From chemistry-request@server.ccl.net Tue Jan 4 15:16:18 2000 Received: from ccshst04.cs.uoguelph.ca (ccshst04.cs.uoguelph.ca [131.104.96.17]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id PAA11377 for ; Tue, 4 Jan 2000 15:16:18 -0500 Received: from ccshst01 (ccshst01.cs.uoguelph.ca [131.104.96.81]) by ccshst04.cs.uoguelph.ca (8.9.3/8.9.3) with SMTP id OAA03573 for ; Tue, 4 Jan 2000 14:22:54 -0500 (EST) Date: Tue, 4 Jan 2000 14:07:42 -0500 (EST) From: WeiQuan Tian X-Sender: wtian@ccshst01 To: CHEMISTRY@ccl.net Subject: Need help for ACSSCF SOC calculation in G98! Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear All: I used test301 in G98 to test the triplet SOC calculation ( I changed the original siglet to triplet). The following is the main output: ********************************************* %chk=test301 ------------------ #p uhf/sto-3g test ------------------ 1/38=1/1; 2/17=6,18=5/2; 3/11=2,25=1,30=1/1,2,3; 4/7=2/1; 5/5=2,32=1,38=4/2; 6/7=2,8=2,9=2,10=2,28=1/1; 99/5=1,9=1/99; Leave Link 1 at Tue Jan 4 13:56:24 2000, MaxMem= 0 cpu: 0.2 (Enter /g98/l101.exe) -------------------------------------------- Gaussian Test Job 301 (Part 1): FORMALDEHYDE -------------------------------------------- Symbolic Z-matrix: Charge = 0 Multiplicity = 3 C O 1 RCO X 1 1. 2 90. X 1 RCX 3 LXC 2 180. 0 H 4 RXH 1 LXH 3 180. 0 X 4 1. 5 90. 1 180. 0 H 4 RXH 6 90. 5 180. 0 Variables: RCX 0.595 RXH 0.9268 RCO 1.212 LXC 90. LXH 90. Leave Link 101 at Tue Jan 4 13:56:25 2000, MaxMem= 6291456 cpu: 0.3 (Enter /g98/l202.exe) ...... ...... %chk=test301 %nosave ------------------------------------------------------ #p cas(2,2,spin)/6-31g** 5d guess=read geom=check test ------------------------------------------------------ 1/29=2,38=1/1; 2//2; 3/5=1,6=6,7=101,8=1,25=1,32=1/1,2,3,19; 4/5=1,7=6,17=2,18=2,21=10/1,5; 5/5=2,17=11000000,28=2,32=1,47=2/10; 6/7=2,8=2,9=2,10=2,28=1/1; 99/5=1,9=1/99; Leave Link 1 at Tue Jan 4 13:56:39 2000, MaxMem= 0 cpu: 0.3 (Enter /g98/l101.exe) .... ..... Initial guess read from the checkpoint file: test301.chk Guess basis functions will be translated to current atomic coordinates. Initial guess orbital symmetries: Occupied (A1) (A1) (A1) (A1) (B2) (B1) (A1) (B2) (B1) Virtual (A1) (B2) (A1) (A1) (B1) (B2) (A1) (A1) (B1) (B2) (A1) (A1) (B1) (B2) (A1) (A2) (A1) (B1) (B2) (A1) (A1) (B1) (B2) (A1) (A2) (A1) (B2) (A2) (B2) Leave Link 401 at Tue Jan 4 13:56:53 2000, MaxMem= 6291456 cpu: 0.6 (Enter /g98/l405.exe) Truncation Level= 99999 a= 0 b= 2 c= 0 a=N/2 - s b=2s c=n- (a+b) no. active orbitals (n) 2 no. active ELECTRONS (N)= 2 SLATER DETERMINANT BASIS IRREPS TO BE RETAINED = 1 2 3 4 GROUP IRREP. MULT. TABLE 1 2 3 4 2 1 4 3 3 4 1 2 4 3 2 1 IRREP. LABELS FOR ORBITALS 4 3 BOTTOM WEIGHT= 3 TOP WEIGHT= 3 PRIMARY BASIS FUNCTION= 1 2 NO OF BASIS FUNCTIONS = 1 NO TO BE DELETED = 0 TAPE READ ERROR TAPE READ ERROR TAPE READ ERROR The calculation stayed at l405 for initionizing the MCSCF forever with the error : TAPE READ ERROR . This was the same for another triplet calculations. However, no problem with singlet calculation. Thanks a lot for any suggestion! Wei Quan Tian Univ. of Guelph Canada From chemistry-request@server.ccl.net Tue Jan 4 16:01:09 2000 Received: from socrates.cgl.ucsf.edu (socrates.cgl.ucsf.edu [128.218.27.3]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id QAA11550 for ; Tue, 4 Jan 2000 16:01:08 -0500 Received: (from ross@localhost) by socrates.cgl.ucsf.edu (8.9.3/8.9.3/GSC1.6) id LAA247561 for CHEMISTRY@ccl.net; Tue, 4 Jan 2000 11:52:33 -0800 (PST) Date: Tue, 4 Jan 2000 11:52:33 -0800 (PST) From: Bill Ross Message-Id: <200001041952.LAA247561@socrates.cgl.ucsf.edu> To: CHEMISTRY@ccl.net Subject: Announcing AMBER 6 It is with great pleasure that we announce the availability of AMBER 6. AMBER--one of the most widely licensed molecular modeling and simulation packages in the world--provides high powered facilities for a large number of new simulation-based methods. Highlights of AMBER 6 include many new and useful features, as detailed below. It is our belief that these new features add great value to AMBER and fully justify the introduction of a new version of the package. We hope you agree and choose to license AMBER 6. Note that funds from licensing AMBER 6 support research by the authors of the package, and thus your fees support further development of new features. The academic price for licensing is the same as for AMBER 5, $400. (This fee may be reduced or waived in special circumstances.) The industrial price is $20,000 for new licensees and $15,000 for those who have licensed AMBER 5. To proceed with ordering AMBER 6, go to the AMBER web site, http://www.AMBER.ucsf.edu/amber This site has much additional information, including the manual and tutorials. To order AMBER, you can download the license agreement from the web site, sign it, and send with an appropriate check or money order made out to the Regents of the University of California, to Willa Crowell (willa@cgl.ucsf.edu), Department of Pharmaceutical Chemistry, University of California, San Francisco, 94143. Overview of AMBER 6: AMBER 6 has a number of very exciting capabilities which should prove very powerful in structure-based ligand design and in the understanding of structure and free energy in any complex molecular system. New methods such as Chemical Monte Carlo/Molecular Dynamics (CMC/MD) allow the consideration of many molecules simultaneously and are a powerful complement to more qualitative approaches in drug design. One can imagine using DOCKing methods to screen databases of ligands and, after