented approach was followed by using the Python 2.7 programming language. A modular procedure was pursued making the introduction of new developments in the source code straightforward. New algorithms were designed for rigorously (i) calculating chemical equivalencing for charge equivalencing versus charge averaging, (ii) determining the molecular topology, (iii) controlling the optimized geometries and electrostatic potentials computed by quantum mechanics, (iv) describing numerous RESP and ESP charge models using predefined and user defined options, which lead to highly reproducible charge values, (v) defining models of dummy atoms (i. e. extra-points) and united carbon atoms, (vi) building force field topology databases (or set of force field libraries) for large ensembles of molecules, as well as for natural and chemically engineered polymers (i. e. biopolymers and functionalized carbon nanotube polymers), (vii) correcting rounding-off errors in agreement with the different charge constraints used during the charge fitting step, (viii) performing atom typing for the Amber force fields, as well as (ix) generating, adapting and rationalizing force field parameters ready to be loaded within the LEaP program using a dedicated script. The whole procedure handles multiple orientations, multiple conformations as well as multiple molecules. It is not limited to biomolecules, and is now compatible with most of the elements of the periodic table. R.E.D. Python will be first open to academics by November 2013 through R.E.D. Server Development at http://q4md-forcefieldtools.org. The core of this program will be distributed under the GNU General Public License.

R.E.D. Python: Object oriented programming for Amber force fields

247th National Meeting (2014)

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