Dear Jmol users, I am pleased to announce the release of the RESP ESP charge DDataBase (or R.E.DD.B.) @ http://www.u-picardie.fr/labo/lbpd/REDDB/.
RESP and ESP charges centered on atoms are needed in many molecular mechanics and docking studies, and used in many force field based simulations. These atomic charges are recognized as highly efficient to reproduce many molecular properties. However, no real system allows to rigorously define the charge derivation conditions, and store, compare and distribute the corresponding charge values. The RESP ESP charge DDataBase is a new source of RESP or ESP charge values for small structures and model systems. Its goals are multiple. R.E.DD.B. allows to freely store and distribute RESP and ESP charges of high quality and high reproduciblility in the scientific community. However, R.E.DD.B. can also be seen as a tool devoted to reproduce, compare, criticize and improve the different RESP and ESP models. Many different procedures are used to derive such RESP or ESP charges, and the charge values are affected by many parameters (QM programs, algorithms, molecular orientation, molecular conformation, human errors, etc...). Thus, R.E.DD.B. not only stores RESP or ESP charge values, but also the structures (Cartesian coordinates optimized by QM) and detailed information about the method used to derive the charges. Two types of the data or projects can be found in R.E.DD.B. * WHOLE MOLECULE type projects, "W-$n", which corresponds to an intact (un-broken) molecule. Examples are small organic or inorganic molecules such as solvent molecules (Dimethylsulfoxide, Ethanol, Cyclohexane etc...), or ligands of proteins or nucleic acids. * MOLECULE FRAGMENT type projects, "F-$n", which corresponds to a part (or fragment) of an organic or inorganic macro-molecule. Examples are amino-acid fragments 'NH-CH(R)-CO' (AA) where the atomic charges are generally derived using capped amino acids 'ACE-AA-NME', nucleotide fragments originating from the fusion between dimethylphosphate and the corresponding nucleosides, or monosaccharide fragments. These fragments are generally compatible with previously existing ones (available in force field topology databases), and used to construct macro-molecules such as proteins, nucleic acids or polysaccharides. DESCRIPTION OF R.E.DD.B.: - A R.E.DD.B. project code is automatically attributed to each project submitted in R.E.DD.B. once it has been sucessfully uploaded. This code should to be used by its author(s) to reference the R.E.DD.B. project in the corresponding publication. Consequently, the R.E.DD.B. project code provides a rigorous link between the charge values and the corresponding publication insuring the definition/reproducibility of the published results. - A tool has been developped allowing the author(s) of a project (i) to fully describe the computational conditions she/he used in the charge derivation procedure and (ii) to upload the files required to characterize this project. - A second tool has been written to efficiently search projects within R.E.DD.B. and download the corresponding projects. - FAQ are available to describe the project submission procedure, the data and files required for a submission, the ways of searching projects in R.E.DD.B. and much more. - A list of references about RESP and ESP charges is also available. - Each whole molecule and molecule fragment and its corresponding charge values is visualized within HTML pages using the Jmol program, http://jmol.sourceforge.net/, and J2SE Runtime Environment, http://java.sun.com/j2se/1.5.0/download.jsp. - For each molecule name and project name provided in a project a link to Wikipedia, the Free Encyclopedia, http://en.wikipedia.org/wiki/Main_Page/ is generated providing general information. - The R.E.DD.B.2t ("bis & test") internet site, http://www.u-picardie.fr/labo/lbpd/REDDB2t/ has been designed to track bugs in the system. It can also be used by anyboby interested in learning how to submit projects in the official RESP ESP charge DDatabase. Thus, this "bis & test" web site is useful for knowing the information required before/for an official R.E.DD.B. by performing and recording