From owner-chemistry@ccl.net Fri Jul 4 00:08:01 2008 From: "Antonio G De Crisci antonio.decrisci ~ utoronto.ca" To: CCL Subject: CCL:G: SCF is confused? Message-Id: <-37290-080704000638-8456-DOdPtMNg4UTE9qECz8C22w|-|server.ccl.net> X-Original-From: "Antonio G De Crisci" Date: Fri, 4 Jul 2008 00:06:34 -0400 Sent to CCL by: "Antonio G De Crisci" [antonio.decrisci[-]utoronto.ca] I also had this problem (for a UHF calculation). Using the quadratic SCF (as stated below: scf=qc or scf=xqc) and taking of symmetry by using the NoSymm keyword solved the issue for me. Hope that helps. Antonio De Crisci, Ph.D. Candidate Department of Chemistry University of Toronto > "McGaughey, Georgia B. georgia_mcgaughey*|*merck.com" wrote: > > Sent to CCL by: "McGaughey, Georgia B." [georgia_mcgaughey{}merck.com] > Sarah, > > Have you tried any other key words? For calculating dimer interactions > using MP2/aug-cc-pvdz, I typically use the Counterpoise=3D2 keyword (in > Gaussian) along w/ SCF=3D(qc,tight,maxcycle=3D512). I too had "SCF is > confused" in my output on occasion prior to adding in the SCF syntax. > > -Georgia=20 > > -----Original Message----- > > From: owner-chemistry!=!ccl.net [mailto:owner-chemistry!=!ccl.net]=20 > Sent: Monday, June 30, 2008 8:39 AM > To: McGaughey, Georgia B. > Subject: CCL:G: SCF is confused? > > > Sent to CCL by: "Sarah R Whittleton" [SWhittleton|dal.ca] > Hi CCL, > > I am trying to run a BSSE single-point calculation (counterpoise) using > MP2 on an organotin compound. The tin atom is described using the > Stuttgart ECP and an augmented, triple-zeta basis set. After running > for 11 hours the calculation dies uncompleted and the output (copied > below) says that Density matrix is not changing but DIIS error and the > SCF is confused. I have run similar calculations with the same method > on different organotin compounds and this is the only one giving me > trouble. I want to keep the method (MP2) and basis set consistent > between compounds is there anything I can do to make resolve this > problem and allow the calculations to complete normally? I have also > included the first lines of the input file for this calculation. > > I thank you all in advance for any suggestions, > Sarah Whittleton > =09 > ******************************** > Ph.D. Candidate > Department of Chemistry > Dalhousie University > Halifax, NS B3H 4J3 > > > THE END OF THE OUTPUT FILE: > The electronic state of the initial guess is 2-A. > of initial guess=3D 0.7500 > Requested convergence on RMS density matrix=3D1.00D-08 within 128 cycles. > Requested convergence on MAX density matrix=3D1.00D-06. > Requested convergence on energy=3D1.00D-06. > No special actions if energy rises. > Restarting incremental Fock formation. > Density matrix is not changing but DIIS error=3D 1.23D-06 > CofLast=3D-1.58D-02. > The SCF is confused. > Error termination via Lnk1e in /usr/local/gaussian/g03/l502.exe at Tue > Jun 24 22:30:03 2008. > Job cpu time: 0 days 11 hours 8 minutes 18.9 seconds. > File lengths (MBytes): RWF=3D 65118 Int=3D 0 D2E=3D 0 Chk=3D = > 8 > Scr=3D 1 > > > THE INPUT FILE: > %mem=3D2GB > %nprocs=3D3 > %chk=3DMP2-test.chk > # MP2/GenECP Pseudo=3DRead counterpoise=3D2 maxdisk=3D200GB > > > > -=3D This is automatically added to each message by the mailing script =3D-http://www.ccl.net/cgi-bin/ccl/send_ccl_messageSubscribe/Unsubscribe:=20Job: http://www.ccl.net/jobs=20http://www.ccl.net/spammers.txtNotice: This e-mail message, together with any attachments, contains > information of Merck & Co., Inc. (One Merck Drive, Whitehouse Station, > New Jersey, USA 08889), and/or its affiliates (which may be known > outside the United States as Merck Frosst, Merck Sharp & Dohme or > MSD and in Japan, as Banyu - direct contact information for affiliates is > available at http://www.merck.com/contact/contacts.html) that may be > confidential, proprietary copyrighted and/or legally privileged. It is > intended solely for the use of the individual or entity named on this > message. If you are not the intended recipient, and have received this > message in error, please notify us immediately by reply e-mail and > then delete it from your system. > > From owner-chemistry@ccl.net Fri Jul 4 06:44:01 2008 