reducing the number of possible leads to leads ~100, using this method to more accurately estimate the binding free energy for these 100 compounds. Another major development has been the use of continuum methods combined with explicit MD and molecular mechanics. The method of computational Alanine scanning by Massova and Kollman (JACS, 121:8133, 1999) reflects the exciting possibility of modeling many protein mutants at once. In the era of genomics, use of MM-PBSA (Molecular mechanics- Poisson Bolzmann Surface Area) using molecular dynamics should lead to more accurate protein models and, when combined with homology modeled protein structures, should aid computer assisted design of tight binding ligands by making the protein structure more reliable and robust. The methodology of locally enhanced sampling (LES) has already been shown to be very powerful in protein structure refinement (Simmerling et al, JACS, submitted). New dynamics simulation methods to aid in ligand design(OWFEG and PROFEC) are available in AMBER 6. As additional bonuses, the excellent software for NMR refinement, the latest in force field models and parameters and the capabilities to model enzyme mechanisms (Stanton et al, JACS, 120:3448, 1998) are also part of the code. Below are some more technical details and references. An overview of some of the new capabilities of AMBER 6: 1. LES with PME AMBER 5 contained the capability for Locally Enhanced Sampling (LES) and Particle Mesh Ewald (PME), but not both together. These have been integrated and used in promising ways in prediction of RNA structure (Simmerling et al, JACS, 120:7149, 1998) and protein structure (Simmerling et al, JACS,submitted) as well as in free energy calculations of carbohydrate systems (Simmerling et al, JACS, 120:5771, 1998, and work in progress). We anticipate this methodology will be very powerful in structure prediction of complex molecules in solution, since, in contrast to most other methods, explicit water molecules can be included and thus the solvation effect considered at the highest level of accuracy. 2. CMC/MD Chemical Monte Carlo/Molecular Dynamics(CMC/MD) is a new approach to ligand design, which can consider many molecules at once and is a powerful complement to more qualitative approaches. In papers published by Pitera and Kollman (JACS, 120:7557, 1998) and by Eriksson et al. (J. Med. Chem., 42:868, 1999), it has been shown to be accurate and leads in both cases to a ligand which was predicted to bind more strongly to the target than the previous best one considered experimentally. 3. OWFEG free energy grid The OWFEG(One Window Free Energy Grid) method has been incorporated into the SANDER module of AMBER 6. OWFEG(Pearlman, J. Med. Chem., 42, 4313, 1999) allows one to generate an approximate free energy grid about any ligand from a single molecular dynamics trajectory. OWFEG is based on the PROFEC approach(Radmer and Kollman, J. Comput-Aided Mol. Des., 12,215, 1998), but has been generalized to be suitable for use with flexible ligands. As demonstrated in the OWFEG and PROFEC publications, such grids can provide very useful guidance in drug design. 4. MM-PBSA (Molecular Mechanics-Poisson Bolzmann/Surface Area) Case et al. (JACS 120:9401, 1998) have shown that a combination of molecular dynamics simulations and continuum calculations can be very powerful in estimating free energy differences even between systems on which one cannot use free energy perturbation calculations. This methodology is automated in AMBER 6. This method has proven to be very accurate in calculations of protein-ligand interactions (Chong et al, PNAS, in press), in protein-peptide interactions (Massova and Kollman, JACS, 121:8133, 1999), RNA-protein interactions (Reyes and Kollman, JMB, in press) and protein folding (Lee et al, Proteins, submitted.) 5. GB/SA Generalized Born surface area(GB/SA) is a way to put solvation effects implicitly into calculations of complex systems and recently Tsui and Case have incorporated this into AMBER 6 for use in minimization and molecular dynamics calculations. This approach allows one to greatly reduce the number of atoms in the system by representing solvent implicitly rather than explicitly. It is estimated that this saves more than an order of magnitude in simulations of proteins in aqueous solution. 6. Revised PME implementation AMBER 6 contains a major re-write of the particle-mesh-Ewald (PME) implementation for molecular dynamics in SANDER. This now accurately This now supports alternative box shapes(such as the truncated octahedron), allows polarizable potentials to be used in conjunction with PME and accurately conserves energy (in the NVE ensemble) over long trajectories. The user interface for PME calculations has been greatly simplified, so that in most cases the default parameters should give efficient yet acceptably accurate results. A variety of accuracy checks and comparisons to "regular" Ewald summation results are available. 7. NMR refinements NMR refinements can be carried out with restraints derived from residual dipolar coupling measurements or with "ambiguous" restraints whose corresponding NMR spectra are not fully assigned, or for "multiple-conformer" models generated using the LES algorithm. Routines to generate restraint input and to interface to NMR data-processing programs have been considerably expanded. 