From owner-chemistry@ccl.net Thu Nov 24 12:40:01 2011 From: "Olivier roy oliroy63^_^gmail.com" To: CCL Subject: CCL: G09 - PES scan followed by SP at higher level for every scan point Message-Id: <-45920-111124085333-17482-Meeuiruwx+L00SgORBgwGg..server.ccl.net> X-Original-From: "Olivier roy" Date: Thu, 24 Nov 2011 08:53:30 -0500 Sent to CCL by: "Olivier roy" [oliroy63---gmail.com] Dear CCL Users, I would like to do a PES scan (on a dihedral angle) at HF/6-31G(d) level followed by single point energy calculation at B3LYP/6-311G+(d,p) level for every scan point. I have tried this route: # B3LYP/6-311G+(d,p)//HF/6-31G(d) geom=modredundant But the single point is done only for the last scan point. Could you help me. thx O. Roy From owner-chemistry@ccl.net Thu Nov 24 15:00:00 2011 From: "FyD fyd*_*q4md-forcefieldtools.org" To: CCL Subject: CCL: q4md-forcefieldtools.org announcement Message-Id: <-45921-111124115939-7625-pNhmntXPTuOr6ODLLFC6aQ- -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: Thu, 24 Nov 2011 17:59:29 +0100 MIME-Version: 1.0 Sent to CCL by: FyD [fyd- -q4md-forcefieldtools.org] Dear All, I am pleased to announce the official release of the latest developments at http://q4md-forcefieldtools.org. q4md-forcefieldtools.org regroups an ensemble of tools, server, database and tutorials related to empirical force field developments. Theses developments are designed for the AMBER and GLYCAM force fields, but can also have applications in CHARMM and OPLS force field based simulations. At the basis of our work is the RESP and ESP charge Derive (R.E.D.) program devoted to RESP and ESP charge derivation and force field library building for new molecules and potentially any type of molecular fragments. The approach leads to reproducible charge values independently of the quantum chemistry program interfaced or initial structure chosen by the user. In complex approaches, multiple molecules, multiple conformations and multiple orientations are involved in charge derivation and force field library building, and a large set of force field libraries or Force Field Topology DataBase (FFTopDB) is generated. The procedure is now compatible with any type of biomolecules and bioinorganic molecules (nucleic acids, proteins, glycoconjugates, organic and bioinorganic structures in the ground or excited states; covalently or non-covalently bound; natural structures as well as chemically engineered or artificial analogs). . The standalone version of the R.E.D. tools is available at http://q4md-forcefieldtools.org/RED/. . R.E.D. Server available at http://q4md-forcefieldtools.org/REDS/ is a Web server, which provides all required software and hardware for charge derivation and force field library building. It interfaces the latest versions of the Ante_R.E.D. and R.E.D. programs. . R.E.DD.B. is a database of RESP and ESP charges and force field libraries available at http://q4md-forcefieldtools.org/REDDB/. . Related tutorials are at http://q4md-forcefieldtools.org/Tutorial/. * New web tools have been developed in R.E.D. Server allowing the automatic and simultaneous generation of force field libraries for the nucleotide or amino-acid fragments. . N-terminal, C-terminal and central fragments for a new amino-acid residue from a single dipeptide http://q4md-forcefieldtools.org/Tutorial/Tutorial-3.php#25 . 5'-terminal, 3'-terminal and central fragments for a new nucleotide residue from a single nucleoside http://q4md-forcefieldtools.org/Tutorial/Tutorial-3.php#27 * A new R.E.D. Server version named "R.E.D. Server Development" has been developed. R.E.D. Server Development allows RESP and ESP charge derivation and force field library building for new molecules and fragments involving all the elements of the periodic table. Several user defined options have been also incorporated in this server. See http://q4md-forcefieldtools.org/REDS-Development/ http://q4md-forcefieldtools.org/REDS-Development/faq.php http://q4md-forcefieldtools.org/REDS-Development/faq.php#17 * New R.E.DD.B. features have been developed representing the first step toward R.E.DD.B. 2.0, a database of Force Field Topology DataBase. New scripts have been written allowing the automatic submission in R.E.DD.B. of data generated by the R.E.D. tools and R.E.D. Server. See http://q4md-forcefieldtools.org/REDDB/faq.php#5 PubMed ID indexation is now incorporated in R.E.DD.B. New Force Field Topology DataBases are available. Among others see representative examples: http://q4md-forcefieldtools.org/REDDB/projects/F-88/ http://q4md-forcefieldtools.org/REDDB/projects/F-87/ http://q4md-forcefieldtools.org/REDDB/projects/F-85/ * A new force field library file format has been developed within the LEaP program (AmberTools 1.5). The mol3 force field library file format was developed. This file format merge some advantages of the Tripos mol2 and AMBER OFF file formats within t/xLEaP. See http://q4md-forcefieldtools.org/Tutorial/leap-mol3.php * Updated RESP version 2.2 for charge fitting for metal complexes and large set of molecules, conformations and orientations. See http://q4md-forcefieldtools.org/RED/resp/ * Tutorials have been updated accordingly to these new features. * The articles describing R.E.DD.B., R.E.D. and R.E.D. Server are all freely available under the following PubMed Central reference number: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2238896/ http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2918240/ http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3125739/ All our tools and data are open to all, and are in agreement with the GNU General Public License 3.0. regards, Francois F.-Y. Dupradeau --- http://q4md-forcefieldtools.org/FyD/