From: "elite elite158[#]gmail.com" To: CCL Subject: CCL: "Computational Medicinal Chemistry" Masters degree - Requesting sugges Message-Id: <-37291-080704064052-1037-hnR6G9kgjLoPyytDwVW8Og ~~ server.ccl.net> X-Original-From: "elite " Date: Fri, 4 Jul 2008 06:40:48 -0400 Sent to CCL by: "elite " [elite158-,-gmail.com] Dear CClers and academic stalwarts, I write to you this mail in anticipation of receiving your esteemed opinions. I have completed my graduate studies (4 years) in pharmaceutical sciences sometime back, and since then working in the same industry (for the past 4 years). My current employment is as a senior research associate in a training company which uses a certain commercial suite of software programs for training participants in 'computational molecular modeling and drug design'. I believe I have hit a dead-end with just a bachelors degree and I presume my career path would be good if I earn a masters degree in a relevant area. With afore mentioned academic history and work experience, I am currently looking for a Masters program, especially in the area of "computational medicinal chemistry". Also, after masters, I want to do an advanced program (perhaps a PhD) which would provide me required skills in the domain of computational nanotechnology. My current financial condition prohibits me from exploring any academic opportunity without proper graduate assistantship. It would be great if anyone could help me suggest a department that would provide me the required financial assistantship either through research or teaching and also would help me add value to the department through my previous work experience. Although I have spent considerable time looking through various University websites and searching using google, I still seek your kind pointers and helpful suggestions. Kindly excuse me if this mail seems to be naive. Regards, elite158 (at) g m a i l . c o m From owner-chemistry@ccl.net Fri Jul 4 09:58:01 2008 From: "Simon Halstead shalstead]*[hit.edu.cn" To: CCL Subject: CCL: MM3 forcefield format Message-Id: <-37292-080704001156-10425-bvNxekP5mXUoFpr+u4/7vQ(_)server.ccl.net> X-Original-From: "Simon Halstead" Date: Fri, 4 Jul 2008 00:11:52 -0400 Sent to CCL by: "Simon Halstead" [shalstead-#-hit.edu.cn] Dear all, I am trying to perform some simulations using the MM3 forcefield. However, I cannot find any explanation of the format of the forcefield. Could anyone please give me a brief description of the format of the forcefield (the form of the different terms and the various units too)? I already have all the different parameters, but unfortunately I only have access to journals that are available online. (My apologies if this is a repost, but I have not seen my original message appear) Thank you for your help, Simon Halstead From owner-chemistry@ccl.net Fri Jul 4 10:32:00 2008 From: "mohamed aish mhmdaish..yahoo.com" To: CCL Subject: CCL:G: Check file Message-Id: <-37293-080704101247-19395-zUfUj5h9O5ZahE99Nz7NbA],[server.ccl.net> X-Original-From: mohamed aish Content-Type: text/plain; charset=us-ascii Date: Fri, 4 Jul 2008 07:12:32 -0700 (PDT) MIME-Version: 1.0 Sent to CCL by: mohamed aish [mhmdaish|a|yahoo.com] Hi All; Can We use more than one check file in G03? If the answer is yes; please give examples for all possible cases. Thank you From owner-chemistry@ccl.net Fri Jul 4 12:38:01 2008 From: "Alessandro Curioni cur .. zurich.ibm.com" To: CCL Subject: CCL: NEW CPMD version 3.13.1 available for download Message-Id: <-37294-080704123235-8476-rqhiD4e5KPL0qU1fLkCUyA(0)server.ccl.net> X-Original-From: "Alessandro Curioni" Date: Fri, 4 Jul 2008 12:32:31 -0400 Sent to CCL by: "Alessandro Curioni" [cur.:.zurich.ibm.com] Dear Collegues, it is with pleasure to announce that finally the new cpmd version 3.13.1 is available for download - I suggest everybody to download and install the new version since it contains many improvement , new features and bug fixes. This version is accompanied by a significantly revised manual now including a small theory section, brief tutorials and other discussions of practical issues of the manual (thanks to A. Kohlmeyer and J. Hutter), an exteded pseudopotential library, more contributed tools ( e.g. metadynamics free