8. QM/MM Capabilities. The ROAR 2.0 module contains QM/MM capabilities to carry out QM/MM minimizations, MD simulations and reaction path following studies. Semiempirical (PM3, AM1 and MNDO) theory is used for the QM part of the calculations, while the AMBER force field is the MM part of the calculation. Minimization can be done using steepest descent, conjugate gradient or through the use of a limited memory BFGS approach. The latter approach can also be used in fully classical minimizations. 9. Multiple Time-Step (MTS) Capabilities The ROAR module contains the capability to carry out MTS simulations using the methodology of Berne and co-workers. Conservatively this allows a doubling of the time-step used, while is special cases much longer time-steps (e.g., 5fs) can be used. This option is also coupled with the Nose-Hoover Chain approach to constant T and P simulations and is designed to work with either standard Ewald or with PME. This option is only set up to run on condensed phases at this time. In addition to the capabilities in AMBER 6, a major effort is going on to broaden the applicability of the force field to more functional groups of organic molecules, such that one has an accurate representation of both the conformational and non-bonded interactions of any organic molecule. A paper in this area has been submitted to J. Comp. Chem. (Junmei Wang and PAK, submitted) and Wang is further developing the program ANTECHAMBER to enable efficient handling of many molecules at a time. AMBER authors David A. Case David A. Pearlman James W. Caldwell Thomas E. Cheatham, III Wilson S. Ross Carlos Simmerling Tom Darden Kenneth M. Merz Robert V. Stanton Ailan Chen James J. Vincent Mike Crowley Vicke Tsui Randall Radmer Yong Duan Jed Pitera Irina Massova George L. Seibel (for contributions to AMBER 3A) U. Chandra Singh (for contributions to AMBER 2 and 3) Paul Weiner (for contributions to AMBER 1) Peter A. Kollman From chemistry-request@server.ccl.net Tue Jan 4 16:25:16 2000 Received: from smtp.csc.fi (pobox5.csc.fi [193.166.0.99]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id QAA11632 for ; Tue, 4 Jan 2000 16:25:15 -0500 Received: from isosirri (isdn-60.csc.fi [193.166.2.60]) by smtp.csc.fi (8.9.3/8.9.3/CSC) with SMTP id WAA20826 for ; Tue, 4 Jan 2000 22:16:39 +0200 From: "Leif Laaksonen" To: "Chemistry@Ccl. Net" Subject: Numerical 2D program x2dhf (new version available) Date: Tue, 4 Jan 2000 22:18:36 +0200 Message-ID: MIME-Version: 1.0 Content-Type: multipart/mixed; boundary="----=_NextPart_000_0000_01BF5701.A5033D60" X-Priority: 3 (Normal) X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook IMO, Build 9.0.2416 (9.0.2910.0) Importance: Normal X-MimeOLE: Produced By Microsoft MimeOLE V5.00.2919.6600 This is a multi-part message in MIME format. ------=_NextPart_000_0000_01BF5701.A5033D60 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit Dear x2dhf Users, The newest version of the x2dhf program is available. The main corrections and extensions include: - homonuclear cases are treated correctly due to proper assignment of g/u symmetry, - multipole moments (dipole, quadrupole, octopole and hexadecapole) relative to the centre of mass are calculated as a default, - Gaussian94 program should provide good starting values for molecular orbitals due to cleaup of procedures reading its output files, - when initialization of molecular orbitals is done via the linear combination of atom-centred hydrogen-like functions the zeta parameter can be specified as either an effective nuclear charge or a nuclear charge screening factor (as readily obtained form the output of Froese-Fischer's MCHF program) - there are more examples (both closed and open-shell) of input data which should make the usage of the program easier. A number of minor changes were also incorporated in this version. For example, ttime routine should now work correctly on PCs running Linux and using g77, the table of atomic masses (see blk_data.inc) was updated and extended to fermium atom, etc. The program, documentation and examples are available for download at: http://www.csc.fi/~laaksone/2d/ The program is kindly provided by Dr. Jacek Kobus to whom all technical questions and comments should be sent. Yours, -leif laaksonen Ps. As you possible have seen the old http://laaksonen.csc.fi/ site has been closed down. The gOpenMol, YARL, x2dhf ... stuff can now be found at http://www.csc.fi/~laaksone/. ------=_NextPart_000_0000_01BF5701.A5033D60 Content-Type: text/x-vcard; name="Leif Laaksonen.vcf" Content-Transfer-Encoding: 7bit Content-Disposition: attachment; filename="Leif Laaksonen.vcf" BEGIN:VCARD VERSION:2.1 N:Laaksonen;Leif FN:Leif Laaksonen ORG:Center for Scientific Computing;FUNET TITLE:Network Information Services Manager NOTE:My personal Web page: http://www.csc.fi/~laaksone/ TEL;WORK;VOICE:+358 9 457 2378 TEL;CELL;VOICE:+358 +358400425203 TEL;WORK;FAX:+358 9 457 2302 ADR;WORK;ENCODING=QUOTED-PRINTABLE:;;Tekniikantie 15 a D=0D=0AP.O.Box 405;Espoo;;FIN-02101;Finland LABEL;WORK;ENCODING=QUOTED-PRINTABLE:Tekniikantie 15 a D=0D=0AP.O.Box 405=0D=0AEspoo FIN-02101=0D=0AFinland URL:http://laaksonen.csc.fi/ URL:http://www.csc.fi/ EMAIL;PREF;INTERNET:Leif.Laaksonen@csc.fi EMAIL;INTERNET:Leif.Laaksone@csc.fi REV:19991226T172416Z END:VCARD ------=_NextPart_000_0000_01BF5701.A5033D60-- From chemistry-request@server.ccl.net Tue Jan 4 18:04:30 2000 Received: from lrz.uni-muenchen.de (lsajca1-ar3-012-122.biz.dsl.gtei.net [4.3.12.122]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id SAA12162 for ; Tue, 4 Jan 2000 18:04:29 -0500 Received: (from eugene.leitl@localhost) by lrz.uni-muenchen.de (8.8.8/8.8.8) id OAA14725; Tue, 4 Jan 2000 14:50:44 -0800 Resent-From: Eugene Leitl MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Resent-Message-ID: <14450.31044.213957.508918@lrz.uni-muenchen.de> Resent-Date: Tue, 4 Jan 2000 14:50:44 -0800 (PST) Resent-To: , Message-Id: From: To: fork@xent.ics.uci.edu Subject: New SPEC benchmarks Date: Mon, 3 Jan 2000 12:58:50 +0100 (MET) From: Robert Harley SPECint95 and SPECfp95 are now superceded by CINT2000 and CFP2000: http://www.specbench.org/osg/cpu2000/results/cpu2000.html Good to see Alpha out there kicking ass as usual. Rob. From chemistry-request@server.ccl.net Tue Jan 4 13:57:21 2000 Received: from terra.ifi.unicamp.br (terra.ifi.unicamp.br [143.106.6.20]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id NAA11084 for ; Tue, 4 Jan 2000 13:57:17 -0500 Received: from ifi.unicamp.br (lua [143.106.6.13]) by terra.ifi.unicamp.br (8.9.3/8.9.3) with ESMTP id PAA09013 for ; Tue, 4 Jan 2000 15:46:31 -0200 (BDB) Received: (from daemon@localhost) by ifi.unicamp.br (8.9.3/8.9.3) id PAA14734 for ; Tue, 4 Jan 2000 15:46:31 -0200 (BDB) Received: from giselle.ifi.unicamp.br(143.106.72.217), claiming to be "giselle" via SMTP by lua.ifi.unicamp.br, id smtpdAAAa003aC; Tue Jan 4 15:46:30 2000 Message-Id: <4.1.20000104153801.00a36390@lua.ifi.unicamp.br> X-Sender: dasf@lua.ifi.unicamp.br X-Mailer: QUALCOMM Windows Eudora Pro Version 4.1 Date: Tue, 04 Jan 2000 15:43:52 -0200 To: CHEMISTRY@ccl.net From: Demetrio Antonio da Silva Filho Subject: G98 question Mime-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id NAA11085 Dear CCL'ers, Does anybody knows how can I set the total energy number of decimal places in a CIS calculation ( E(CIS) ) using G98? I need to increase this number to make energy comparisons. Thanks in advance, Demetrio FIlho _____________________________________ Demetrio A. da Silva Filho UNICAMP - IFGW Prédio D - Sala 17 CEP 13083-970 C.Postal 6165 Campinas - SP - Brasil _____________________________________ "Se não houver frutos, valeu a beleza das flores. Se não houver flores, valeu a sombra das folhas. Se não houver folhas, valeu a intenção da semente." Henfil From chemistry-request@server.ccl.net Wed Jan 5 05:05:16 2000 Received: from sc2a.unige.ch (sc2a.unige.ch [129.194.48.4]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id FAA15434 for ; Wed, 5 Jan 2000 05:05:15 -0500 Received: from pcdavid ([129.194.49.167]) by sc2a.unige.ch (PMDF V5.2-32 #37940) with SMTP id <01JKCAVZLOH000037G@sc2a.unige.ch> for chemistry@ccl.net; Wed, 5 Jan 2000 09:56:30 MET-DST Date: Wed, 05 Jan 2000 09:56:09 +0100 From: David De Vito Subject: ADF file visualisation To: chemistry@ccl.net Message-id: <004901bf575a$b6a67a60$a731c281@unige.ch> Organization: Quantum Chemical Labs MIME-version: 1.0 X-MIMEOLE: Produced By Microsoft MimeOLE V5.00.2314.1300 X-Mailer: Microsoft Outlook Express 5.00.2314.1300 Content-type: text/plain; charset=iso-8859-1 Content-transfer-encoding: 7bit X-Priority: 3 X-MSMail-priority: Normal Good Morning and Happy New Year !! I have heard that a it is possible to find in Internet an ADF-visualisation program for PC. Does anyone the address where I can find this "treasure" ? Thank you very much for your help ! Best regards, D. De Vito. **************************************************************** D. De Vito Department of Physical Chemistry Group of Prof. Weber (Computational Chemistry) University of Geneva Office 106 - Sciences II 30, Quai Ernest-Ansermet 1211 Geneva 4 / Switzerland +4122 / 702.65.35 (Office) +4122 / 328.92.16 (Home) +4176 / 532.47.40 (Mobile) http://lcta.unige.ch/~devito (Personal Page) http://www.unige.ch/sciences/chimie (Web Master) **************************************************************** From chemistry-request@server.ccl.net Wed Jan 5 10:41:44 2000 Received: from rrzd1.rz.uni-regensburg.de (root@rrzd1.rz.uni-regensburg.de [132.199.1.6]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id KAA17631 for ; Wed, 5 Jan 2000 10:41:43 -0500 Received: from kunz.chemie.ngate.uni-regensburg.de (rchnw3.chemie.uni-regensburg.de [132.199.48.203]) by rrzd1.rz.uni-regensburg.de (8.9.3/8.9.3-KLW-Linux-0.1) with ESMTP id PAA12141 for ; Wed, 5 Jan 2000 15:32:50 +0100 Received: from RCHNW3/SpoolDir by kunz.chemie.ngate.uni-regensburg.de (Mercury 1.44); 5 Jan 00 15:32:54 +0100 Received: from SpoolDir by RCHNW3 (Mercury 1.44); 5 Jan 00 15:32:48 +0100 From: "Georg Schmeer" Organization: Universitaet Regensburg To: CHEMISTRY@ccl.net Date: Wed, 5 Jan 2000 15:32:44 +0100 MIME-Version: 1.0 Content-type: text/plain; charset=US-ASCII Content-transfer-encoding: 7BIT Subject: Transition states Priority: normal X-mailer: Pegasus Mail for Windows (v2.54) Message-ID: <15C8F50562F9@kunz.chemie.ngate.uni-regensburg.de> Dear CCLers, during the calculation of the imidazole catalyzed ester hydrolysis in the gas phase with GAUSSIAN 94/98 we get, going from the reactants to the products, two saddle points - characterized by one neative eigenvalue of the Hessian matrix of the SCF-energy -, and one intermediate (local minimum of the SCF-energy) in between. The reaction paths were determined by IRC-calculations from the two transition states. The intermediate was found from both transition states and has a lower SCF-energy than the two transition states. Structurally the three structures are very similar. If we calculate the Gibbs energies, however, the G-values of the intermediate is higher than that of the transition states. In this context I have some questions: - Which energy (E-SCF or Delta-G) should be taken into account for the discussion of reaction energy barriers? - It seems, that the positive change in Delta-G is caused by the special degree of freedom, which