From chemistry-request@server.ccl.net Tue Feb 13 01:17:04 2001 Received: from mcmail.cis.mcmaster.ca ([130.113.64.66]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f1D6H3w17965 for ; Tue, 13 Feb 2001 01:17:03 -0500 Received: from localhost (mattacf@localhost) by mcmail.cis.mcmaster.ca with ESMTP id BAA09055 for ; Tue, 13 Feb 2001 01:14:48 -0500 (EST) Date: Tue, 13 Feb 2001 01:14:48 -0500 (EST) From: "C.F. Matta" To: CHEMISTRY@ccl.net Subject: Volume of a molecule contained within an isosurface In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi everyone, I wonder is someone knows of a free program that calculates the volume of a molecule contained within a particular density envelope (e.g. the 0.001 a.u. density envelope) from a GAUSSIAN94 wavefunction or cube ? ( The volume I want to calculate is the INTEGRATED volume within the envelope of choice AND NOT the volume computed from intersecting spheres NOR the "solvent accessible volume"). Thank you very much, I will summarize the answers. Cherif ___________________________________________________________________________ Cherif F. Matta tel. (905) 525-9140 ext. 22502 Chemistry Department fax (905) 522-2509 McMaster University Hamilton, Ontario, CANADA L8S 4M1. ___________________________________________________________________________ From chemistry-request@server.ccl.net Tue Feb 13 01:27:06 2001 Received: from century.fen.bilkent.edu.tr (century.fen.bilkent.edu.tr [139.179.97.100]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f1D6R4w18020 for ; Tue, 13 Feb 2001 01:27:05 -0500 Received: from pinar (pinar [139.179.97.99]) by century.fen.bilkent.edu.tr (8.9.1/8.9.1) with ESMTP id IAA25782; Tue, 13 Feb 2001 08:26:22 +0200 (EET) Date: Tue, 13 Feb 2001 08:32:47 +0200 (EET) From: Ulrike Salzner X-Sender: salzner@pinar To: Christos Garoufalis cc: CHEMISTRY@ccl.net Subject: Re: CCL:g98 oscillator strengths In-Reply-To: <002201c094f8$fde7c8c0$0b9e8c96@milon.physics.upatras.gr> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII There is a brand new article by Hsu, Hirata, and Head-Gordon, J. Phys. Chem. A, 2001, 105, 451-458 on TDDFT excitation energies and oscillator strength of linear polyenes. There are also references and comparisons with other methods and wit experiment. Best wishes, Ulrike Salzner =================================================================== Dr. Ulrike Salzner Associate Professor Department of Chemistry Tel.: (312) 290-2122 Bilkent University Fax.: (312) 266-5097 06533 Bilkent, Ankara e-mail: salzner@fen.bilkent.edu.tr Turkey ==================================================================== On Mon, 12 Feb 2001, Christos Garoufalis wrote: > Dear CCL'ers > How reliable are the oscillator strengths derived by a TDDFT > calculation with g98? Does anyone has any experience with it? And how can one force g98 to print them out > with more decimal digits? > > Thanks in advance > _________________________ > C. S. Garoufalis, > Department of Physics, > University of Patras, Greece > _________________________ > From chemistry-request@server.ccl.net Tue Feb 13 03:17:37 2001 Received: from gate.syntem-sa.fr (gate.syntem-sa.fr [146.19.248.65]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f1D8HZw18311 for ; Tue, 13 Feb 2001 03:17:35 -0500 Received: (from uucp@localhost) by gate.syntem-sa.fr (980427.SGI.8.8.8/980728.SGI.AUTOCF) id JAA80432; Tue, 13 Feb 2001 09:14:31 +0100 (MET) Received: from syntem-sa.fr(10.0.0.2) by gate.syntem-sa.fr via smap (4.1) id xma180812; Tue, 13 Feb 01 09:14:14 +0100 Received: from victoria.syntem-sa.fr (victoria.syntem-sa.fr [10.0.0.44]) by laetitia.syntem-sa.fr (980427.SGI.8.8.8/980728.SGI.AUTOCF) via ESMTP id JAA57337; Tue, 13 Feb 2001 09:11:45 +0100 (MET) Received: from syntem-sa.fr (localhost [127.0.0.1]) by victoria.syntem-sa.fr (980427.SGI.8.8.8/980728.SGI.AUTOCF) via ESMTP id JAA11192; Tue, 13 Feb 2001 09:17:20 +0100 (MET) Sender: dturner@syntem-sa.fr Message-ID: <3A88ED90.89EC1676@syntem-sa.fr> Date: Tue, 13 Feb 2001 09:17:20 +0100 From: David Turner Reply-To: dturner@syntem.com Organization: Computational Drug Design, Syntem X-Mailer: Mozilla 4.7C-SGI [en] (X11; I; IRIX 6.5 IP32) X-Accept-Language: en MIME-Version: 1.0 To: Ivan CC: chemistry@ccl.net Subject: Re: CCL:Second negative frequency References: <003401c09484$54ceb240$71df05d4@duron-k-7> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Your second value (36 cm-1) could easily be positive given the error associated with normal mode calculations (+/-50 cm-1 or so). Perhaps you have only one imaginary frequency ... David Ivan wrote: > > Dear CCL'ers > > I am working with programme GAMESS and an present time I am facing some > problems with TS.I am simulating H-transfer from NH3 bonded to the rest of > molecule to another "free" NH3 forming "free"NH4. > In TS there are two imaginary frequencies ( 1. - value about 975, that > correspond to H-transfer and 2.- value about 36 ) and can't get rid of > this second little negative frequency. Firstly I tried to use keywords > PURIFY in $STATPT and $FORCE groups to purify hessian matrix but with no > results. Then I tried several approachs to find better TS, but all resulted > to the same TS. And IRC calculations in both directions are correct, because > according to IRC's this TS connects appropriate minimas on both side of the > hill.Finally I wanted to to perform IRC folowing the second negative > frequency, but GAMESS did not accept the specified frequency ( in $IRC > group ). > > I would very appreciate any help,advice or trick. > > Stanislav Ivan > student > > -= This is automatically added to each message by mailing script =- > CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins > MAILSERV@ccl.net -- HELP CHEMISTRY or HELP SEARCH > CHEMISTRY-SEARCH@ccl.net -- archive search | Gopher: gopher.ccl.net 70 > Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net -- ________________________________________________________________ David Turner Synt:em Senior Modeling Scientist Parc Scientifique G.Besse Computational Drug Discovery 30000 Nimes email: dturner@syntem.com France Tel: Switchboard: +33 (0)4 66 04 86 66 Fax: +33 (0)4 66 04 86 67 Direct Line: +33 (0)4 66 04 22 85 ________________________________________________________________ Discover New Drugs, Discover Synt:em http://www.syntem.com ________________________________________________________________ From chemistry-request@server.ccl.net Tue Feb 13 05:09:20 2001 Received: from info.cyf-kr.edu.pl (root@info.cyf-kr.edu.pl [149.156.4.11]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f1DA9Fw18946 for ; Tue, 13 Feb 2001 05:09:19 -0500 Received: from kinga.cyf-kr.edu.pl (IDENT:8304@kinga.cyf-kr.edu.pl [149.156.2.32]) by info.cyf-kr.edu.pl (8.9.3/8.9.3) with ESMTP id LAA24989 for ; Tue, 13 Feb 2001 11:09:13 +0100 (MET) Received: (from mynowak@localhost) by kinga.cyf-kr.edu.pl (8.9.3/8.9.3) id LAA07604; Tue, 13 Feb 2001 11:09:11 +0100 (MET) Date: Tue, 13 Feb 2001 11:09:10 +0100 (MET) From: Mateusz Nowak To: Subject: Pair list generation problem in GROMOS96 Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear CCL I'm trying to run a regular MD simulation in GROMOS96. My system is 107 aa protein in a box of SPC water with 4 NA+ ions added. PBC are applied, and the box sizes are ~ 4*5*6 nm. Bonds involving hydrogens are shaken. In an output i'm getting following warnings: NONBML: WARNING, NOT ALL EXCLUDED NEIGHBOUR WERE SCANNED IN THE PAIR-LIST NONBML: WARNING, NOT ALL THIRD NEIGHBOUR WERE SCANNED IN THE PAIR-LIST Kinetic and non-bonded potental energy terms are not being calculated ("nan" instead of a value) in an initial (t=0) step. In next steps pair list contains 0 elements instead of ~300000, as it is in initial step. According to manual this warning occures when cut-off for pair list construction (RCUTP) is not reasonably large. In my case it has 1.0 nm (acctually twin rang cut-off 1.0/1.6 is used). I tried to run the same simulation with pair list construction cut-off 1.2 and 1.6 nm, but the same warning occures. Has anybody experienced similar problem? Any help will be appreciated. Mateusz Nowak Jagiellonian Univ. Krakow POLAND From chemistry-request@server.ccl.net Tue Feb 13 05:44:14 2001 Received: from rzumail2.unizh.ch (rzumail2.unizh.ch [130.60.128.10]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f1DAiEw19083 for ; Tue, 13 Feb 2001 05:44:14 -0500 Received: from zisgi.unizh.ch (zisgi.unizh.ch [130.60.19.17]) by rzumail2.unizh.ch (8.9.3/8.9.3/08) with ESMTP id LAA18211; Tue, 13 Feb 2001 11:44:12 +0100 (MET) From: "Dr. Peter Burger" Received: [(chburger@localhost) by zisgi.unizh.ch (SGI-8.9.3/SMI-IRIX6.2/USAR_MAIL_V2) id LAA42365; Tue, 13 Feb 2001 11:44:12 +0100 (MET)] Message-Id: <200102131044.LAA42365@zisgi.unizh.ch> Subject: Re: CCL:Second negative frequency To: dturner@syntem-sa.fr (David Turner) Date: Tue, 13 Feb 2001 11:44:12 +0100 (CET) Cc: chemistry@ccl.net In-Reply-To: <3A88ED90.89EC1676@syntem-sa.fr> from "David Turner" at Feb 13, 1 09:17:20 am X-Mailer: ELM [version 2.4 PL25 PGP2] MIME-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Good point, however, what are you going to do about it? I spent alot computer time in reoptimizing using the calculated hessian / recalculating the second derivatives (sometimes several times) and had the excact same question. I analyzed these low frequencies and in my case quite often these were just rotations of methyl groups etc. in the peripheral positions, while the larger imaginary frequency was corresponding to the TS. Anyways, this made me wonder how this is handled in publications. Are these sometimes small frequencies sometimes ignored? Will this be always mentioned in the paper, would the referees accept additional imaginary frequencies if they had been analyzed thoroughly? Sorry, for this question I do not want to blame anyone - but being originally not trained as an theoretical chemist, I am just curious. So far, I was lucky to get rid of all additional negative frequencies, by reoptimization, but considering the usual error bars of these frequencies as mentioned in the last post and the size of some of my systems (DFT on 50-130 atoms with numerical second derivatives by finite difference), I could be tempted to just mention in the paper that that there is a residual small imaginary frequency, which I cannot get rid of with reasonable computational effort, e.g. redo the force calculation a third or forth time. Any comments? Peter > Your second value (36 cm-1) could easily be positive given the error > associated with normal mode calculations (+/-50 cm-1 or so). Perhaps > you have only one imaginary frequency ... From chemistry-request@server.ccl.net Tue Feb 13 06:55:27 2001 Received: from mx1.ustc.edu.cn ([61.132.182.1]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f1DBtMw20209 for ; Tue, 13 Feb 2001 06:55:23 -0500 Received: from mail.ustc.edu.cn (mail.ustc.edu.cn [202.38.64.10]) by mx1.ustc.edu.cn (8.8.7/8.8.6) with SMTP id UAA26876 for ; Tue, 13 Feb 2001 20:37:46 -0800 Received: (qmail 1557 invoked by uid 1944); 13 Feb 2001 11:46:42 -0000 Date: Tue, 13 Feb 2001 19:46:42 +0800 (CST) From: Zhiyong Zhang X-X-Sender: To: cc: Subject: One article Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi, everyone: Now, I am eager to get one article: Title: "Free energy calculations on binding and catalysis by alpha-lytic protease: the role of substrate size in the P1 pocket." Authors: "Caldwell JW, Agard DA, and Kollman PA." Journal: "PROTEINS: Structure, Function and Genetics" Date: "1991; 10(2): 140-148 Can anyone tell me a site to download this article? Or any other suggestions would be appreciated. Thank you in advance. Regards Zhiyong ******************************************************** Zhiyong Zhang, Ph.D student of Professor Yunyu Shi, Laboratory of Structural Biology, School of Life Science, University of Science and Technology of China (USTC), Hefei, Anhui 230027, P.R. China. Tel: +86-551-3603754 or +86-551-3630875 Fax: +86-551-3603754 Email: zzy@mail.ustc.edu.cn ******************************************************** From chemistry-request@server.ccl.net Tue Feb 13 00:51:33 2001 Received: from iitkgp.iitkgp.ernet.in ([202.141.127.2]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f1D5pUw17868 for ; Tue, 13 Feb 2001 00:51:31 -0500 Received: from cts.iitkgp.ernet.in (cts.iitkgp.ernet.in [144.16.192.220]) by iitkgp.iitkgp.ernet.in (8.9.3/8.9.3) with ESMTP id LAA12527 for ; Tue, 13 Feb 2001 11:19:43 -0500 (GMT) Received: from localhost (rajarshi@localhost) by cts.iitkgp.ernet.in (8.9.3/8.9.3) with ESMTP id LAA08860 for ; Tue, 13 Feb 2001 11:08:59 +0530 X-Authentication-Warning: cts.iitkgp.ernet.in: rajarshi owned process doing -bs Date: Tue, 13 Feb 2001 11:08:59 +0530 (IST) From: Rajarshi Guha X-X-Sender: To: CompuChem List Subject: z matrix to cartesian Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi, does anybody know any command line utility that would convert a z matrix to cartesian coords? ------------------------------------------------------------------------ Rajarshi Guha | Circumstances rule men; men do not rule Dept Of Chemistry, | circumstances. IIT Kharagpur. | | -- Herodotus email: rajarshi@presidency.com | web : www.psynet.net/jijog | ------------------------------------------------------------------------- From chemistry-request@server.ccl.net Tue Feb 13 02:18:11 2001 Received: from mserv.itpa.lt (mserv.itpa.lt [193.219.53.20]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f1D7Ghw18159 for ; Tue, 13 Feb 2001 02:16:50 -0500 Received: from localhost (tamulis@localhost) by mserv.itpa.lt (8.11.1/8.11.0) with ESMTP id f1D7Cvx29753; Tue, 13 Feb 2001 09:13:12 +0200 (EET) (envelope-from tamulis@itpa.lt) Date: Tue, 13 Feb 2001 09:12:56 +0200 (EET) From: Arvydas Tamulis To: "Cust. Service Doug" cc: , , Jelena Tamuliene Subject: Re: CCL:Paramagnetically shifted 1H NMR spectra In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear Dauoglas Fox and other Netters who responded me during last days concerning calculations of paramagnetically shifted 1H NMR spectra possessing up to 135 ppm values. During last days I clearified that for large (100 ppm) paramagnetic 1H shifts are responsible not good basis sets (only few ppm) and not electron correlations (only tens ppm) but including relativistic effects: 'electron spin-orbit', 'electron spin-spin', and 'electron spin - proton spin', etc. couplings. I do not know what relativism it is included in DALTON and DIRAC packages (maybe here can respond experts from these teams) but for my opinion if it is included 'electron spin - proton spin' coupling that should give these 100 ppm paramagnetic shifts in 1H NMR spectra. Maybe in other programs people are doing such a inclusions of 'electron spin - proton spin couplings'? I would be appreciate if somebody will allow me to perform trial calculations of biliverdin CuOEB molecule 1H NMR spectrum using DALTON, DIRAC or other program with implemented as much as possible relativistic effects. Thanking your in advance for further discussions and advises. Yours sincerely, Arvydas Tamulis Enclosed please find X-Ray geometry of CuOEB molecule in Angstroms: Cu1 0. 0. 0. O2 0.2239 -2.96653 -1.55039 N3 1.38133 -1.33544 -0.35323 N4 1.38119 1.34207 0.36885 C5 1.22628 -2.58553 -0.97483 C6 2.51385 -3.33756 -0.86868 C7 3.37827 -2.55016 -0.22896 C8 2.67395 -1.28282 0.09472 C9 3.26426 -0.17877 0.65202 C10 2.68854 1.08761 0.70813 C11 3.38244 2.34651 0.96318 C12 2.50269 3.34699 0.72477 C13 1.25013 2.71593 0.35196 C14 0.0751 3.37078 0. C15 2.68652 -4.68205 -1.49633 C16 3.05674 -4.56912 -2.96369 C17 4.84657 -2.77602 0.04178 C18 5.72923 -2.08939 -1.00856 C19 4.85471 2.43112 1.27447 C20 5.69449 2.34802 0.0041 C21 2.72592 4.83225 0.72854 C22 2.87181 5.41601 -0.67222 H23 4.13917 -0.29105 1.00274 H24 0.09707 4.35684 0. H25 1.8737 -5.18468 -1.40342 H26 3.37402 -5.20107 -1.07412 H27 3.13618 -5.45897 -3.37019 H28 2.36288 -4.06322 -3.3895 H29 3.87718 -4.07992 -3.05734 H30 5.00432 -3.74715 0.00503 H31 5.07799 -2.46117 0.91361 H32 6.64112 -2.28581 -0.82449 H33 5.51113 -2.4159 -1.88189 H34 5.58593 -1.11668 -0.96462 H35 5.10459 1.68705 1.84642 H36 5.03303 3.27735 1.73233 H37 6.61722 2.41078 0.21711 H38 5.52484 1.4978 -0.44582 H39 5.45344 3.10135 -0.56135 H40 3.50226 5.01567 1.24612 H41 1.98737 5.25961 1.1645 H42 3.01354 6.38803 -0.58859 H43 3.62122 5.00544 -1.10604 H44 2.09038 5.25163 -1.1876 N45 -1.43943 -1.27259 0.35323 N46 -1.32005 1.40226 -0.36885 C47 -1.12793 2.76892 -0.35196 C48 -1.34022 -2.52835 0.97483 C49 -2.72843 -1.16245 -0.09472 C50 -2.63743 1.20627 -0.70813 C51 -2.35113 3.45514 -0.72477 O52 -0.3558 -2.95361 1.55039 C54 -2.66 -3.22228 0.86868 C55 -3.4885 -2.39716 0.22896 C56 -3.26899 -0.0332 -0.65201 C57 -3.27458 2.49484 -0.96318 C58 -2.50799 4.94886 -0.72854 C59 -2.89238 -4.55775 1.49633 C60 -4.9654 -2.5574 -0.04178 H61 -4.14802 -0.1064 -1.00274 C62 -4.74161 2.64493 -1.27447 C63 -2.62775 5.53854 0.67222 H64 -3.2754 5.16668 -1.24612 H65 -1.75115 5.34291 -1.1645 C66 -3.2572 -4.42844 2.96368 H67 -2.10276 -5.09608 1.40342 H68 -3.60232 -5.04563 1.07412 C69 -5.8166 -1.83214 1.00856 H70 -5.16625 -3.52054 -0.00503 H71 -5.18257 -2.23255 -0.91362 C72 -5.58426 2.59932 -0.0041 H73 -5.02439 1.91273 -1.84642 H74 -4.88207 3.49828 -1.73233 H75 -2.72604 6.51592 0.58859 H76 -3.3947 5.16177 1.10604 H77 -1.85441 5.33953 1.1876 H78 -3.37619 -5.31387 3.37019 H79 -2.5415 -3.95395 3.3895 H80 -4.05504 -3.90319 3.05734 H81 -6.73633 -1.98774 0.82449 H82 -5.61326 -2.16804 1.88189 H83 -5.63012 -0.86678 0.96462 H84 -6.50328 2.70312 -0.21711 H85 -5.45265 1.74239 0.44582 H86 -5.3099 3.34117 0.56135 *********************************************************** > On Mon, 12 Feb 2001, Cust. Service Doug wrote: > > Dr. Tamulis, > > I don't have ready access to this journal at my office. Can > you send the structure you used? Have you