From owner-chemistry@ccl.net Mon Jan 12 09:16:01 2009 From: "FyD fyd__q4md-forcefieldtools.org" To: CCL Subject: CCL:G: Release of the R.E.D.-III.1 tools Message-Id: <-38416-090112080201-12112-ae/6tO0PX5kVwkFNoljqxg]^[server.ccl.net> X-Original-From: FyD Content-Disposition: inline Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=ISO-8859-1; DelSp="Yes"; format="flowed" Date: Mon, 12 Jan 2009 12:59:14 +0100 MIME-Version: 1.0 Sent to CCL by: FyD [fyd],[q4md-forcefieldtools.org] Dear All, January, 12th, 2009. I am pleased to announce the release of the program RESP ESP charge =20 Derive version III.1 (or R.E.D. III.1) and its related tools =20 (Ante_R.E.D.-1.1 & X R.E.D. III.1) available (-) =20 http://q4md-forcefieldtools.org/RED/. New features available: - Bug corrections in Ante_R.E.D. & R.E.D.-III, - Better handling/display of system variables, - Better interface for PC-GAMESS/Firefly & GAMESS-US (Ante_R.E.D., =20 R.E.D. & X_R.E.D.), - Portability on Mac OS X platforms (Thanks to T. Patko's work - =20 California State University, Long Beach, CA, USA), - Better compatibility with R.E.D. Server. This new distribution contains a mini-HowTo and a tutorial about =20 charge derivation and force field library building for whole molecules =20 and molecule fragments using the R.E.D.-III.1 tools. A person who is already registered as a R.E.D.-III tools user does not =20 need to register again: She/he can use her/his R.E.D.-III tools =20 login/passwd obtained previously to download the R.E.D.-III.1 tools. RESP and ESP charge derivation for a new structure is an =20 important step in molecular dynamics simulations based on AMBER, =20 CHARMM, GLYCAM and OPLS force fields. To derive such atom-centered =20 charges three steps need to be followed: - First, the molecule studied is optimized to determine a stable =20 minimum (using a quantum chemistry software). - Then, this minimized structure is used to calculate a Molecular =20 Electrostatic Potential (MEP) on a three-dimensional grid (using again =20 a quantum chemistry software). - Finally, this grid is exported into the "RESP program" (also =20 downloadable from the CCL software database) which is used to fit =20 atom-centered charges to the MEP. Although this method is now used 'routinely' to obtain =20 partial charges for molecules, in our opinion, it suffers from a =20 number of limitations: - To apply this strategy, which requires the described above steps but =20 also numerous format conversions between the different programs used, =20 a significant number of scripts, programs and compilers are needed and =20 used sequentially. Consequently, the procedure is tedious, =20 time-consuming, and numerous errors can be introduced without having a =20 real way to check them. - Although it is admitted that any quantum chemistry programs could be =20 used to minimize the starting structure and to calculate the MEP, the =20 "Amber" developers mainly use the "Gaussian" program, which is a quite =20 expensive proprietary software. The "GAMESS" academic program, which =20 is provided at no cost and which provide similar functionality for =20 'RESP' and 'ESP' charges development than "Gaussian", is not =20 officially used to derive 'RESP' or 'ESP' charges. Indeed, it is known =20 that partial charges calculated using "GAMESS", are 'different' than =20 those determined using "Gaussian". - Finally, starting from different sets of Cartesian coordinates for a =20 same molecule, the 'RESP' or 'ESP' partial charges are, in somes =20 cases, not reproducible even using "Gaussian", making errors in the =20 protocol difficult to detect. Thus, we developed the R.E.D. I (RESP ESP charge Derive, =20 version 1.0) program to automatically derive 'RESP' and 'ESP' charges =20 starting from an un-optimized PDB structure. R.E.D. sequentially =20 executes (i) either the "GAMESS" program or the "Gaussian" program to =20 minimize the target structure and to compute the corresponding MEP, =20 and (ii) the "RESP" program to fit the atom-centered charges to the =20 grid previously determined. Format conversions needed during the =20 procedure and "GAMESS", "Gaussian" and "RESP" inputs are automatically =20 generated by R.E.D. By controlling the molecular orientation of the =20 optimized geometry, a new RESP fitting procedure based on =20 multi-orientation feature is proposed and results in highly =20 reproducible 'RESP' and 'ESP' charges independently of the QM software =20 or the initial Cartesian coordinate set. With R.E.D. II (version 2.0), multi-conformation RESP and ESP =20 fit has been implemented. Such an approach permits to make the atom =20 charge values more 'general' and effective, and is useful in molecular =20 dynamics simulations where the whole conformational space needs to be =20 explored. Thus with R.E.D.-II, 'multi-conformation' and =20 'multi-orientation' RESP fit can be performed together or =20 independently according to the user choice. 'Standard' but also =20 'non-standard' RESP inputs can also be generated. Finally, RESP and =20 ESP charges can be derived for chemical elements having up to a total =20 number of electrons, Z =3D 35. With R.E.D. III.x (version 3.x), the control of charge =20 constraints for atoms and groups of atoms in a molecule =20 (intra-molecule charge constraint) or between two molecules =20 (inter-molecule charge constraint and inter-molecular charge =20 equivalencing) has been incorporated allowing for the derivation of =20 the RESP and ESP atom charge values for molecule fragments and sets of =20 molecules. Fitting procedures involving multiple molecules, and for =20 each molecule, multiple conformations, and for each conformation, =20 multiple orientations, can now be automatically carried out. =20 Moverover, eight different charge derivation procedures using =20 different MEP computation algorithms (Connolly surface and CHELPG =20 algorithms) and different fitting procedures (with or without =20 hyperbolic restraints) are now available. Potentially, an infinite =20 number of approaches can be developed by simply changing a few words =20 in the R.E.D. III.x source code. Such procedures can be used in =20 simulations based on AMBER, CHARMM, GLYCAM and OPLS force fields. Once the R.E.D. execution is completed, the charge values are =20 available in Tripos mol2 file(s) which can be considered as precursors =20 of AMBER OFF and CHARMM RFT or PSF force field libraries. R.E.D. makes =20 the development of the 'RESP' and 'ESP' charges a straightforward, =20 simple and highly reliable procedure. R.E.D. interfaces the GAMESS-US or Gaussian program and RESP =20 program. R.E.D. III.x is now fully compatible with GAMESS-US, =20 PC-GAMESS/Firefly and Gaussian 1994, 1998 and 2003 versions. R.E.D. III.x is distributed with two other programs: - X R.E.D. is a graphical user-friendly interface, which has =20 been developed to graphically execute R.E.D. and modify R.E.D. =20 variables. - Ante_R.E.D. is a program useful for preparing R.E.D. =20 inputs, and in particular the "P2N" files. The P2N file format is a =20 new file format introduced with R.E.D. III. It corresponds to the PDB =20 file format with a second column of atom names. R.E.D. III.x, Ante_R.E.D.-1.1, and X R.E.D. III.1 constitute =20 the R.E.D. III.x tools. R.E.D. (versions 1, 2 and 3.x) and Ante_R.E.D. have been =20 written with the "Perl" programming language (See also the O'REILLY =20 web site), while X R.E.D. has been developed using the "tcl/tk" =20 programming language. "Perl" and "tcl/tk" are interpreted programming =20 languages, meaning that the programs written with these languages do =20 not need to be compiled. This makes R.E.D., Ante_R.E.D. and X R.E.D. =20 simple to use, highly flexible and portable. They have been tested on =20 PC-LINUX and SGI-IRIX workstations, and should work on all other UNIX =20 platforms. The R.E.D. III.x tools are not "FREE" programs (i. e. in the =20 sense of "freedom"; see the GNU web site for a clear definition). They =20 are provided at no cost for ACADEMIC users involved in NON-PROFIT =20 RESEARCH after signing a license. Industrial/COMMERCIAL users are =20 asked to pay 3000.00 ? for using the R.E.D.III.x tools. The PI =20 (Principal Investigator or Director) of a laboratory