From chemistry-request@server.ccl.net Fri Mar 14 05:09:42 2003 Received: from iris.chimfarm.unipg.it ([141.250.13.4]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h2EA9g523355 for ; Fri, 14 Mar 2003 05:09:42 -0500 Received: from apollo.chimfarm.unipg.it ([141.250.13.72] helo=apollo) by iris.chimfarm.unipg.it with esmtp (Exim 2.04 #2) id 18tuXS-0002Mi-00 for chemistry@ccl.net; Fri, 14 Mar 2003 11:08:19 -0800 From: "Daniele Bellocchi" To: Subject: CCL:An error in the TS optimization Date: Fri, 14 Mar 2003 11:05:44 +0100 Message-ID: <000001c2ea11$4792ecb0$480dfa8d@apollo> MIME-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: 7bit X-Priority: 3 (Normal) X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook, Build 10.0.2627 Importance: Normal X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2600.0000 Dear All, I started an eigenvalue-following transition state optimization in g98 but the run failed giving the following error message: ------------------------------------------------------------------------ -------------------- dumping /fiocom/, unit = 3 NFiles = 1 SizExt = 524288 WInBlk = 512 defal = T LstWrd = 66048 FType=2 FMxFil=10000 Number 0 Base 20480 End 66048 End1 66048 Wr Pntr 20480 Rd Pntr 20480 Error termination in NtrErr: NtrErr Called from FileIO. ------------------------------------------------------------------------ --------------------- I used the following route for TS search: # PM3 test opt=(EF,TS,calcfc,ModRed) scf=direct freq Can anybody tell me how to solve this problem?Thanks a lot! Regards, Daniele Bellocchi University of Perugia Italy From chemistry-request@server.ccl.net Fri Mar 14 06:36:32 2003 Received: from cuces.unisi.it ([193.205.4.2]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h2EBaV525931 for ; Fri, 14 Mar 2003 06:36:31 -0500 Received: from CONVERSION-DAEMON.cuces.unisi.it by cuces.unisi.it (PMDF V6.1-1 #30546) id <01KTIJKFZYCW000GVH@cuces.unisi.it> for chemistry@ccl.net; Fri, 14 Mar 2003 12:34:00 +0100 (MET) Received: from pc-val9.unisi.it (pc-val9.chim.unisi.it [172.16.3.109]) by cuces.unisi.it (PMDF V6.1-1 #30546) with ESMTP id <01KTIJK5KQV0000LP4@cuces.unisi.it> for chemistry@ccl.net; Fri, 14 Mar 2003 12:33:08 +0100 (MET) Date: Fri, 14 Mar 2003 12:34:14 +0100 From: Elena Molteni Subject: CCL: magnetic susceptibility tensor X-Sender: molteni@mailsrv.unisi.it To: chemistry@ccl.net Message-id: <5.2.0.9.0.20030314115033.00a0ed80@mailsrv.unisi.it> MIME-version: 1.0 X-Mailer: QUALCOMM Windows Eudora Version 5.2.0.9 Content-type: text/plain; charset=us-ascii; format=flowed Dear all, I am working on a system with a Fe(II) ion in high spin state. Dr. Marcel Swart kindly helped me by performing with ADF a single point calculation on this system (which I couldn't get to converge with Gaussian98). Now, I have to use the obtained results as input to calculate the magnetic susceptibility tensor. Does any of you know how one can calculate this tensor (ADF doesn't support this option, as I read in the manual), with Gaussian or any other program, and which kind of information is needed as input (spin densities,.....) ? (with Gaussian I know how to do that only if I have the complete output of a previous Gaussian calculation...) Thanks in advance Elena Molteni From chemistry-request@server.ccl.net Fri Mar 14 08:10:05 2003 Received: from celebris04.cetem.gov.br ([200.20.105.10]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h2EDA5528720 for ; Fri, 14 Mar 2003 08:10:05 -0500 Received: by correio.cetem.gov.br with Internet Mail Service (5.5.2653.19) id ; Fri, 14 Mar 2003 10:15:32 -0300 Message-ID: <216FE3CA3D4DD611AE2600105AD16BDFD56AD9@correio.cetem.gov.br> From: Ian Hovell To: "'chemistry@ccl.net'" Subject: solvating using gaussian98 Date: Fri, 14 Mar 2003 10:15:22 -0300 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2653.19) 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 h2EDA6528721 Good Morning Colleages, I am using GaussianW98 I am trying to solvate a molecule in a liquid other than the ones described in the manual with the following input line # opt=tight hf/sto-3g* scrf=(pcm,dielectric=34.9) geom=connectivity It seem to ignore the dielectric value and reverts to water. Iam doing something wrong here I know but I cant see it. I have tried placing the delectric value in the description of the molecule such as # opt=tight hf/sto-3g* scrf=(pcm,read) geom=connectivity molecule description blank line eps=34.9 but it all ways comes back with an error Also I would like to run this at room temperature. I am using gaussianview to create my inputs. Any help would be extremely