has a negative Hessian eigenvalue in the transition state, and which contributes with positive sign to the vibrational partition function of the intermediate, having nearly the same strucuture. What are the consequences of this difference for the determination of the Gibbs energy of activation? - Does anyone met this problem, too? I would appreciate any comments and hints to this problem and will summarize the answers if possible. With best regards G.Schmeer Prof. Dr. Georg Schmeer Institut fuer Physikalische und Theoretische Chemie Universitaet Regensburg D-93040 Regensburg Georg.Schmeer@chemie.uni-regensburg.de Tel: 0941-943-4745 Fax: 0941-943-4532 From chemistry-request@server.ccl.net Wed Jan 5 10:06:07 2000 Received: from alpha.luc.ac.be (alpha.luc.ac.be [193.190.2.30]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id KAA17502 for ; Wed, 5 Jan 2000 10:06:07 -0500 Received: from sbg-ts (sbg-ts.luc.ac.be [193.190.1.15]) by alpha.luc.ac.be (8.9.3/8.9.3) with SMTP id OAA10443 for ; Wed, 5 Jan 2000 14:57:15 +0100 (MET) Date: Wed, 5 Jan 2000 14:57:15 +0100 (MET) Message-Id: <200001051357.OAA10443@alpha.luc.ac.be> X-Sender: skwasnie@mail.luc.ac.be X-Mailer: Windows Eudora Pro Version 2.1.2 Mime-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" To: chemistry@ccl.net From: sergiusz kwasniewski Subject: Summary of convergence problem with TDDFT in G98 Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id KAA17503 Hi all, Thanks for the many responses I got. I did not try any of the propositions yet, because of a temporary lack of cpu time. I'll keep you informed if I still can't manage to run the calculations... I've read about level shift in some CASPT2 calculations ... But if I'm not mistaken, this should be handled with care, and you would need some experience in it in order to be able to apply it in a correct way. What is it about actually ? Are there some nice references that cover this shift ? As mentioned before I would summarize all the answers that I would get to the following problem: (BTW: TD-DFT stands for time-dependent density functional theory) < I've been trying a TD-DFT calculation (SP) with Gaussian98 and I've got the following message: << Requested convergence on RMS density matrix=1.00D-08 within 64 cycles. Requested convergence on MAX density matrix=1.00D-06. Restarting incremental Fock formation. Restarting incremental Fock formation. Restarting incremental Fock formation. >>>>>>>>>> Convergence criterion not met. SCF Done: E(RB+HF-LYP) = -543.828916188 A.U. after 65 cycles Convg = 0.3546D+01 -V/T = 2.0021 S**2 = 0.0000 Convergence failure -- run terminated. Error termination via Lnk1e in /usr/local/bin/g98.a7/l502.exe >> What keyword is best used to be able to solve this problem ? >Maxcycle ? Perhaps it's a problem with the grid ? All suggestions are >welcome. I'll summarize. > ********** Hello serge, Obviously your criteria of convergence (convg) is not good at all, even after 65 cycles. Probably that the SCF procedure is oscillating. If it is so, it is useless to increase the number of cycles with the keyword "maxcyc". You could check it by introducing the keyword "p" in the command line and see how the SCF procedure behaves at each cycle. The complete command is: #p RHF/basis B3LYP ... Then, if the SCF procedure oscillates, you could try to apply a level shift. This is often usefull for large systems. The syntax is explained in the keyword "SCF". Hope this help, best wishes Pascal Boulet ********** Hi, to help you i need your input-line. These are just guesses: MAXCYCLE may be good, but sometimes even this wont work, then there could be something wrong with your starting geometry. by the way: what is a TD-DFT-Calculation?? hope you get along tim Jödicke ********** Dear Serge: I will use scf=qc (sometimes include maxcycle=XXXX XXXX: a larger number), although it takes me long time, it works. The usual thought is using scf=v-shift, but for non-degeneracy (non-near-degeneracy) and with large LUMO-HOMO gap, it's better to use qc. This problem occurs often for pure DFT( I mean no exact exchange mixed). Hope it helpful. Wei Quan Tian ********** Dear Sergiusz, I don't think that keywords like qc or am will help you. These errors occur mostly because of the stupid Hueckel guess. I would try to start >from a smaller unpolarized BS without any diffuse functions (and scf=(maxcycle=900) ). Afterwards you can read the guess from that calculation. If you are dealing with transition metals or huge pi-systems and a very small HOMO-LUMO gap, the vshift command might help. I hope that will help! Ciao, Alexander Wittkopp ********** Dear; Please use the iop option of iop(5/13=1) Although you fail the convergence of SCF uou can keep your calculation for TD-DFT and finally get some stuffs for excitations. Otherwise you can increase SCF cycle! Good luck! Ohyun Kwon ********** Dr. Kwasniewski, The information here is minimal so the analysis must of course be limited but given the fact that the convergence criteria is down only to 3.5 I highly doubt that increasing cycles will have any positive effect. You don't state which basis set you are trying or any details on the chemistry but I suspect you have a metal or some other system with low lying virtual and it may well be oscillating. Further you likely have an extended basis set which gives the SCF more degrees of freedom to flounder in. My best suggestion would be a series of calculations naming the checkpoint file and the recovering SCF information at each step. 1) #P B3LYP/STO-3g single point and look at the eigenvalues and make sure you have a HOMO/LUMO gap, best if eigenvalues change sign and the gap is 0.2 or greater. 