has to be =20 registered as a R.E.D. III or R.E.D. III.x user to be authorized to =20 download the R.E.D. III.x tools (indeed, we do not accept anymore user =20 agreement from students or post-doc). During the registration =20 procedure, the PI has to select a license among the four different =20 licenses available: (1) License for Academic user & Non-profit research - User from north =20 & south America, (2) License for Academic user & Non-profit research - User from Europe =20 & the rest of the world, (3) License for Profit research (academic & non-academic user) - User =20 > from north & south America, (4) License for Profit research (academic & non-academic user) - User =20 > from Europe & the rest of the world. Please, see the Register section from the R.E.D. home page to =20 register, and display these licenses. If you have questions about the R.E.D. III.x tools, please, =20 first check the documentation available (i. e. the manuals and FAQ). =20 Basic tutorials are available in the R.E.D. I and R.E.D. II manuals, =20 and new Tutorials have been written to describe Ante_R.E.D.-1.1, =20 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 =20 general public help is now provided with the q4md-forcefieldtools =20 mailing list. Any researcher can participate in this mailing list by =20 answering and/or sending queries at q4md-fft(-)q4md-forcefieldtools.org =20 after registration at sympa(-)q4md-forcefieldtools.org. To register in =20 the q4md-fft mailing list just send an email to =20 sympa(-)q4md-forcefieldtools.org with "subscribe q4md-fft" in the email =20 subject or body (to un-subscribe just send "unsubscribe q4md-fft"). =20 Archives of the q4md-fft mailing list are public. We are also registered in the AMBER and CCL mailing lists, =20 and we will answer to the queries about the q4md force field tools in =20 these two mailing lists as well. If you have any suggestions about the R.E.D. III.x tools or =20 if you find a bug, send us an e-mail: contact(-)q4md-forcefieldtools.org regards, Francois F.-Y. Dupradeau --- http://q4md-forcefieldtools.org/FyD/ From owner-chemistry@ccl.net Mon Jan 12 16:09:01 2009 From: "Curt M. Breneman brenec^_^rpi.edu" To: CCL Subject: CCL: First Announcement: ACS COMP Division's "Emerging Technologies in Computaional Chemistry" competition symposium - Sponsored by Schrodinger, Inc Message-Id: <-38417-090112160322-9259-CglknIgecFvzZMTVLsr37w/./server.ccl.net> X-Original-From: "Curt M. Breneman" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="us-ascii" Date: Mon, 12 Jan 2009 14:57:06 -0500 MIME-Version: 1.0 Sent to CCL by: "Curt M. Breneman" [brenec[-]rpi.edu] $1,000 prize to be awarded at the 238th ACS national meeting, Washington, D.C. The Computers in Chemistry Division (COMP) of the ACS will hold the eighth annual Symposium on Emerging Technologies in Computational Chemistry at the American Chemical Society National Meeting, Boston, MA, August 19-23, 2007. The objective of the symposium is to stimulate, reward, and publicize major methodological advances in computational chemistry. The talks will be evaluated by a Panel of Experts on the quality of the presentation and the impact that the research will have on the future of computational chemistry and allied sciences. The symposium is ideal for presenting your latest and best research on new techniques, applications and software development. Schrodinger, Inc. sponsors the $1,000 award for the best talk at the symposium. All are invited to participate. To enter the competition, please submit a regular short ACS abstract via http://oasys.acs.org/ prior to the OAsys deadline (believe it or not, OAsys opens for the Washington, D.C. meeting on January 19th). It is also necessary to email a long (~1,000-word) abstract to the organizer. The presentations must be original, novel and concise. After receipt, the long abstracts will be evaluated by experts to determine which individuals will be selected to give oral presentations at the symposium. Finalists will be notified well in advance of the meeting. Presentations submitted through OAsys that cannot be part of the Emerging