blind tests. EXAMPLES OF PROJECT AVAILABLE IN R.E.DD.B.: We have already submitted close to 140 projects involving multi-orientation, multi-conformation and/or multi-molecule RESP or ESP fit. Below, is a short listing of some projects available in R.E.DD.B.: * RESP atomic charges for 10 solvent molecules based on the Connolly surface algorithm and the HF/6-31G* theory level: Project "W-46", http://www.u-picardie.fr/labo/lbpd/REDDB/up/W-46/info.html with many links to Wikipedia: http://en.wikipedia.org/wiki/Organic_solvent, http://en.wikipedia.org/wiki/Ethanol, http://en.wikipedia.org/wiki/Dimethylsulfoxide etc... * RESP atomic charges for 10 solvent molecules based on the CHELPG algorithm and the HF/6-31G* theory level: Project "W-47". * ESP atomic charges for 10 solvent molecules based on the Connolly surface algorithm and the HF/6-31G* theory level: Project "W-48". * ESP atomic charges for 10 solvent molecules based on the CHELPG algorithm and the HF/6-31G* theory level: Project "W-49". * RESP atomic charges for the 4 DNA and RNA nucleosides based on the Connolly surface algorithm and the HF/6-31G* theory level: Projects "W-69" and "W-74". * RESP atomic charges for the 4 DNA and RNA nucleosides based on the CHELPG algorithm and the HF/6-31G* theory level (following a strategy similar to that applied in the GLYCAM 2004 force field, http://glycam.ccrc.uga.edu/index.jsp): Projects "W-73" and "W-78". * RESP atomic charges for the central, (+)NH3-terminal, (-)OOC-terminal, NH2-terminal and HOOC-terminal fragments of the dimethylalanine amino acid based on the Connolly surface algorithm and the HF/6-31G* theory level: Project F-3, http://www.u-picardie.fr/labo/lbpd/REDDB/up/F-3/info.html and Projects "F-7", "F-11", "F-15" "F-19", respectively. * Similar data are available for the O-methyl-L-tyrosine amino acid, http://www.scripps.edu/newsandviews/e_20011029/schultz1.html involving the Connolly surface and the CHELPG algorythm (RESP and ESP charges): Projects "F-23" up to "F-44". * RESP atomic charges based on the Connolly surface algorithm and the HF/6-31G* theory level for the 16 components of a force field topology database useful for modeling regular DNA: Project "F-45", http://www.u-picardie.fr/labo/lbpd/REDDB/up/F-45/info.html with a LEaP script, http://www.u-picardie.fr/labo/lbpd/REDDB/up/F-45/leaprc-mol2tooff.ff to convert the library precursors (Tripos format) into OFF files. * RESP atomic charges based on the CHELG algorithm and the HF/6-31G* theory level for the 16 components of a force field topology database useful for modeling regular DNA (following a strategy similar to that applied in the GLYCAM 2004 force field): Project "F-49". * Same as project F-45, but the phosphate is located at the O3' position instead of the O5' one: Project "F-50". * RESP atomic charges based on the Connolly surface algorithm and the HF/6-31G* theory level for the 16 components of a force field topology database useful for modeling regular RNA: Project "F-51" with a LEaP script to convert the library precursors (Tripos format) into OFF files (up to "F-56" for other RNA force field topology databases). * Unusual nucleotide projects: "F-57", "F-58" and "F-59". More projects are available, see the download section... These projects have been carried out using the R.E.D. program (version III), http://www.u-picardie.fr/labo/lbpd/RED/. We hope the community will find R.E.DD.B. interesting and will participate to its development. We encourage researchers to submit projects in R.E.DD.B. involving multi-orientations, multi-conformations and multi-molecules and not only single-orientation, single-conformation and single molecule projects which are more limited. This email is available @ http://www.u-picardie.fr/labo/lbpd/REDDB/release.php with all the links to the R.E.DD.B. projects reported. Best regards, Francois -- * F.-Y. Dupradeau * DMAG EA 3901 & Faculte de Pharmacie, Amiens, France **** http://www.u-picardie.fr/labo/lbpd/FyD.htm ------------------------------------------------------- This SF.net email is sponsored by: Splunk Inc. Do you grep through log files for problems? Stop! 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