2) If small or inverted HOMO/LUMO gap try # B3LYP/STO-3G Guess=Read STABLE=OPT to confirm you got the true ground state before continuing. 3) Once you are convinced you have the ground state use # B3LYP/6-31G(d) Guess=Read SCF=Tight or some other intermediate basis set with tighter SCF convergence. If the HOMO/LUMO gap is still small consider SCF=(Tight,VShift=300) to help control mixing. 4) Finally shift to your extended basis set. If you have a lot of diffuse functions consider adding SCF=(NoVarAcc,Tight) along with GUESS=Read. You can add TD at this point as well. If this is still not successful please let me know and include more details of the system. (Gaussian help ) ********** The optimal strategy depends on what actually happens. (1) The energy is almost constant (changing by 1E-6 a.u.). This might indicate you need a better integration grid (2) The energy osscillates. --> Try larger vshift (3) The energy is monotonic, but converges slowly --> Increase MaxCycle (4) Nothing helps. Run a HF calculation, and use the HF orbitals from the checkpoint file as starting orbitals in DFT ********** Hi Serge, probably you have a bad starting geometry. So you have two choices: first: Maybe the convergence will be reached within more than 64 cycles, so try the keyword "SCF(MaxCycle=200)" second: you can try to improve the geometry while reducing the cutoff values for the SCF procedure. So I would try the combination of keywords "SCF=Sleazy" and "Opt(MaxCycle=3)". Then you perform a geometry optimization with reduced cutoff values which takes 3 cycles and will provide you an improved geometry for further calculations. Bye Thomas Mehnert _________________________________________________ Sergiusz Kwasniewski LUC SBG/TS Universitaire Campus Gebouw D 3590 Diepenbeek BELGIUM tel(direct): 011/268315 fax : 011/268301 email : sergiusz.kwasniewski@luc.ac.be _________________________________________________ From chemistry-request@server.ccl.net Wed Jan 5 12:00:05 2000 Received: from mail1.manquehue.net (root@mail1.manquehue.net [216.72.16.5]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id MAA18096 for ; Wed, 5 Jan 2000 12:00:02 -0500 Received: from carlos (tc1-279.manquehue.net [216.72.18.22]) by mail1.manquehue.net (8.9.3/8.9.3) with ESMTP id MAA04805 for ; Wed, 5 Jan 2000 12:51:09 -0300 Message-Id: <200001051551.MAA04805@mail1.manquehue.net> From: "Carlos Robles V. " To: "=?ISO-8859-1?Q?Lista_de_Qu=EDmica?=" Subject: I'm looking for a translator Date: Wed, 5 Jan 2000 12:49:15 -0600 X-MSMail-Priority: Normal X-Priority: 3 X-Mailer: Microsoft Internet Mail 4.70.1155 MIME-Version: 1.0 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Hi, everybody: I have files which list topology of the molecule as a list of atoms (given as elements) and a list of bonds between them for example: atoms 8 atom C1 0.000 0.000 0.000 atom C2 0.000 0.000 0.000 atom H3 0.000 0.000 0.000 atom H4 0.000 0.000 0.000 atom H5 0.000 0.000 0.000 atom H6 0.000 0.000 0.000 atom H7 0.000 0.000 0.000 atom H8 0.000 0.000 0.000 bonds 7 bond C1 C2 simple bond C1 H3 simple bond C1 H4 simple bond C1 H5 simple bond C2 C1 simple bond C1 H6 simple bond C1 H7 simple bond C1 H8 simple bond H3 C1 simple bond H4 C1 simple bond H5 C1 simple As can you see, the coordinates values zero, so I need to translate my input file into a file with the real (or approximate) spacial coordinates for that molecule. I don't need a program that display the structure (I'll do by myself after). I know that there is a program called CONCORD http://www.tripos.com/software/concord.html which takes SMILEs and creates an approximate 3D structure. But i see that is a commercial program, and I need a freeware or shareware program (under LINUX), cause it's for educational and research purposes. Thanks a lot . Carlos Robles V. From chemistry-request@server.ccl.net Wed Jan 5 12:01:12 2000 Received: from chaos.cns.uni.edu (chaos.cns.uni.edu [134.161.241.2]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id MAA18128 for ; Wed, 5 Jan 2000 12:01:12 -0500 Received: from jim.macmillan (macmillan.chem.uni.edu [134.161.240.102]) by chaos.cns.uni.edu (8.9.1b+Sun/8.9.1) with SMTP id JAA13649 for ; Wed, 5 Jan 2000 09:48:01 -0600 (CST) Reply-To: From: "James G. Macmillan" To: Subject: Software for a PC Cluster Date: Wed, 5 Jan 2000 09:50:22 -0600 Message-ID: <000701bf5794$936c7c40$66f0a186@jim.macmillan> MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit X-Priority: 3 (Normal) X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook 8.5, Build 4.71.2173.0 X-MIMEOLE: Produced By Microsoft MimeOLE V4.72.2106.4 Importance: Normal CCL, Could someone give me some advice on software that runs under linux on a PC Parallel Cluster? My experience is with SPARTAN under UNIX and NT. Several people in Math, Physics, and Computer Science are planning a PC Cluster and I have been asked what software I might what to use on the system. Since SPARTAN does not compile under linux I will need to find a software package. You may want to send your replies directly to me as I am not sure this is of general interest. Jim Macmillan ********************************************** James G. Macmillan, Ph.D. Department of Chemistry University of Northern Iowa Cedar Falls, IA 50614-0423 Ph: (319) 273-2476 FAX: (319) 273-7127 E-mail: macmillan@uni.edu ICQ: 10405682 ******************************************** Wine improves with age. The older I get, the better I like it. - Anonymous From chemistry-request@server.ccl.net Wed Jan 5 12:46:31 2000 Received: from mail2.organik.uni-erlangen.de (lesath.chemie.uni-erlangen.de [131.188.127.212]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id MAA18495 for ; Wed, 5 Jan 2000 12:46:30 -0500 Received: from wtewael.chemie.uni-erlangen.de (wtewael [131.188.127.223]) by mail2.organik.uni-erlangen.de (8.8.8/8.1.4-FAU) with ESMTP id RAA12233; Wed, 5 Jan 2000 17:35:44 +0100 (MET) Received: (from wdi@localhost) by wtewael.chemie.uni-erlangen.de (8.8.7/8.1.59-FAU) id QAA22435; Wed, 5 Jan 2000 16:35:47 GMT From: "Wolf-Dietrich Ihlenfeldt" Message-Id: <10001051735.ZM22433@torvs.ccc.uni-erlangen.de> Date: Wed, 5 Jan 2000 17:35:45 +0000 In-Reply-To: "Carlos Robles V. " "CCL:I'm looking for a translator" (Jan 5, 12:49) References: <200001051551.MAA04805@mail1.manquehue.net> Reply-To: Wolf-Dietrich.Ihlenfeldt@CCC.Chemie.Uni-Erlangen.DE X-Phones: +49-9131-85-26579 X-Fax: +49-9131-85-26566 X-Mailer: Z-Mail (3.2.3 08feb96 MediaMail) To: "Carlos Robles V. " Subject: Re: CCL:I'm looking for a translator Cc: Johann.Gasteiger@CCC.Chemie.Uni-Erlangen.DE, Christof.Schwab@CCC.Chemie.Uni-Erlangen.DE, CHEMISTRY@ccl.net Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 8bit On Jan 5, 12:49, Carlos Robles V. wrote: > Subject: CCL:I'm looking for a translator > Hi, everybody: > > I have files which list topology of the molecule as a list of > atoms (given as elements) and a list of bonds between them > for example: > > atoms 8 > atom C1 0.000 0.000 0.000 > atom C2 0.000 0.000 0.000 > atom H3 0.000 0.000 0.000 > atom H4 0.000 0.000 0.000 > atom H5 0.000 0.000 0.000 > atom H6 0.000 0.000 0.000 > atom H7 0.000 0.000 0.000 > atom H8 0.000 0.000 0.000 > > bonds 7 > bond C1 C2 simple > bond C1 H3 simple > bond C1 H4 simple > bond C1 H5 simple > bond C2 C1 simple > bond C1 H6 simple > bond C1 H7 simple > bond C1 H8 simple > bond H3 C1 simple > bond H4 C1 simple > bond H5 C1 simple > > As can you see, the coordinates values zero, so I need to translate my > input file into a file with the real (or approximate) spacial coordinates > for that molecule. I don't need a program that display the structure (I'll > do by myself after). I know that there is a program called CONCORD > > http://www.tripos.com/software/concord.html > > which takes SMILEs and creates an approximate 3D structure. But i see that > is a commercial program, and I need a freeware or shareware program (under > LINUX), cause it's for educational and research purposes. If your structures are not top secret, and you feel comfortable to transfer them via the Internet, you are welcome to use our free CORINA coordinate generator (http://www2.ccc.uni-erlangen.de/services/3d.html) through its Web interface or an email-based batch processor. Alternatively, you could also download the 'csed' molecule editor ( contained in ftp://www2.ccc.uni-erlangen.de/pub/cactvs/Linux2.2/cactvstools-Linux2.2-3.58.tar.gz ), which allows you to draw a structure in 2D and then have the CORINA coordinates computed remotely on our server in realtime. Note that this feature only works if you are not behind a firewall (ports 16520 and 16521 must be open) > > Thanks a lot . > > Carlos Robles V. >-- End of excerpt from Carlos Robles V. -- Dr. Wolf-D. Ihlenfeldt Computer Chemistry Center, Institute for Organic Chemistry, University of Erlangen-Nuremberg Naegelsbachstrasse 25, D-91052 Erlangen (Germany) Tel (+49)-(0)9131-85-26579 Fax (+49)-(0)9131-85-26566 http://www2.ccc.uni-erlangen.de/wdi/ From chemistry-request@server.ccl.net Wed Jan 5 11:19:06 2000 Received: from lightning.mgl.ca (root@lightning.mgl.ca [216.94.24.2]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id LAA17913 for ; Wed, 5 Jan 2000 11:19:06 -0500 Received: from server1.nanodesign.com (www.nanode.com [216.94.27.130]) by lightning.mgl.ca (8.8.5/8.6.12) with ESMTP id KAA09938 for ; Wed, 5 Jan 2000 10:22:42 -0500 Received: by server1.nanodesign.com with Internet Mail Service (5.0.1457.3) id ; Wed, 5 Jan 2000 10:10:50 -0500 Message-ID: From: Miklos Feher To: "'chemistry@server.ccl.net'" Subject: quantum chemistry textbook Date: Wed, 5 Jan 2000 10:10:47 -0500 X-Priority: 3 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.0.1457.3) Content-Type: text/plain Dear All, I posted a message yesterday on the CCL about our new textbook in quantum chemistry. The response was very positive but almost everyone pointed out that $150 is far too expensive for students. Unfortunately, the price of the book is not under our control. I discussed this issue with the publisher last month when the price became known. They ensured me that they give substantial discounts (around 50%) in two cases: if 6 or more copies are ordered simultaneously, or to individual students if the book is adopted for a course. They are also prepared to send inspection copies to those interested in adopting the book for a course, Kluwer should be contacted directly with the request. Thanks very much to all those who responded. Miklos ************************************************ Dr. Miklos Feher senior scientist, computational chemistry Nanodesign Inc., Suite 300, Research Park Centre 150 Research Lane, Guelph, ON, N1G 4T2, Canada Tel: 519-823-9088 Fax: 519-823-9401 e/mail:mfeher@nanodesign.com ************************************************ From chemistry-request@server.ccl.net Wed Jan 5 14:08:33 2000 Received: from mailhost.lanl.gov (mailhost.lanl.gov [128.165.3.12]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id OAA19354 for ; Wed, 5 Jan 2000 14:08:32 -0500 Received: from [128.165.22.209] (machgs.lanl.gov [128.165.22.209]) by