verified that the > environment around these protons is reasonably described by this > input structure? > > Generally the shifts in proton NMR calculations are good only to > about 10% which makes them less appropriate for structural studies > but the wide range you report from the experiment should be reproduced > at least qualitatively. > > > > > Dear Netters, > > > > We did not succeeded to calculate paramagnetically shifted 1H NMR spectrum > > of biliverdin molecule CuOEB using Gaussian 98 (see experimental data in > > J. Am. Chem.Soc., vol. 115, p. 12206 (1993)). > > > > We have optimized geometry of TeMeSilane molecule and obtained from NMR > > calculation the Isotropic Shielding values for H atoms (in ppm): > > > > H Isotropic = 31.9027 Anisotropy = 9.6413 > > XX= 29.4642 YX= 0.2951 ZX= -0.7329 > > XY= 0.4642 YY= 32.9871 ZY= -5.1492 > > XZ= -0.8947 YZ= -5.1015 ZZ= 33.2567 > > Eigenvalues: 27.9348 29.4430 38.3302 > > > > We have used Density Functional Theory B3PW91/6-311G** > > > > We have taken geometry of CuOEB from X-Ray experiment. > > Our B3PW91\6-311G** calculated CuOEB NMR Hm shielding values (ppm): > > 23 H Isotropic = 28.4781 Anisotropy = 10.0683 > > XX= 24.0637 YX= -1.2135 ZX= -.8179 > > XY= -.0906 YY= 35.1141 ZY= -2.2717 > > XZ= 9.0739 YZ= 1.6948 ZZ= 26.2566 > > Eigenvalues: 20.8808 29.3633 35.1904 > > > > 60 H Isotropic = 27.5216 Anisotropy = 12.3793 > > XX= 22.4061 YX= 2.7621 ZX= -1.0495 > > XY= -.3733 YY= 35.4454 ZY= 2.7019 > > XZ= 10.0293 YZ= -6.4196 ZZ= 24.7134 > > Eigenvalues: 18.6646 28.1258 35.7745 > > > > and shielding Hm' value: > > 24 H Isotropic = 25.8868 Anisotropy = 16.3237 > > XX= 36.5750 YX= -.6396 ZX= 4.7813 > > XY= -.0379 YY= 23.9614 ZY= .1694 > > XZ= -.9100 YZ= 2.3766 ZZ= 17.1241 > > Eigenvalues: 16.7005 24.1907 36.7693 > > > > It means that our calculated chemical shifts for Hm and Hm' are equal to > > few ppm while CuOEB experimental NMR chemical shift values for Hm and Hm' in > > J. Am. Chem.Soc., vol 115, p. 12206 are equal approximately to 135 ppm and > > -100 ppm. > > > > Why so badly we have calculated paramagnetically shifted 1H NMR spectrum > > for CuOEB molecule? > > Maybe GAUSSIAN is not able to calculate paramagnetically shifted 1H NMR > > spectra? > > Which program is suitable for calculations of paramagnetically shifted 1H > > NMR spectra? > > > > Thanking your in advance. > > With best regards, Arvydas Tamulis & Jelena Tamuliene > > ******************************************************* > > Arvydas Tamulis > > > > Doctor of Natural Sciences, senior research fellow > > > > Institute of Theoretical Physics and Astronomy, > > Theoretical Molecular Electronics Research Group, > > A. Gostauto 12, Vilnius 2600, Lithuania > > e-mail: TAMULIS@ITPA.lt; WEBsite: http://www.itpa.lt/~tamulis/ > > fax: +(370-2)-225361 or +(370-2)-224694 > > Phone: +(370-2)-620861 > > Home address: Didlaukio 27-40, Vilnius 2057, Lithuania > > Phone: +(370-2)-778743 > > > > > > > > > > > > > > -= This is automatically added to each message by mailing script =- > > CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins > > MAILSERV@ccl.net -- HELP CHEMISTRY or HELP SEARCH > > CHEMISTRY-SEARCH@ccl.net -- archive search | Gopher: gopher.ccl.net 70 > > Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net > > > > > > > > > > > > > -- > > Douglas J. Fox > Technical Support > Gaussian, Inc. > help@gaussian.com > > From chemistry-request@server.ccl.net Tue Feb 13 04:41:23 2001 Received: from merlin2.unizar.es (root@merlin2.unizar.es [155.210.208.12]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f1D9fMw18798 for ; Tue, 13 Feb 2001 04:41:22 -0500 Received: from posta.unizar.es (root@merlin2.unizar.es [155.210.208.12]) by merlin2.unizar.es (8.11.1/8.11.1) with ESMTP id f1D9fFi29100 for ; Tue, 13 Feb 2001 04:41:15 -0500 (EST) Received: from qo_ttf-p3 ([155.210.88.182]) by posta.unizar.es (8.9.1/8.9.1) with SMTP id KAA08435 for ; Tue, 13 Feb 2001 10:39:23 +0100 (MET) Message-ID: <005601c095a1$1ed25cf0$b658d29b@qo_ttf-p3> From: "Jesus Orduna" To: "CCL" Subject: DFT Hyperpolarizabilities in G98:Summary. Date: Tue, 13 Feb 2001 10:41:20 +0100 MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_0053_01C095A9.80615D10" X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 4.72.3612.1700 X-MimeOLE: Produced By Microsoft MimeOLE V4.72.3612.1700 This is a multi-part message in MIME format. ------=_NextPart_000_0053_01C095A9.80615D10 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Hi all, A few days ago I made a question on the calculation of = hyperpolarizabilities using DFT in Gaussian 98. According to the answers I have recieved DFT hyperpolarizabilities can = be calculated as second numerical derivatives of the dipole moment using = the keywords polar=3Denonly or as numerical derivatives of the = polarizability using published methods. Here is the original question = and the answers. Thanks to everybody who responded Original question: Hi all, I am interested in the calculation of DFT first hyperpolarizabilities = (beta). To the best of my knowledge, G98 is not able to calculate = analytical hyperpolarizabilities by dft methods (even though the manual = is rather confussing concerning this point). The only way I have been = able to calculate beta is using the keyword POLAR=3DEnOnly, that causes = the calculation of beta as the second numerical derivative of the dipole = moment with respect to the electric field. Since analytical = polarizabilities (alfa) are available in G98 I wonder if there is a way = to calculate beta as the first numerical derivative of alfa which should = lead to a more rapid and precise calculation. A second question concerns the calculation of second = hyperpolarizabilities (gamma). Can they be calculated in G98 using = either HF or DFT methods. Regards Answers: Dear Jesus:=20 how about using the ADF code?=20 See: http://www.scm.com/=20 and a couple of papers such as:=20 S J A van Gisbergen, J G Snijders, and E J Baerends, Comput. Phys. = Commun. 118, 119, (1999)=20 S J A van Gisbergen, J G Snijders, and E J Baerends, J. Chem. Phys. = 109, 10644 (1998)=20 S J A van Gisbergen, J G Snijders, and E J Baerends, Phys. Rev. = Lett. 78, 3097 (1997)=20 Best regards, Georg=20 Here is one more reference:=20 Van Gisbergen SJA, Guerra CF, Baerends EJ=20 Towards excitation energies and (hyper)polarizability calculations = of large molecules. Application of parallelization=20 and linear scaling techniques to time-dependent density functional = response theory=20 J COMPUT CHEM 21: (16) 1511-1523 DEC 2000=20 --Dr. Georg Schreckenbach phone: +44-1925-603849 CLRC Daresbury Laboratory FAX: +44-1925-603634 Daresbury, Warrington, Cheshire, WA4 4AD, UK h.g.schreckenbach@dl.ac.uk http://www.geocities.com/gschreckenbach/ si colocas #P polar(numer,enonly)=20 te calcula alpha y beta como la derivada num=E9rica de la energ=EDa con = respecto al camp=F2 aplicado. Existe un m=E9todo llamado campo finito. El cual est=E1 muy bien = explicado en el siguiente articulo: Kurtz, H; Stewart, J; Dieter, K. = Journal of computational Chemistry, Vol. 11, No. 1,(1990), pp. 82-87. si deseas algunos detalles me puedes escribir Espero que sea de ayuda. P.D. Disculpa que no te haya contestado en ingl=E9s, pero en vista de = que eres de Espa=F1a creo que para m=ED es m=E1s sencillo explicarte en = nuestro idioma :o) --=20 N=E9stor Cubill=E1n Laboratorio de Electr=F3nica Molecular La Universidad del Zulia Maracaibo-Venezuela Hello Jesus, We are used to run Gaussian to get these alpha, beta and gamma values at different levels of approximation. Maybe you would like to have a look at these papers: JCP, 109, 10489 (1998), JPC A 104, 4755 (2000), CPL, 284, 24 (1998), J. Molec. Struct. 528, 151 (2000). Best regards, Beno=EEt Dr. Benoit CHAMPAGNE CTA Lab FUNDP Rue de Bruxelles, 61 B-5000 Namur BELGIUM http://www.scf.fundp.ac.be/~bchampag/ Tel : 00 32 81 724554 Fax : 00 32 81 724567 Yes, you are right. What you should do, if possible, is just calculate = the analytical alfa, in several jobs, where you change the electric field in steps of = 1.0*10-4 a.u. The minimum number of jobs would then be 7. A second question concerns the calculation of second = hyperpolarizabilities (gamma). Can they be calculated in G98 using = either HF or DFT methods. With HF, that should be no problem, but with DFT probably not, since you = can not even calculate the first hyperpolarizability. Recuerdos, Marcel. --=20 Marcel Swart Theoretische Chemie (MSC) / Moleculaire Dynamica (GBB) Rijksuniversiteit Groningen Nijenborgh 4 9747 AG Groningen The Netherlands m.swart@chem.rug.nl http://go.to/m.swart Dear Jesus, to calculate beta and gamma components you can see the expansion series and the finite-field expressions as reported in: J.Phys.Chem. 97, 1993, 1158; J. Chem. Phys. 103, 1995, 4157 Best regards Andrea ------=_NextPart_000_0053_01C095A9.80615D10 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable

Hi all,

A few days ago I made a question on the calculation of = hyperpolarizabilities using DFT in Gaussian 98.

According to the answers I have recieved DFT=20 hyperpolarizabilities can be calculated as second numerical derivatives = of the=20 dipole moment using the keywords polar=3Denonly or as numerical = derivatives of the=20 polarizability using published methods. Here is the original question = and the=20 answers.

Thanks to everybody who responded

Original question:

Hi all,

I am interested in the calculation of DFT first=20 hyperpolarizabilities (beta). To the best of my knowledge, G98 is not = able to=20 calculate analytical hyperpolarizabilities by dft methods (even though = the=20 manual is rather confussing concerning this point). The only way I have = been=20 able to calculate beta is using the keyword POLAR=3DEnOnly, that causes = the=20 calculation of beta as the second numerical derivative of the dipole = moment with=20 respect to the electric field. Since analytical polarizabilities (alfa) = are=20 available in G98 I wonder if there is a way to calculate beta as the = first=20 numerical derivative of alfa which should lead to a more rapid and = precise=20 calculation.

A second question concerns the calculation of second=20 hyperpolarizabilities (gamma). Can they be calculated in G98 using = either =20 HF or DFT methods.

Regards

Answers:

Dear Jesus:

how about using the ADF code?

See: http://www.scm.com/=20

and a couple of papers such as:

     S J A van Gisbergen, J G = Snijders, and=20 E J Baerends, Comput. Phys. Commun. 118, 119, (1999)=20
     S J A van Gisbergen, J G Snijders, and E J=20 Baerends, J. Chem. Phys. 109, 10644 (1998)
     = S J A=20 van Gisbergen, J G Snijders, and E J Baerends, Phys. Rev. Lett. 78, 3097 = (1997)=20

Best regards, Georg

Here is one more reference:

Van Gisbergen SJA, Guerra CF, Baerends EJ=20
     Towards excitation energies and=20 (hyper)polarizability calculations of large molecules. Application of=20 parallelization
     and linear scaling = techniques to=20 time-dependent density functional response theory =
     J=20 COMPUT CHEM 21: (16) 1511-1523 DEC 2000

--Dr. Georg=20 Schreckenbach          = phone:=20 +44-1925-603849CLRC Daresbury Laboratory      = FAX:=20 +44-1925-603634Daresbury, Warrington, Cheshire, WA4 4AD, UK h.g.schreckenbach@dl.ac.uk   http://www.geocities.co= m/gschreckenbach/

si colocas #P polar(numer,enonly)
te calcula alpha = y beta=20 como la derivada num=E9rica de la energ=EDa con respecto al camp=F2=20 aplicado.

Existe un m=E9todo llamado campo finito. El cual = est=E1 muy bien=20 explicado en el siguiente articulo: Kurtz, H; Stewart, J; Dieter, K. = Journal of=20 computational Chemistry, Vol. 11, No. 1,(1990), pp. 82-87.

si = deseas=20 algunos detalles me puedes escribir

Espero que sea de = ayuda.

P.D.=20 Disculpa que no te haya contestado en ingl=E9s, pero en vista de que = eres de=20 Espa=F1a creo que para m=ED es m=E1s sencillo explicarte en nuestro = idioma=20 :o)

--
N=E9stor Cubill=E1n
Laboratorio de Electr=F3nica = Molecular
La=20 Universidad del Zulia
Maracaibo-Venezuela

Hello Jesus,

We are used to run Gaussian to get = these=20 alpha, beta
and gamma values at different levels of = approximation.
Maybe=20 you would like to have a look at these papers:
JCP, 109, 10489 = (1998),
JPC=20 A 104, 4755 (2000),
CPL, 284, 24 (1998),
J. Molec. Struct. 528, = 151=20 (2000).

Best regards,

Beno=EEt

Dr. Benoit = CHAMPAGNE
CTA=20 Lab
FUNDP
Rue de Bruxelles, 61
B-5000 Namur
BELGIUM
http://www.scf.fundp.ac.be= /~bchampag/
Tel=20 : 00 32 81 724554
Fax : 00 32 81 724567

Yes, you are right. What you should do, if possible, = is just=20 calculate the analytical alfa,
in several jobs, where you change the electric field = in steps=20 of 1.0*10-4 a.u.
The minimum number of jobs would then be = 7.

 
 A second question concerns the calculation = of second=20 hyperpolarizabilities (gamma). Can they be calculated in G98 using=20 either  HF or DFT methods.

 
With HF, that should be no problem, but with DFT = probably not,=20 since you can not even calculate the first = hyperpolarizability.

 
Recuerdos,

 
Marcel.
--
Marcel Swart

 
Theoretische Chemie (MSC) / Moleculaire Dynamica=20 (GBB)
Rijksuniversiteit Groningen
Nijenborgh 4
9747 AG Groningen
The Netherlands
m.swart@chem.rug.nl
http://go.to/m.swart

Dear Jesus,

to calculate beta and gamma = components you=20 can see the expansion series
and the finite-field expressions as = reported=20 in:

J.Phys.Chem. 97, 1993, 1158; J. Chem. Phys. 103, 1995,=20 4157

Best regards

Andrea





 
------=_NextPart_000_0053_01C095A9.80615D10-- From chemistry-request@server.ccl.net Tue Feb 13 04:52:10 2001 Received: from web9613.mail.yahoo.com (web9613.mail.yahoo.com [216.136.131.12]) by server.ccl.net (8.11.0/8.11.0) with SMTP id f1D9qAw18855 for ; Tue, 13 Feb 2001 04:52:10 -0500 Message-ID: <20010213095209.59533.qmail@web9613.mail.yahoo.com> Received: from [161.142.10.11] by web9613.mail.yahoo.com; Tue, 13 Feb 2001 01:52:09 PST Date: Tue, 13 Feb 2001 01:52:09 -0800 (PST) From: sohail qamar Subject: Re: CCL:AMBER6*COMPILATION ON SUN* To: Cory Pye Cc: chemistry@ccl.net In-Reply-To: MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii --- Cory Pye wrote: > On Sat, 10 Feb 2001, sohail qamar wrote: > > > I am getting errors with f77 compiler.I have > installed > > the licenses properly(as far as I know) but still > its > > giving me an output of missing licence file in > > flexlm/licences/licences.dat If I put the > appropriate > > license files in path it still give me errors. > > > > It also give an error of setting domain name to 1 > or > > to use etc/resolve.configfile but I have none in > my > > sun. > > > This might be called /etc/resolv.conf ? > > It typically has a list like: > > domain > nameserver > nameserver > > The , and information > you will need to get from > your network administrator. > It sounds as though you might have a network > misconfiguration. > > The resolv.conf file, if used, basically tells the > computer what network it > belongs to and what host to use as a nameserver > (certain hosts on a network > give out information which matches a symbolic name > to an assigned IP address > (of course real IP addresses must use numbers > expressible in 8 bits, > 0 > See examples > satan.word98.hell.com 666.666.666.666 > god.latex.heaven.ca 3.3.3.3 > fibonacci.math.edu 2.3.5.8 > > The nameserver would be given a numeric IP address, > because at this point, the computer doesn't know > anything about names. > > domain heaven.ca. > nameserver 3.3.2.1 ; > stpeter.pearlygates.heaven.ca > > What might be happening is that the licencing > software needs to know the > hostname in order to generate some internal code, > which it can't get. > > > > > If any friend has compiled amber6 on sun.sparc > please > > give me some idea. > > > > sohail. > > > > __________________________________________________ > > Do You Yahoo!? > > Get personalized email addresses from Yahoo! Mail > - only $35 > > a year! http://personal.mail.yahoo.com/ > > > > > > -= This is automatically added to each message by > mailing script =- > > CHEMISTRY@ccl.net -- To Everybody | > CHEMISTRY-REQUEST@ccl.net -- To Admins > > MAILSERV@ccl.net -- HELP CHEMISTRY or HELP SEARCH > > CHEMISTRY-SEARCH@ccl.net -- archive search | > Gopher: gopher.ccl.net 70 > > Ftp: ftp.ccl.net | WWW: > http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net > > > > > > > > > > > > > > ************* ! Dr. Cory C. Pye > ***************** ! Assistant Professor > *** ** ** ** ! Theoretical and Computational > Chemistry > ** * **** ! Department of Chemistry, > Saint Mary's University > ** * * ! 923 Robie Street, Halifax, NS > B3H 3C3 > ** * * ! cpye@crux.stmarys.ca > http://apwww.stmarys.ca/cpye > *** * * ** ! Ph: (902)-420-5654 > FAX:(902)-496-8104 > ***************** ! > ************* ! Les Hartree-Focks (Apologies > to Montreal Canadien Fans) > > Dr. cory, I amm still getting errors after solving various. especially there is no lib file in my system, f77: Cannot find /usr/lib/v8plusa/libm.il. i am getting the following errors.can u giveany suggestion. cd addles; make install ../Compile L0 -P lesmain.f cat lesmain.f | /lib/cpp -P -DSPARC -DISTAR2 -DMEM_ALLOC > _lesmain_.f /usr/lang/f77 -c -Nl50 -fast -O1 _lesmain_.f f77: Warning: Optimizer level changed from 1 to 3 to support dependence based tr ansformations f77: Warning: -xarch=v8plusa is not portable _lesmain_.f: MAIN: "_lesmain_.f", line 237: Warning: local variable "tntheta" never used "_lesmain_.f", line 239: Warning: local variable "tifcap" never used "_lesmain_.f", line 314: Warning: local variable "inlist" never used "_lesmain_.f", line 320: Warning: local variable "title" never used "_lesmain_.f", line 324: Warning: local variable "tx" never used "_lesmain_.f", line 324: Warning: local variable "ty" never used "_lesmain_.f", line 324: Warning: local variable "tz" never used "_lesmain_.f", line 326: Warning: local variable "tvx" never used "_lesmain_.f", line 326: Warning: local variable "tvy" never used "_lesmain_.f", line 326: Warning: local variable "tvz" never used "_lesmain_.f", line 337: Warning: local variable "ncop" never used "_lesmain_.f", line 341: Warning: local variable "revpoint" never used "_lesmain_.f", line 341: Warning: local variable "poiatom" never used "_lesmain_.f", line 342: Warning: local variable "tlesid" never used "_lesmain_.f", line 342: Warning: local variable "tnlev" never used "_lesmain_.f", line 343: Warning: local variable "tbfach" never used "_lesmain_.f", line 343: Warning: local variable "tbfac" never used "_lesmain_.f", line 343: Warning: local variable "tafach" never used "_lesmain_.f", line 343: Warning: local variable "tafac" never used "_lesmain_.f", line 344: Warning: local variable "ttfach" never used "_lesmain_.f", line 344: Warning: local variable "ttfac" never used "_lesmain_.f", line 345: Warning: local variable "nexcl" never used "_lesmain_.f", line 345: Warning: local variable "tnexcl" never used "_lesmain_.f", line 346: Warning: local variable "j1" never used "_lesmain_.f", line 346: Warning: local variable "i2" never used "_lesmain_.f", line 346: Warning: local variable "i3" never used "_lesmain_.f", line 346: Warning: local variable "k5" never used "_lesmain_.f", line 346: Warning: local variable "i4" never used "_lesmain_.f", line 369: Warning: local variable "i1" never used "_lesmain_.f", line 370: Warning: local variable "chgbox" never used f77: Cannot find /usr/lib/v8plusa/libm.il *** Error code 1 make: Fatal error: Command failed for target `lesmain.o' Current working directory /export/home/sohail/AMBER/amber6/src/addles *** Error code 1 make: Fatal error: Command failed for target `install' *** Select Close or Exit from the window menu to close this window *** __________________________________________________ Do You Yahoo!? Get personalized email addresses from Yahoo! Mail - only $35 a year! http://personal.mail.yahoo.com/ From chemistry-request@server.ccl.net Tue Feb 13 08:12:04 2001 Received: from vytautas.vdu.lt (vytautas.vdu.lt [193.219.38.33]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f1DDA8w20570 for ; Tue, 13 Feb 2001 08:11:34 -0500 Received: from vaidila.vdu.lt ([193.219.38.52] ident=root) by