ESP and ESP charge derivation for a new structure is an important step in molecular dynamics simulations based on AMBER, CHARMM, GLYCAM and OPLS force fields. To derive such atom-centered charges three steps need to be followed:
- First, the molecule studied is optimized to determine a stable minimum (using a quantum chemistry software).
- Then, this minimized structure is used to calculate a Molecular Electrostatic Potential (MEP) on a three-dimensional grid (using again a quantum chemistry software).
- Finally, this grid is exported into the "RESP program" (also downloadable from the CCL software database or from q4md-forcefieldtools) which is used to fit atom-centered charges to the MEP.

        Although this method is now used 'routinely' to obtain partial charges for molecules, in our opinion, it suffers from a number of limitations:
- To apply this strategy, which requires the described above steps but also numerous format conversions between the different programs used, a significant number of scripts, programs and compilers are needed and used sequentially. Consequently, the procedure is tedious, time-consuming, and numerous errors can be introduced without having a real way to check them.
- Although it is admitted that any quantum chemistry programs could be used to minimize the starting structure and to calculate the MEP, the "Amber" developers mainly use the "Gaussian" program, which is a quite expensive proprietary software. The "GAMESS" academic program, which is provided at no cost and which provide similar functionality for 'RESP' and 'ESP' charges development than "Gaussian", is not officially used to derive 'RESP' or 'ESP' charges. Indeed, it is known that partial charges calculated using "GAMESS", are 'different' than those determined using "Gaussian".
- Finally, starting from different sets of Cartesian coordinates for a same molecule, the 'RESP' or 'ESP' partial charges are, in somes cases, not reproducible even using "Gaussian", making errors in the protocol difficult to detect.


        Thus, we developed the R.E.D. I (RESP ESP charge Derive, version 1.0) program to automatically derive 'RESP' and 'ESP' charges starting from an un-optimized PDB structure. R.E.D. sequentially executes (i) either the "GAMESS" program or the "Gaussian" program to minimize the target structure and to compute the corresponding MEP, and (ii) the "RESP" program to fit the atom-centered charges to the grid previously determined. Format conversions needed during the procedure and "GAMESS", "Gaussian" and "RESP" inputs are automatically generated by R.E.D. By controlling the molecular orientation of the optimized geometry, a new RESP fitting procedure based on multi-orientation feature is proposed and results in highly reproducible 'RESP' and 'ESP' charges independently of the QM software or the initial Cartesian coordinate set.

        With R.E.D. II (version 2.0), multi-conformation RESP and ESP fit has been implemented. Such an approach permits to make the atom charge values more 'general', and is useful in molecular dynamics simulations where the whole conformational space needs to be explored. Thus with R.E.D.-II, 'multi-conformation' and 'multi-orientation' RESP fit can be performed together or independently according to the user choice. 'Standard' but also 'non-standard' RESP inputs can also be generated. Finally, RESP and ESP charges can be derived for chemical elements having up to a total number of electrons, Z = 35.

        With R.E.D. III.x (version 3.x), the control of charge constraints for atoms and groups of atoms in a molecule (intra-molecule charge constraint) or between two molecules (inter-molecule charge constraint and inter-molecular charge equivalencing) has been incorporated allowing for the derivation of the RESP and ESP atom charge values for molecule fragments and sets of molecules. Fitting procedures involving multiple molecules, and for each molecule, multiple conformations, and for each conformation, multiple orientations, can now be automatically carried out. Moverover, eight different charge derivation procedures using different MEP computation algorithms (Connolly surface and CHELPG algorithms) and different fitting procedures (with or without hyperbolic restraints) are now available. Potentially, an infinite number of approaches can be developed by simply changing a few words in the R.E.D. III.x source code. Such procedures can be used in simulations based on AMBER, CHARMM, GLYCAM and OPLS force fields.

        Once the R.E.D. execution is completed, the charge values are available in Tripos mol2 file(s) which can be considered as precursors of AMBER OFF and CHARMM RFT or PSF force field libraries. R.E.D. makes the development of the 'RESP' and 'ESP' charges a straightforward, simple and highly reliable procedure.


        R.E.D. interfaces the GAMESS-US or Gaussian program and RESP program. R.E.D. III.x is now fully compatible with GAMESS-US (and its WinGAMESS version), Firefly and the Gaussian 1994, 1998, 2003 and 2009 versions on UNIX, MacIntosh and Windows plateforms.

        R.E.D. III.x is distributed with two other programs:
        - X R.E.D. is a graphical user-friendly interface, which has been developed to graphically execute R.E.D. and modify R.E.D. variables.
        - Ante_R.E.D. is a program useful for preparing R.E.D. inputs, and in particular the "P2N" files. The P2N file format is a new file format introduced with R.E.D. III. It corresponds to the PDB file format with a second column of atom names.
        R.E.D. III.x, Ante_R.E.D.-1.x, and X R.E.D. III.x constitute the R.E.D. III.x tools.

        R.E.D. (versions I, II and III.x) and Ante_R.E.D. have been written with the "Perl" programming language (See also the O'REILLY web site), while X R.E.D. has been developed using the "tcl/tk" programming language. "Perl" and "tcl/tk" are interpreted programming languages, meaning that the programs written with these languages do not need to be compiled. This makes R.E.D., Ante_R.E.D. and X R.E.D. simple to use, highly flexible and portable. They are fully functional on UNIX, MacIntosh and Windows plateforms.

        The R.E.D. III.5 tools are now distributed under the GNU General Public License after a simple Register & Download procedure.

        If you have questions about the R.E.D. III.x tools, please, first check the documentation available (i. e. the manuals and FAQ). Basic tutorials are available in the R.E.D. I and R.E.D. II manuals, and new Tutorials have been written to describe Ante_R.E.D.-1.x, R.E.D. III.x and also R.E.DD.B..

        If you need help about using the R.E.D. III.x tools, a general public help is now provided with the q4md-forcefieldtools mailing list. Any researcher can participate in this mailing list by answering and/or sending queries at q4md-fft@q4md-forcefieldtools.org after registration at sympa@q4md-forcefieldtools.org. To register in the q4md-fft mailing list just send an email to sympa@q4md-forcefieldtools.org with "subscribe q4md-fft" in the email subject or body (to un-subscribe just send "unsubscribe q4md-fft"). Archives of the q4md-fft mailing list are public.

        We are also registered in the AMBER and CCL mailing lists, and we will answer to the queries about the q4md force field tools in these two mailing lists as well.

        If you have any suggestions about the R.E.D. III.x tools or if you find a bug, send us an e-mail: