From owner-chemistry@ccl.net Wed Feb 22 08:17:00 2012 From: "Dimitrios Vlachakis dvlachakis]^[bioacademy.gr" To: CCL Subject: CCL: Call for Papers: JOURNAL OF MOLECULAR BIOCHEMISTRY Message-Id: <-46355-120222033500-14604-8A7PWutEn+Q9E29Nn4SLQw-x-server.ccl.net> X-Original-From: "Dimitrios Vlachakis" Date: Wed, 22 Feb 2012 03:34:42 -0500 Sent to CCL by: "Dimitrios Vlachakis" [dvlachakis..bioacademy.gr] Dear Scientists, The JOURNAL OF MOLECULAR BIOCHEMISTRY (JMolBiochem; ISSN: 2241-0090) is a new peer-reviewed journal that is currently accepting manuscripts for publication. JMolBiochem publishes high-quality scientific articles, in English, in all areas of MOLECULAR BIOCHEMISTRY. Call for Papers JMolBiochem will cover all major areas of the field of Molecular Biochemistry. The journal welcomes the submission of scientific manuscripts of high standard that meet the criteria for scientific excellence. Our Journal will publish: Original and novel scientific articles in basic and applied research Case studies in Molecular Biochemistry Articles involving statistics, surveys, opinions and commentaries in Molecular Biochemistry Letters to the editor Reviews and Essays We invite you to submit your manuscript(s) to our on-line submission system at www.jmolbiochem.com Our goal is to provide authors with a decision about their manuscript(s) within no-more of six weeks upon submission. Given that the article is accepted, it will appear on our online archive index, will be issued a DOI and will be published in our next issue. Instruction for authors, conditions and all other important details are available on our Author Guidelines section. Dimitrios Vlachakis Spyridon Champeris-Tsaniras Editors-In-Chief Journal of Molecular Biochemistry www.jmolbiochem.com ///////////////////////////////////// JMolBiochem is an Open Access Journal. The Journal of Molecular Biochemistry, is serving the novel purpose of worldwide unrestricted access to research publications. Therefore JMolBiochem is an open access journal and is member of the Lorem Ipsum Press. We believe that subscription-based journals constrain the flow of scientific knowledge by limiting the visibility and impact of published works. Indexing and retrieval of all scientific papers is top priority. All articles will be issued a DOI and will be indexed and freely available on our website upon acceptance. JMolBiochem supports the Open Access Initiative (OAI) in academic publishing. From owner-chemistry@ccl.net Wed Feb 22 08:52:00 2012 From: "FyD fyd|,|q4md-forcefieldtools.org" To: CCL Subject: CCL:G: Release of the R.E.D. III.5 tools Message-Id: <-46356-120222055441-11716-HKmCiUfuy7+mnAxPOfZzNg++server.ccl.net> X-Original-From: FyD Content-Disposition: inline Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1; DelSp="Yes"; format="flowed" Date: Wed, 22 Feb 2012 11:54:31 +0100 MIME-Version: 1.0 Sent to CCL by: FyD [fyd||q4md-forcefieldtools.org] Dear All, We are pleased to announce the release of the program RESP ESP charge Derive version III.5 (or R.E.D. III.5) and its related tools (Ante_R.E.D.-1.5 and X R.E.D. III.5) available _._ http://q4md-forcefieldtools.org/RED/. New features available: - Bug corrections and code cleaning, - Update of the Mini-HowTo & Tutorials, - Better handling of Gaussian, GAMESS and Firefly error messages, - Charge value rounding off errors automatically corrected at 10-6 up to 10-2 depending on the user choice, - Handling geometrical constraints in the P2N file format (geometry optimization using the Gaussian program), - Two new scripts for data submission in R.E.DD.B., - New version for the RESP program: version 2.2 with updated documentation. The R.E.D. III.5 tools are distributed under the GNU General Public License after a simple Register & Download procedure. The article describing the R.E.D. tools is available _._ http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2918240/. News about the latest developments of R.E.D. IV can be found _._ http://q4md-forcefieldtools.org/RED/popup/news.php. RESP 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 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 at contact_._q4md-forcefieldtools.org. regards, Francois F.-Y. Dupradeau --- http://q4md-forcefieldtools.org/FyD/ From owner-chemistry@ccl.net Wed Feb 22 11:52:01 2012 From: "Ly Minh Nguyen nguyenminhly2209#%#yahoo.com" To: CCL Subject: CCL: SN1 Reaction Message-Id: <-46357-120222111402-23364-GyuDu+/fWHKSE7wpl7drag#%#server.ccl.net> X-Original-From: "Ly Minh Nguyen" Date: Wed, 22 Feb 2012 11:14:01 -0500 Sent to CCL by: "Ly Minh Nguyen" [nguyenminhly2209-$-yahoo.com] Dear sir, I'm Ly, Viet Nam I have a problem with SN1 reaction. I want to optimize transition state of SN1 subtitution reaction ( 2 structure ) but I don't know how to do this. Can I use QST2 and QST3 key word for optimizing ? Please help me. Thanks From owner-chemistry@ccl.net Wed Feb 22 12:26:00 2012 From: "Vera Cathrine vera.cathrine|*|yahoo.com" To: CCL Subject: CCL: G09: TDDFT frequncy restart Message-Id: <-46358-120222115431-11352-5tHrVfTFXE04V4vaWBcYyQ- -server.ccl.net> X-Original-From: "Vera Cathrine" Date: Wed, 22 Feb 2012 11:53:59 -0500 Sent to CCL by: "Vera Cathrine" [vera.cathrine]^[yahoo.com] Dear List Members, I have run some TDDFT frequency calculations in the excited state using G09-A2. My goal is to compute the derivatives of the electric transition dipole for further vibronic analysis. If things work properly, the el-dipoles should contain 6N+1 lines (if N is the number of atoms) each reporting the three x, y, z components of the transition electric dipole at a different geometry. I have supplied following route section: #p freq=(savenm,noraman,hpmodes) td cam-b3lyp/6-31g(d) nosymm geom=connectivity But my job has been killed because of our cluster wall time and I restarted the jobs until normal termination (after 45 days on 8 cpu) by #p freq=restart td cam-b3lyp/6-31g(d) nosymm geom=connectivity I expected to extract 6N+1 (dipole at the initial geometry reported in excited-state equilibrium and the next 6N lines report the dipole at geometries obtained displacing sequentially a single coordinate) in the out file as usual which is not the case. I have just part of this analysis. I need this data printed out to use externally for HT and FCHT analyis (not with G09). I am wondered yo ask whether these information are stored in the chk file? and is there any way to retrieve this data? It seems that this data can be used in G09 internally by readfch command for HT or FCHT analysis. Is that right? I appreciate your time and kind reply. Best regards, Vera