vytautas.vdu.lt with esmtp for chemistry@server.ccl.net id 14Sf9q-0002iB-00; Tue, 13 Feb 2001 15:06:14 +0200 Received: from vaidila.vdu.lt (vejas.vdu.lt [193.219.38.82]) by vaidila.vdu.lt (8.9.3/8.9.3) with ESMTP id PAA11485 for ; Tue, 13 Feb 2001 15:06:44 +0200 (GMT) Message-ID: <3A8896D7.77AC3A6B@vaidila.vdu.lt> Date: Tue, 13 Feb 2001 03:07:20 +0100 From: "art'" X-Mailer: Mozilla 4.7 [en] (Win98; I) X-Accept-Language: en MIME-Version: 1.0 CC: chemistry@server.ccl.net Subject: CCL: reference on polarizabilities vs. molecular reactivity/electronic structure ? References: <200008231930.PAA03790@comppub.com> Content-Type: text/plain; charset=koi8-r Content-Transfer-Encoding: 7bit Hi, CCL'ers, Is there any reference on relation between polarizabilities and molecular reactivity or electronic structure ? Have a nice day Arturas Z. From chemistry-request@server.ccl.net Tue Feb 13 09:06:44 2001 Received: from argyle.richmond.edu (argyle.richmond.edu [141.166.188.18]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f1DE6iw21049 for ; Tue, 13 Feb 2001 09:06:44 -0500 Received: from sabrash (lfa222012.richmond.edu [141.166.222.12]) by argyle.richmond.edu (8.11.2/8.11.2) with SMTP id f1DE0TO15257; Tue, 13 Feb 2001 09:00:29 -0500 (EST) Message-Id: <3.0.5.32.20010213085728.008af680@facstaff.richmond.edu> X-Sender: sabrash@facstaff.richmond.edu X-Mailer: QUALCOMM Windows Eudora Light Version 3.0.5 (32) Date: Tue, 13 Feb 2001 08:57:28 -0500 To: "Dr. Peter Burger" , dturner@syntem-sa.fr From: "Samuel A. Abrash" Subject: Re: CCL:Second negative frequency Cc: chemistry@ccl.net In-Reply-To: <200102131044.LAA42365@zisgi.unizh.ch> References: <3A88ED90.89EC1676@syntem-sa.fr> Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Of course there is the possibility that it is real. I haven't looked at the molecule under discussion but many molecules have internal rotation degrees of freedom, or other degrees of freedom in which the potential energy surface is very flat. In those cases, it can be very difficult to locate the minimum of the PES in that coordinate. Another possibility is that the symmetry that the calculation is being carried out in may be too high to allow a true minimum to be reached. Perhaps the symmetry needs to be relaxed. Best regards, Sam Abrash At 11:44 AM 02/13/2001 +0100, Dr. Peter Burger wrote: >Good point, > >however, what are you going to do about it? I spent alot computer time >in reoptimizing using the calculated hessian / recalculating the second >derivatives (sometimes several times) and had the excact same question. >I analyzed these low frequencies and in my case quite often these were >just rotations of methyl groups etc. in the peripheral positions, while >the larger imaginary frequency was corresponding to the TS. > >Anyways, this made me wonder how this is handled >in publications. Are these sometimes small frequencies >sometimes ignored? Will this be always mentioned >in the paper, would the referees accept additional imaginary >frequencies if they had been analyzed thoroughly? > > Sorry, for this question I do not want to >blame anyone - but being originally not trained >as an theoretical chemist, I am just curious. So far, >I was lucky to get rid of all additional negative frequencies, >by reoptimization, but considering the usual error bars of these >frequencies as mentioned in the last post and the size of some of my >systems (DFT on 50-130 atoms with numerical second derivatives by finite >difference), I could be tempted to just mention in the paper that >that there is a residual small imaginary frequency, which I >cannot get rid of with reasonable computational effort, e.g. redo the >force calculation a third or forth time. > >Any comments? > >Peter > >> Your second value (36 cm-1) could easily be positive given the error >> associated with normal mode calculations (+/-50 cm-1 or so). Perhaps >> you have only one imaginary frequency ... > > >-= This is automatically added to each message by mailing script =- >CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins >MAILSERV@ccl.net -- HELP CHEMISTRY or HELP SEARCH >CHEMISTRY-SEARCH@ccl.net -- archive search | Gopher: gopher.ccl.net 70 >Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net > > > > > Samuel A. Abrash Associate Professor Department of Chemistry University of Richmond Richmond, VA 23173 Phone: (804) 289-8248 Fax: (804) 287-1897 E-mail: sabrash@richmond.edu http://www.richmond.edu/~sabrash "The time it takes to complete a scientific project is given by the equation t = 2a + b, where a is the original estimate, 2 is a correction factor, and b is a number large compared to 2a." From chemistry-request@server.ccl.net Tue Feb 13 09:35:50 2001 Received: from relay.it.northwestern.edu (relay.acns.nwu.edu [129.105.16.56]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f1DEZow21204 for ; Tue, 13 Feb 2001 09:35:50 -0500 Received: (from mailnull@localhost) by relay.it.northwestern.edu (8.9.3/8.9.3) id IAA11075; Tue, 13 Feb 2001 08:35:49 -0600 (CST) Received: from [129.105.9.174] (pine-4-009174.nuts.nwu.edu [129.105.9.174]) by relay.acns.nwu.edu via smap (V2.0) id xma010416; Tue, 13 Feb 01 08:35:38 -0600 Mime-Version: 1.0 X-Sender: hutchisn@mercury.chem.northwestern.edu Message-Id: In-Reply-To: References: Date: Tue, 13 Feb 2001 08:35:29 -0600 To: Rajarshi Guha From: Geoff Hutchison Subject: Re: CCL:z matrix to cartesian Cc: CompuChem List Content-Type: text/plain; charset="us-ascii" ; format="flowed" At 11:08 AM +0530 2/13/01, Rajarshi Guha wrote: > does anybody know any command line utility that would convert a z >matrix to cartesian coords? Sure. There are various z-matrix formats and Cartesian formats handled by babel. -- -- -Geoff Hutchison Ratner/Marks Groups Northwestern Chemistry http://www.chem.nwu.edu/ From chemistry-request@server.ccl.net Tue Feb 13 10:34:24 2001 Received: from interlock.herc.com (interlock.herc.com [199.221.7.2]) by server.ccl.net (8.11.0/8.11.0) with SMTP id f1DFYMw21439 for ; Tue, 13 Feb 2001 10:34:23 -0500 Received: from csdnsg1.herc.com ([147.116.14.51]) by interlock.herc.com with SMTP id KAA14308 (InterLock SMTP Gateway for ); Tue, 13 Feb 2001 10:34:07 -0500 Subject: polymer structures To: chemistry@ccl.net Cc: X-Mailer: Lotus Notes Release 5.0.2b December 16, 1999 Message-Id: From: Goutam.Das@betzdearborn.com Date: Tue, 13 Feb 2001 09:32:35 -0600 X-Priority: 3 (Normal) X-Mimetrack: Serialize by Router on CSDNSG1/Servers/Herc(Release 5.0.1b|September 30, 1999) at 02/13/2001 10:21:06 AM Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Dear CCL'ers Could anyone of you send me pointers on calculated structures of EVA copolymers, polyalkyl acrylates/methacrylates, Ethylyne, vinyl acetate, isobutylene terpolymers. Do they exist at all in litera ture? I did find some studies on poly alkyl acrylates but that is all. What is the best way (level of theory, etc) to calculate the structure of a "unit cell" of e.g. Polyoctadecyl acrylate? Thanks in anticipation Goutam Das Staff Scientist BetzDearborn Division of Hercules The Woodlands, TX 77380 281.367.6201 ext 425 From chemistry-request@server.ccl.net Tue Feb 13 11:22:57 2001 Received: from schrodinger.com (root@thermidore.schrodinger.com [192.156.98.99]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f1DGMuw22099 for ; Tue, 13 Feb 2001 11:22:56 -0500 Received: from erica.schrodinger.com (erica.schrodinger.com [192.156.98.3]) by schrodinger.com (8.8.5/8.8.5) with SMTP id IAA00745; Tue, 13 Feb 2001 08:22:54 -0800 Date: Tue, 13 Feb 2001 08:22:54 -0800 (PST) From: Schrodinger Technical Support Reply-To: Schrodinger Technical Support To: Jamal Uddin cc: chemistry@ccl.net Subject: Re: diasort: Not enough e- to doubly occupy core | 010209o In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi Jamal, When Jaguar uses the special initial guess routines for a transition metal- containing molecule, it typically tries to obtain closed-shell configurations for the ligands. In your scandium complex, scandium's 3 valence electrons are used to make closed-shells for the three ligands, but then the required +1 charge for the molecule can't be reconciled with the number of electrons in the ECP. You can guide the TM initial guess by using an &atomic section that specifies where the unpaired electron and formal charge should go, but in this case it's probably easiest to just use the default initial guess algorithm, iguess=10. Note that the 'iacc=1' and 'iacscf=1' settings in your input file apply only to the pseudospectral method, which you have turned off with 'nops=1'. You can actually do this optimization with the following &gen section: &gen gdftmed=-13 gdftfine=-13 gdftgrad=-13 iacc=1 idft=22111 iguess=10 igeopt=1 molchg=1 multip=2 basis=LACV3P**++ & On the other hand, if you are trying to obtain the ultimate accuracy in this calculation, replace 'iacc=1' with 'nops=1'. Sincerely, Dale Braden ---------------------------------------------------------------------- Schrodinger Technical Support | http://www.schrodinger.com help@schrodinger.com | 503-299-1150 | 503-299-4532 (fax) Schrodinger, Inc. | 1500 SW First Ave. Suite 1180, Portland OR 97201 ---------------------------------------------------------------------- On Mon, 12 Feb 2001, Jamal Uddin wrote: -------- Original Message -------- Subject: CCL:Not enough e- to doubly occupy core Date: Mon, 12 Feb 2001 12:50:25 -0600 (EST) From: Jamal Uddin To: CHEMISTRY@ccl.net Hello, In optimizations of cationic transition metal complexes using JAGUAR I get the following error message: start of program hfig initial wavefunction generated automatically from atomic wavefunctions ERROR: fatal error -- debug information follows diasort: Not enough e- to doubly occupy core For transition metal, there is an effective core potential which I used for the calculation of neutral molecules too but there were no error message. I would appreciate any suggestion or help. Thanks, Jamal Uddin From chemistry-request@server.ccl.net Tue Feb 13 10:45:16 2001 Received: from hope.edu (webmail.hope.edu [198.110.98.17]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f1DFjGw21658 for ; Tue, 13 Feb 2001 10:45:16 -0500 Received: from [198.110.101.2] (polik@hope.edu); Tue, 13 Feb 2001 10:45:30 -0500 X-WM-Posted-At: hope.edu; Tue, 13 Feb 01 10:45:30 -0500 Message-Id: <4.2.2.20010213103855.01b653f0@webmail.hope.edu> X-Sender: polik@webmail.hope.edu X-Mailer: QUALCOMM Windows Eudora Pro Version 4.2.2 Date: Tue, 13 Feb 2001 10:43:40 -0500 To: chemistry@ccl.net From: "William F. Polik" Subject: WebMO: WWW-based interface to Gaussian, GAMESS, MOPAC Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii"; format=flowed WebMO version 2.1 has been officially released and is available for FREE download at http://www.webmo.net WebMO is a web-based interface to popular computational chemistry programs including Gaussian, MOPAC, and GAMESS. WebMO permits users to build 3-D molecular structures, submit multiple jobs, monitor job progress, and view text and graphical results all from within a standard web-browser. WebMO has a very fast learning curve for novices, yet offers total control over every job for experts. A tour of screenshots and a working demo are available at the WebMO website. WebMO features include: * Entirely web-based (no software or plug-ins to install on clients) * True 3-D molecular editor for building input structures * Built-in support for Gaussian 94/98, GAMESS, MOPAC 6/7 * Automatic parsing of output files for calculated properties * Vibrational mode and partial charge visualization * IR and NMR spectra visualization * Job queuing, monitoring, and control * Web-based administration of user accounts, time limits, job control, etc. For a detailed list of features, system requirements, screenshots, a working demo, download information, installation and upgrade instructions, and general support information, visit the WebMO homepage at http://www.webmo.net In addition, the WebMO website has support material of general interest to the computational chemistry community, including * Detailed Gaussian, GAMESS, and MOPAC installation instructions * East-to-follow Red Hat Linux installation instructions * Computational chemistry course lecture notes and exercises which are available at http://www.webmo.net/support http://www.webmo.net/curriculum Enjoy! The WebMO Team From chemistry-request@server.ccl.net Tue Feb 13 10:43:32 2001 Received: from kanga.INS.cwru.edu (root@kanga.INS.CWRU.Edu [129.22.8.32]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f1DFhWw21612 for ; Tue, 13 Feb 2001 10:43:32 -0500 Received: from raman6 (chem51439.CHEM.CWRU.Edu [129.22.129.103]) by kanga.INS.cwru.edu with SMTP (8.8.8+cwru/CWRU-3.6) id KAA08646; Tue, 13 Feb 2001 10:43:32 -0500 (EST) (from hxt19@po.cwru.edu for ) Message-ID: <007e01c095d4$d193bea0$67811681@cwru.edu> Reply-To: "Hui-Hsu (Gavin) Tsai" From: "Hui-Hsu (Gavin) Tsai" To: Subject: different electronic states Date: Tue, 13 Feb 2001 10:51:22 -0500 MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_007B_01C095AA.E7340960" X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 5.00.2615.200 X-MimeOLE: Produced By Microsoft MimeOLE V5.00.2615.200 This is a multi-part message in MIME format. ------=_NextPart_000_007B_01C095AA.E7340960 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Dear all, I have a question about setting up calaulations at different = electronic states in G98. The first example is how to remove one electron from different = orbitals (e.g. HOMO, HOMO-1....) to calculate=20 different ionization potential energy at different final electronic = states In G98, I use "alter" command to switch two orbitals (say HOMO and = HOMO-1) and let G98 to remove one electron from=20 the "switched HOMO" orbital. Unfortunely, G98 always removes the = "original" HOMO orbital. The another example is about the different spin state of = Fe(II)/Fe(III) (or say transition metal).=20 As you know, iron compunds always have mixed spin sate. The question is = how to setup different spin sate in G98? =20 Could anyone show me how to perform this kind of calculations? Any comment or suggestion is welcomed and appreciated. Gavin ------=_NextPart_000_007B_01C095AA.E7340960 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable
Dear all,
 
       I = have a=20 question about setting up calaulations at different electronic states in = G98.
 
    The first = example is how to=20 remove one electron from different orbitals (e.g. HOMO, HOMO-1....) to = calculate=20
different ionization potential = energy at=20 different final electronic states
In G98, I use "alter" command to switch = two=20 orbitals (say HOMO and HOMO-1) and let G98 to remove one electron from=20
the "switched HOMO"=20 orbital. Unfortunely, G98 always removes the "original" HOMO=20 orbital.
 
   The another example is = about the=20 different spin state of Fe(II)/Fe(III) (or say transition metal). =
As you know, iron compunds always have = mixed spin=20 sate. The question is how to setup different spin sate in = G98?
      =
     Could = anyone show me=20 how to perform this kind of calculations?
Any comment or suggestion is welcomed = and=20 appreciated.
 
Gavin
------=_NextPart_000_007B_01C095AA.E7340960-- From chemistry-request@server.ccl.net Tue Feb 13 12:10:54 2001 Received: from rzumail2.unizh.ch (rzumail2.unizh.ch [130.60.128.10]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f1DHArw22516 for ; Tue, 13 Feb 2001 12:10:53 -0500 Received: from zisgi.unizh.ch (zisgi.unizh.ch [130.60.19.17]) by rzumail2.unizh.ch (8.9.3/8.9.3/08) with ESMTP id SAA20794; Tue, 13 Feb 2001 18:10:51 +0100 (MET) From: "Dr. Peter Burger" Received: [(chburger@localhost) by zisgi.unizh.ch (SGI-8.9.3/SMI-IRIX6.2/USAR_MAIL_V2) id SAA23036; Tue, 13 Feb 2001 18:10:51 +0100 (MET)] Message-Id: <200102131710.SAA23036@zisgi.unizh.ch> Subject: Re: CCL:Second negative frequency To: azhary@ksu.edu.sa (Adel Abbas Ali Elazhary Sci. College) Date: Tue, 13 Feb 2001 18:10:51 +0100 (CET) Cc: CHEMISTRY@ccl.net In-Reply-To: from "Adel Abbas Ali Elazhary Sci. College" at Feb 13, 1 05:55:46 pm X-Mailer: ELM [version 2.4 PL25 PGP2] MIME-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Dear Adel, > I think your problem is with the numerical derivatives. I think using the > analytical would solve you problem. You do not you try small basis set nice try, but in the (yet) absence of this capability in the program I use, i.e. Turbomole I am left with that problem. > with analytical or if you can the smallest of your molecules with > analytical. There are so many paprameters also to vary with the numerical. > Why do not try to vary these (I really do not think it will help but you > may try). Why do not you try tighter geometry optimization. I think that well, sure I do all that kind stuff, tighten SCF-convergence etc., change the stepsize of the finite differences but you see, you do not know the answer in advance after 6n SCF steps and gradients. In my case I may have the answer just after 2-10 days etc. depending on the size of the system (50-130 atoms 500-1500 bfs) and numbers of CPU I use (though it runs perfectly parallel, calculations are done on 8-20 CPUs). Checking for / fighting the numerical noise is not just gratifying considering error bars of at least +-20 cm-1 - so should I stop and relax with a second small imaginary frequency of -20 to -30 cm-1? Peter P.S. Also I forget to point out that a number of people seem to be just happy and get away with the updated approximate hessian they get during the optimization process - is that any better? I do not think so. From chemistry-request@server.ccl.net Tue Feb 13 13:08:39 2001 Received: from mumbai3.mtnl.net.in (mumbai3.mtnl.net.in [203.94.227.53]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f1DI8Yw23188 for ; Tue, 13 Feb 2001 13:08:35 -0500 Received: from bol.net.in by mumbai3.mtnl.net.in (8.9.1/1.1.20.3/27Mar00-0611PM) id XAA0000001743; Tue, 13 Feb 2001 23:36:58 +0530 (IST) Message-ID: <3A0F887E.77F6E895@bol.net.in> Date: Mon, 13 Nov 2000 11:51:50 +0530 From: Prashant Desai X-Mailer: Mozilla 4.5 [en] (Win98; I) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net Subject: Info on Principle Compmonent Analysis Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit I am looking for a nice review article on Principle Component Analysis as applicable to QSAR studies. It should be written for beginners. Name: Prashant Desai e-maol: pradesa@bol.net.in From chemistry-request@server.ccl.net Tue Feb 13 13:11:22 2001 Received: from mumbai3.mtnl.net.in (mumbai3.mtnl.net.in [203.94.227.53]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f1DIBJw23239 for ; Tue, 13 Feb 2001 13:11:20 -0500 Received: from bol.net.in by mumbai3.mtnl.net.in (8.9.1/1.1.20.3/27Mar00-0611PM) id XAA0000017110; Tue, 13 Feb 2001 23:39:44 +0530 (IST) Message-ID: <3A0F8924.A27C0B13@bol.net.in> Date: Mon, 13 Nov 2000 11:54:36 +0530 From: Prashant Desai X-Mailer: Mozilla 4.5 [en] (Win98; I) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net Subject: Review on Principle Component Analysis Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit I am looking for a review article alongwith examples on Principle Component Analysis as applied to QSAR. It should be written for beginners. Name: Prashant desai e-mail: pradesai@bol.net.in From chemistry-request@server.ccl.net Tue Feb 13 13:20:55 2001 Received: from hotmail.com (f14.pav0.hotmail.com [64.4.33.85]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f1DIKtw23416 for ; Tue, 13 Feb 2001 13:20:55 -0500 Received: from mail pickup service by hotmail.com with Microsoft SMTPSVC; Tue, 13 Feb 2001 10:18:54 -0800 Received: from 64.109.129.78 by pv0fd.pav0.hotmail.msn.com with HTTP; Tue, 13 Feb 2001 18:18:54 GMT X-Originating-IP: [64.109.129.78] From: "Orest Macina" To: chemistry@ccl.net Subject: MO Viewer Date: Tue, 13 Feb 2001 13:18:54 -0500 Mime-Version: 1.0 Content-Type: text/plain; format=flowed Message-ID: X-OriginalArrivalTime: 13 Feb 2001 18:18:54.0898 (UTC) FILETIME=[6CA40120:01C095E9] Hello CCL, Does anyone know of a free Molecular Orbital viewer that can read in a MOPAC output file and display HOMO and LUMO? Orest _________________________________________________________________ Get your FREE download of MSN Explorer at http://explorer.msn.com From chemistry-request@server.ccl.net Tue Feb 13 14:56:06 2001 Received: from Mailer.Uni-Marburg.DE (Mailer.Uni-Marburg.DE [137.248.1.76]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f1DJu6w24317 for ; Tue, 13 Feb 2001 14:56:06 -0500 Received: from mailer.uni-marburg.de ([192.168.161.185]) by Mailer.Uni-Marburg.DE (8.11.2/8.11.2) with ESMTP id f1DJu7j23908 for ; Tue, 13 Feb 2001 20:56:07 +0100 Sender: boehm@mailer.uni-marburg.de Message-ID: <3A899156.E5503DD@mailer.uni-marburg.de> Date: Tue, 13 Feb 2001 20:56:07 +0100 From: Markus Boehm Organization: University of Marburg X-Mailer: Mozilla 4.7C-SGI [en] (X11; I; IRIX 6.5 IP32) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net Subject: CCL:Info on Principle Compmonent Analysis Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit > I am looking for a nice review article on Principle Component Analysis > as applicable to QSAR studies. It should be written for beginners. > Name: Prashant Desai > e-maol: pradesa@bol.net.in Have a look at a very nice tutorial: PCA, in: Chemometrics and Intelligent Lab. Systems 2 (1987) 37-52 Greetings, Markus From chemistry-request@server.ccl.net Tue Feb 13 15:58:36 2001 Received: from toto.research.aa.wl.com ([162.48.100.19]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f1DKwZw25764 for ; Tue, 13 Feb 2001 15:58:35 -0500 Received: by toto.research.aa.wl.com with Internet Mail Service (5.5.2650.21) id <17BVWSJK>; Tue, 13 Feb 2001 15:56:36 -0500 Message-ID: <6944FBE0F687D411823D00508B6095FA26B365@aaunderdog.research.aa.wl.com> From: "Whitehead, Christopher" To: "'Prashant Desai'" , chemistry@ccl.net Subject: RE: Review on Principle Component Analysis Date: Tue, 13 Feb 2001 15:46:20 -0500 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2650.21) Content-Type: text/plain; charset="iso-8859-1" Desai, The following reference is not an exact match to your query, but it should help: Geladi, P. and B. R. Kowalski (1986). "Partial Least-Squares Regression: A Tutorial." Analytica Chimica Acta 185: 1-17. Contained in this article, is a brief description of MLR, PCA, PCR, and PLS. Christopher Whitehead -----Original Message----- From: Prashant Desai [mailto:pradesai@bol.net.in] Sent: Monday, November 13, 2000 1:25 AM To: chemistry@ccl.net Subject: CCL:Review on Principle Component Analysis I am looking for a review article alongwith examples on Principle Component Analysis as applied to QSAR. It should be written for beginners. Name: Prashant desai e-mail: pradesai@bol.net.in -= This is automatically added to each message by mailing script =- CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins MAILSERV@ccl.net -- HELP CHEMISTRY or HELP SEARCH CHEMISTRY-SEARCH@ccl.net -- archive search | Gopher: gopher.ccl.net 70 Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net From chemistry-request@server.ccl.net Tue Feb 13 22:42:32 2001 Received: from iitkgp.iitkgp.ernet.in ([202.141.127.2]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f1E3gTw27642 for ; Tue, 13 Feb 2001 22:42:30 -0500 Received: from cts.iitkgp.ernet.in (cts.iitkgp.ernet.in [144.16.192.220]) by iitkgp.iitkgp.ernet.in (8.9.3/8.9.3) with ESMTP id JAA13295 for ; Wed, 14 Feb 2001 09:10:45 -0500 (GMT) Received: from localhost (rajarshi@localhost) by cts.iitkgp.ernet.in (8.9.3/8.9.3) with ESMTP id IAA03145 for ; Wed, 14 Feb 2001 08:58:57 +0530 X-Authentication-Warning: cts.iitkgp.ernet.in: rajarshi owned process doing -bs Date: Wed, 14 Feb 2001 08:58:57 +0530 (IST) From: Rajarshi Guha X-X-Sender: To: CompuChem List Subject: GAMESS? Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi, does anybody know an alternative site for GAMESS-US. The site at http://www.msg.ameslab.gov/GAMESS/ seems to be down. ------------------------------------------------------------------------- Rajarshi Guha | Growing old is mandatory, Dept. of Chemistry | growing wise is optional IIT Kharagpur. | | email: rajarshi@presidency.com | rajarshi@cts.iitkgp.ernet.in | web : www.psynet.net/jijog | ------------------------------------------------------------------------- From chemistry-request@server.ccl.net Tue Feb 13 23:52:04 2001 Received: from lorica.ucc.usyd.edu.au (lorica.ucc.usyd.edu.au [129.78.64.15]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f1E4q2w28300 for ; Tue, 13 Feb 2001 23:52:03 -0500 Received: from alf.chem.usyd.edu.au (alf.chem.usyd.edu.au [129.78.76.34]) by lorica.ucc.usyd.edu.au (8.9.3/8.9.3) with SMTP id PAA17094 for ; Wed, 14 Feb 2001 15:51:38 +1100 (EST) Received: by alf.chem.usyd.edu.au (5.65v4.0/1.1.19.2/16Dec99-0159PM) id AA10667; Wed, 14 Feb 2001 15:52:01 +1100 Received: from equus.chem.usyd.edu.au(129.78.77.235) by alf.chem.usyd.edu.au via smap (V2.1) id xma005890; Wed, 14 Feb 01 15:51:53 +1100 Message-Id: <3.0.5.32.20010214144647.00899550@mailhost> X-Sender: bacskay@mailhost X-Mailer: QUALCOMM Windows Eudora Pro Version 3.0.5 (32) Date: Wed, 14 Feb 2001 14:46:47 +1100 To: chemistry@ccl.net From: George Bacskay Subject: Xenon computers Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Dear all, We at Sydney are considering buying Xenon 700 computers for quantum chemistry (mostly G98) as well as Monte Carlo type applications. We'd be interested to hear from anyone who has such a machine or tested one (single or dual processor Xenon with 1M or 2M cache and varying RAM sizes) and could tell us about its performance. We would particularly like to know how such machines compare with pentium III and/or IV machines. Any information on this will be greatly appreciated. Best regards, George Bacskay School of Chemistry University of Sydney NSW 2006 Australia email: bacskay@chem.usyd.edu.au ***************************************************** Dr George Bacskay School of Chemistry University of Sydney NSW 2006 Australia tel : 61-2- 9351 3777 fax : 61-2- 9351 3329 email : bacskay@chem.usyd.edu.au web : http://www.chem.usyd.edu.au/staffgbb.htm *****************************************************