Technologies Symposium will be rescheduled in another appropriate COMP session at the Washington meeting. Inquiries and applications should sent to: Prof. Curt M. Breneman Director, RECCR Center Department of Chemistry Rensselaer Polytechnic Institute Troy, NY 12180 E-mail: brenec_at_rpi.edu From owner-chemistry@ccl.net Mon Jan 12 17:19:01 2009 From: "Andrew Orry orry.molsoft * gmail.com" To: CCL Subject: CCL: Protein Structure and Drug Design Workshop - MolSoft February 5-6 2009 Message-Id: <-38418-090112145826-3789-nqkkuvMI1L6HN5S86lO+2Q : server.ccl.net> X-Original-From: Andrew Orry Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=windows-1252; format=flowed Date: Mon, 12 Jan 2009 11:59:26 -0800 MIME-Version: 1.0 Sent to CCL by: Andrew Orry [orry.molsoft-,-gmail.com] **We still have some places available at out MolSoft ICM Workshop: "Protein Structure and Drug Discovery" February 5th to 6th 2009 La Jolla, CA.** Please see the following invitation to attend MolSoft's (www.molsoft.com) Protein Structure and Drug Design Workshop on February 5th to 6th 2009 in La Jolla, California USA. For more information and a registration form visit www.molsoft.com/training.html. Our workshops are suitable for chemists and biologists who would like to learn more about computational drug discovery and bioinformatics. No prior knowledge in this field is required to participate. The workshop is presented by Prof. Ruben Abagyan (The Scripps Research Institute) and Dr. Maxim Totrov (MolSoft). The workshops will consist of lectures, demonstrations, and "hands-on" computational experiments and will cover the following topics: - Sequence and Protein Structure Analysis - Protein Modeling and Simulations - Structure Validation and Optimization - Ligand Binding Site Prediction - Small Molecule Docking and Virtual Ligand Screening - Structure-based development of target-specific compound libraries - Cheminformatics, Chemical Clustering, Searching, Superposition etc... - QSAR, Machine Learning - Protein-Protein Docking We will demonstrate and train you in the use of many of our new developments in computational chemistry and biology including: - 3D Ligand Editor - design and optimize ligands interactively - Markush Library Docking - Multiple Receptor Docking (A method to incorporate receptor flexibility) - Automated model building into electron density - Atomic property field chemical superposition - Fast machine learning tools for QSAR - Pharmacophore drawing and searching - Compound library enumeration tools - Screen-grabbing molecular movie making "The objective of this training workshop is to help chemists and biologists solve challenging problems in the area of drug discovery by efficient use of the science and technology present in ICM molecular modeling tools." Prof. Ruben Abagyan (The Scripps Research Institute and Co-Founder of Molsoft LLC) Please see our website at www.molsoft.com for more details or E mail andy~~molsoft.com or call (858) 625 2000 ext.108. Please join the ICM Discussion Forum: http://groups.google.com/group/molsoft-icm-forum Latest Newsletter: http://www.molsoft.com/news.html MolSoft is a La Jolla based company that is a primary source of new breakthrough technologies in computational chemistry and biology. Molsoft is committed to solving intellectually challenging problems in drug discovery and computational biology. From owner-chemistry@ccl.net Mon Jan 12 17:53:00 2009 From: "Curt M Breneman brenec###rpi.edu" To: CCL Subject: CCL: Please note meeting site and date correction - Re: First Announcement: ACS COMP Division's "Emerging Technologies in Computaional Chemistry" competition symposium - Sponsored by Schrodinger, Inc Message-Id: <-38419-090112173724-18669-KHIFoPfBwp2c13Y7XL4TnA^-^server.ccl.net> X-Original-From: "Curt M Breneman" Date: Mon, 12 Jan 2009 17:37:20 -0500 Sent to CCL by: "Curt M Breneman" [brenec[]rpi.edu] > "Curt M. Breneman brenec^_^rpi.edu" wrote: > > Sent to CCL by: "Curt M. Breneman" [brenec[-]rpi.edu] > > $1,000 prize to be awarded at the 238th ACS national meeting, Washington, > D.C. > > The Computers in Chemistry Division (COMP) of the