mailhost.lanl.gov (8.9.3/8.9.3/(cic-5, 2/8/99)) with SMTP id KAA02057 for ; Wed, 5 Jan 2000 10:59:41 -0700 X-Sender: schrecke@t12mail.lanl.gov Message-Id: Mime-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Date: Wed, 5 Jan 2000 11:02:11 -0600 To: CHEMISTRY@ccl.net (CCL) From: schrecke@t12.lanl.gov (Georg Schreckenbach) Subject: Scalar vs. SO relativistic effects Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id OAA19355 Dear all, I got the following message as a response to my earlier post (included below). I thought that it might be of some general interest, so I am posting it, with permission, to the general list. Best regards, Georg >Dear Georg, > >I ws interested in your response below, and wanted to bring to your >attention a couple of papers that Clint Nash and I published this year on a >wonderful ficititious molecule [118]F4 (the paper was published _before_ >[118] was discovered!). With scalar relativistic effects we predict the >molecule to be square planar like XeF4. But when SO effects are included, >the molecule very slightly prefers a tetrahedral geometry. > >The relevant papers: > >C. S. Nash and B. E. Bursten, “Spin-Orbit Coupling vs. the VSEPR Method: >On the Possibility of a Nonplanar Structure for the Super-Heavy Noble-Gas >Tetrafluoride [118]F4,” Angew. Chem., 111, 115-117 (1999); Angew. Chem. >Int. Ed. Engl., 38, 151-153 (1999). > >C. S. Nash and B. E. Bursten, “Spin-Orbit Effects, VSEPR Theory, and the >Electronic Structures of Heavy and Superheavy Group IVA Hydrides and Group >VIIIA Tetrafluorides. A Partial Role Reversal for Elements 114 and 118,” >J. Phys. Chem. A, 103, 402-410 (1999). > >I hope you find them of interest. > >Best regards, Bruce > >>Date: Mon, 3 Jan 2000 11:34:30 -0600 >>To: CHEMISTRY@ccl.net (CCL) >>From: schrecke@t12.lanl.gov (Georg Schreckenbach) >>Subject: CCL:so effects on geometry (was: high-quality GAMESS-US basis set >for >>iodine?) >> >>Dear Valentin and CCL, >> >>>Does anybody know appropriate references on what effect: scalar- >>>relativistic or spin-orbit has more effect on geometry? >> >>There is one paper out by van Lenthe et al. where they compared scalar and >>spin-orbit effects on the geometry and other properties of small molecules. >>For instance, for I2, they find a difference in bond length of 0.019 >Angstrom, >>one of the largest for the set of molecules considered. So, the conclusion >>was that the influence of spin-orbit effects on the geometry of closed- >>shell molecules is modest only. The same is not true, of course, for other >>properties including energetics or NMR. The reference is JCP 1996, 105, 6505. >> >> Besides, it is clear that one needs scalar relativistic effects to get the >>geometries right, cf., e.g., the classic 1988 Chem Rev. review by Pyykkö. >This, >>then, is a point in favor of ECP basis sets for something as heavy as iodine >>:-) >> >>>In most cases using ECP usually gives better agreement in geometry >>>compared to all-electron calculations for iodine containing molecules. >>>For example, one may take a look at recent publications with Stuttgart >>>ECP basis set on iodine. >> >>Best regards, Georg >> >* * * * * * * * * * * * * * * * * * >Bruce E. Bursten >Distinguished University Professor and Department Chair >Department of Chemistry >The Ohio State University >100 W. 18th Avenue >Columbus, OH 43210 > >Chair's office: (614) 292-6723 > (614) 292-3311 >Research office: (614) 292-1866 (voice) > (614) 688-3306 (fax) >E-mail: bursten.1@osu.edu > -- ============================================================== Dr. Georg Schreckenbach Tel: (USA)-505-667 7605 Theoretical Chemistry T-12 FAX: (USA)-505-665 3909 M.S. B268, Los Alamos National E-mail: schrecke@t12.lanl.gov Laboratory, Los Alamos, New Mexico, 87545, USA Internet: http://www.t12.lanl.gov/home/schrecke/ ============================================================== From chemistry-request@server.ccl.net Wed Jan 5 15:38:40 2000 Received: from france.chem.duke.edu (france.chem.duke.edu [152.3.169.99]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id PAA19664 for ; Wed, 5 Jan 2000 15:38:39 -0500 Received: from primo.chem.duke.edu (primo [152.3.170.1]) by france.chem.duke.edu (8.9.3/8.9.3) with ESMTP id OAA25846 for ; Wed, 5 Jan 2000 14:29:48 -0500 (EST) Received: from localhost (shubin@localhost) by primo.chem.duke.edu (8.9.3+Sun/8.9.1) with ESMTP id OAA06795 for ; Wed, 5 Jan 2000 14:29:48 -0500 (EST) X-Authentication-Warning: primo.chem.duke.edu: shubin owned process doing -bs Date: Wed, 5 Jan 2000 14:29:47 -0500 (EST) From: ShuBin Liu X-Sender: shubin@primo To: chemistry@ccl.net Subject: CCL: TDDFT for multiplets Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi, All CCLers: When I perform time-dependent DFT calculations for the singlet or triplet state of some molecule, following error often comes up: !!!Fatal Error: The smallest alpha delta epsilon is -0.30057073D+00 I understand that this line is from L801 when orbital coefficients are checked and can be bypassed by using iop(8/11=1). My questions are why this happens and how one can fix it. If you know the answers to these questions, please kindly let me know. Thank you in advance! Shubin ======================================================================== Shubin Liu, Ph.D. Research Associate Tele: 919-660-1531(Office) Department of Chemistry 919-929-6856(Home) Duke University Email:shubin@chem.duke.edu Durham, North Carolina 27768-0348 shubin@email.unc.edu USA URL: http://www.unc.edu/~shubin ========================================================================