energy surface reconstruction) and a developer automatic test suite ( thanks to G. Matthias and S. Ivanov). New functionality includes additional distributed linear algebra code for initialization, final wavefunction projection and Friesner diagonalization , mean free energy path search method, multiscale shock method, Langevin integrator for metadynamics with extended Lagrangian, calculation of non-adiabatic couplings, Landau-Zener Surface hopping, ROKS-based Slater transition-state density, linear-response DFPT with a ROKS-based reference state, simplified van der Waals correction according to Grimme, simplified ROKS input options with hard-wired variants of modified Goedecker algorithms for ROKS, PBEsol functional, ports to IBM Blue Gene/P and MacOS-X/x86, improved ultrasoft pseudopotential parallelization (VDB) (MPI and OpenMP), optimizations for scalar CPUs, new collective variables for metadynamics, variable cell support in DCD output, isotropic and zflexible cell for Parrinello-Rahman dynamics, damped dynamics and Berendsen thermostats for electrons, ions and cell, support for BO-MD with path integrals, support for completely reproducible outputs for CPMD TestSuite, consistent and updated unit conversions throughout the code, improved energy conservation in MD methods, spin-density Mulliken analysis, aClimax format output of vibrational frequencies, optimization scheme for Goedecker pseudopotential parameters for use as link atoms in QM/MM applications, support for QUENCH BO with PCG MINIMIZE when using VDB potentials, corrections for a number of serious bugs in the Gromos QM/MM code, use of PDB format coordinate files for amber2gromos, task group support for Gromos QM/MM with SPLIT option, BO-MD with EXTRAPOLATE WFN fully restartable, ASPC extrapolation for BO-MD, access to QM and MM energy in QM/MM calculations. I would like to thanks all the (many) people that helped for the shaping of this release and in particular M. Boero, A. Kohlmeyer, N. Nair, C. Bekas, J. Friedrichs, R. Vuilleumier, C. Mundy and J. Hutter. I take the occasion to ask your help for updates of the pubblication list as usual and wish you a good computing time with CPMD - Best Regards, Alessandro Curioni for the CPMD team From owner-chemistry@ccl.net Fri Jul 4 13:13:01 2008 From: "Geoffrey Hutchison geoffh+ ~ pitt.edu" To: CCL Subject: CCL:G: ANNOUNCE: Open Babel 2.2.0 Release Message-Id: <-37295-080704123739-8947-/wBuOQLm8k9jZPH8HyBrwQ ~~ server.ccl.net> X-Original-From: Geoffrey Hutchison Content-transfer-encoding: 8BIT Content-type: text/plain; charset=iso-8859-1 Date: Fri, 04 Jul 2008 12:37:28 -0400 (EDT) MIME-version: 1.0 Sent to CCL by: Geoffrey Hutchison [geoffh+- -pitt.edu] I am very happy to finally announce the release of Open Babel 2.2.0, the latest stable version of the open source chemistry toolbox. Open Babel has been downloaded over 80,000 times and use in over 30 open source chemistry tools. This release represents a major update and should be a stable upgrade, strongly recommended for all users of Open Babel. Highlights include improved force fields and coordinate generation, conformer searching, enhanced plugins including molecular descriptors, filters, and command- line transformations. Many formats are improved or added, including CIF, mmCIF, Gaussian cube, PQR, OpenDX cubes, and more. Improved developer API and scripting support and many, many bug fixes are also included. What's new? See the full release notes at: http://openbabel.org/wiki/Open_Babel_2.2.0 To download, see: http://openbabel.org/wiki/Install For more information, see the project website at: http://openbabel.org/ I would like to personally thank a few people for making this release a great one. In alphabetical order, Jean Bréfort, Andrew Dalke, Marcus Hanwell, Chris Morley, Noel O'Boyle, Kevin Shepherd, Tim Vandermeersch, and Ugo Varetto. This is a community project and we couldn't have made this release without you. Many thanks to all the contributors to Open Babel including those of you who submitted feedback, bug reports, and code. Cheers, -Geoff --- Prof. Geoffrey Hutchison Department of Chemistry University of Pittsburgh tel: (412) 648-0492 email: geoffh\a/pitt.edu web: http://hutchison.chem.pitt.edu/