ACS will hold the eighth > annual Symposium on Emerging Technologies in Computational Chemistry at the > American Chemical Society National Meeting, Washington, D.C., August > 15-20,2009. The objective of the symposium is to stimulate, reward, and > publicize major methodological advances in computational chemistry. > > The talks will be evaluated by a Panel of Experts on the quality of the > presentation and the impact that the research will have on the future of > computational chemistry and allied sciences. The symposium is ideal for > presenting your latest and best research on new techniques, applications > and software development. Schrodinger, Inc. sponsors the $1,000 award for > the best talk at the symposium. > > All are invited to participate. To enter the competition, please submit > a regular short ACS abstract via http://oasys.acs.org/ prior to the OAsys > deadline (believe it or not, OAsys opens for the Washington, D.C. meeting on > January 19th). It is also necessary to email a long (~1,000-word) abstract > to the organizer. The presentations must be original, novel and concise. > After receipt, the long abstracts will be evaluated by experts to determine > which individuals will be selected to give oral presentations at the > symposium. Finalists will be notified well in advance of the meeting. > Presentations submitted through OAsys that cannot be part of the Emerging > Technologies Symposium will be rescheduled in another appropriate COMP > session at the Washington meeting. > > Inquiries and applications should sent to: > Prof. Curt M. Breneman > Director, RECCR Center > Department of Chemistry > Rensselaer Polytechnic Institute > Troy, NY 12180 > E-mail: brenec_at_rpi.edu > > From owner-chemistry@ccl.net Mon Jan 12 18:43:01 2009 From: "TJ O Donnell tjo(_)acm.org" To: CCL Subject: CCL: Book: Design and Use of Relational Databases in Chemistry Message-Id: <-38420-090112183111-23817-AwYmHlWwywaDr900rWo5Hw|-|server.ccl.net> X-Original-From: "TJ O Donnell" Date: Mon, 12 Jan 2009 18:31:07 -0500 Sent to CCL by: "TJ O Donnell" [tjo:acm.org] Dear Colleagues, My new book, Design and Use of Relational Databases in Chemistry has just been published by CRC Press. It provides an introduction to databases and SQL. Rather than use examples of a business or general nature, the emphasis is on scientific data and chemical structure storage and searching. The focus is on the PostgreSQL database, but the disussion applies to any SQL database. I expect it will be of greatest interest to those of you who already use relational databases and wish to expand their usefulness. It should also provide a good introduction to those just starting with databases or those wanting a good overview of the topic. A web site is available at http://www.gnova.com/book This site is meant to accompany the book, not to provide a complete discussion of relational databases in chemistry. The web site provides a Table of Contents for the book and many SQL and other computer language examples. There are several demos available to allow structure searches, explore fragment methods and offer full database access after login credentials are requested. There is a link to amazon (click the book cover) if you are interested in purchasing the book. For more information, contact me at tjo,,gnova.com, or CRC press at http://crcpress.com/shopping_cart/products/product_detail.asp?sku=64428&isbn=9781420064421 TJ O'Donnell From owner-chemistry@ccl.net Mon Jan 12 19:20:01 2009 From: "Sachin Tyagi styagi2!=!uic.edu" To: CCL Subject: CCL:G: How to find bond dissociation energies? Message-Id: <-38421-090112191840-17868-ej/BuVQa6K54IBtIFaa5CQ . server.ccl.net> X-Original-From: "Sachin Tyagi" Date: Mon, 12 Jan 2009 19:18:36 -0500 Sent to CCL by: "Sachin Tyagi" [styagi2],[uic.edu] Hi all, I want to calculate and compare bond dissociation energies in two different organic molecules using gaussian03. Could you please tell me how exactly I can do it with examples if possible. I am synthetic chemist forced to do these calculations, so please forgive me if question appears to be trivial. Thank you all. Regards Sachin