welcome. Ian Hovell - Ph.D. NUCLEO DE MODELAGEM MOLECULAR-NMM Centro de Tecnologia Mineral - CETEM Ministerio da Ciência e da Tecnologia- MCT Avenida Ipê, No 900 - Cidade Universitaria Ilha do Fundão Rio de Janeiro RJ Brasil CEP 21941-590 tel 00 55 (xx) 3865 - 7216 Fax 00 55 (xx) 22602837 ou 2290-4286 e-mail hovell@cetem.gov.br From chemistry-request@server.ccl.net Fri Mar 14 05:48:05 2003 Received: from cascara.uvic.ca ([142.104.5.28]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h2EAm5524447 for ; Fri, 14 Mar 2003 05:48:05 -0500 Received: from [24.65.168.211] ([24.65.168.211]) by cascara.uvic.ca (8.12.8/8.12.8) with ESMTP id h2EAlxDs699662 for ; Fri, 14 Mar 2003 02:48:01 -0800 From: Roy Jensen To: chemistry@ccl.net Subject: SUMMARY: O2(a-X) splitting Date: Fri, 14 Mar 2003 02:48:30 -0800 Message-ID: References: In-Reply-To: X-Mailer: Forte Agent 1.91/32.564 MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii X-UVic-Virus-Scanned: OK - Passed virus scan by Sophos (sophie) on cascara X-Scanned-By: MIMEDefang 2.19 (www . roaringpenguin . com / mimedefang) Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id h2EAm5524449 All Like I said, I was missing something...like the fact that CI _isn't_ multireference. A quick NBO analysis showed that the state obtained is an equal mixture of the 1-delta and 1-sigma states. A multireference (two determinant minimum) approach is needed. ORIGINAL MESSAGE > I was looking at the splitting between the a-1-delta and X-3-sigma states > of oxygen using the UQCISD/6-311++G(d,p) level of theory. The calculated > singlet-triplet spacing is 47 % higher than the experimentally observed > value (11618 vs 7918 cm-1, respectively). I am sure there is a ready > explanation for this; however, I am drawing a blank...any insights > would be greatly appreciated! Thanks to those who responded, Roy Jensen Roy Jensen -----BEGIN PGP PUBLIC KEY BLOCK----- Comment: available at www.consol.ca ------END PGP PUBLIC KEY BLOCK------ From chemistry-request@server.ccl.net Fri Mar 14 03:45:30 2003 Received: from cyber7.cyberworldservers.net ([66.206.20.1]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h2E8jT507516 for ; Fri, 14 Mar 2003 03:45:30 -0500 Received: from rowyna.com (unverified [66.206.20.2]) by cyber7.cyberworldservers.net (Vircom SMTPRS 5.3.232) with ESMTP id for ; Fri, 14 Mar 2003 00:45:36 -0800 Message-ID: <43b512b55aab40cf9b2c87115367ca97.rowyna@rowyna.com> X-EM-APIVersion: 2, 0, 0, 8 X-Priority: 3 (Normal) Reply-To: "Rowyna" From: "Rowyna" To: chemistry@ccl.net Subject: delphi results Date: Fri, 14 Mar 2003 00:45:36 -0800 MIME-Version: 1.0 Content-type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id h2E8jU507517 Hi all, This is regarding Delphi in InsightII(2000). My problem with it is that with results obtained from Delphi, I calculated the change in electrostatic energy between the bound and unbound state of the complex to be about -100 kcal/mol to -150 kcal/mol. This seems like quite a big number even though I have a large protein but the ligand is a small a.a residues only. Recently when I tried between a grid resolution of 0.75 A and 1.00 A, the electrostatic energy of the complex obtained was -650 kt and 125 kt . I didn't think changing the grid resolution slight could produce such a large difference in the electrostatic energy. I've been running the calculations with solute dielectric of 2 and 8 and solvent 80 and zero ionic strength. I keep ending up with such large numbers when it comes to the electrostatic energy changes. It is more worthwhile to use Delphi software package(not the one from accelerys)? I hope that somebody can help. Thank you in advance. Regards, Rowyna From chemistry-request@server.ccl.net Fri Mar 14 18:03:47 2003 Received: from smtp2.ruc.dk ([130.225.220.70]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h2EN3l514025 for ; Fri, 14 Mar 2003 18:03:47 -0500 Received: by smtp2.ruc.dk (Postfix, from userid 504) id 379899A4494; Sat, 15 Mar 2003 00:03:46 +0100 (CET) Received: from virgil.ruc.dk (virgil.ruc.dk [130.225.220.110]) by smtp2.ruc.dk (Postfix) with ESMTP id 230539A4491; Sat, 15 Mar 2003 00:03:45 +0100 (CET) Received: from VIRGIL/SpoolDir by virgil.ruc.dk (Mercury 1.47); 15 Mar 03 00:03:45 +0100 Received: from SpoolDir by VIRGIL (Mercury 1.47); 15 Mar 03 00:03:38 +0100 From: "Jens Spanget-Larsen" Organization: Roskilde Universitetscenter To: Ian Hovell Date: Sat, 15 Mar 2003 00:03:11 +0100 Subject: CCL:solvating using gaussian98 Reply-To: spanget@ruc.dk Cc: chemistry@ccl.net X-Confirm-Reading-To: spanget@ruc.dk X-pmrqc: 1 Priority: normal X-mailer: Pegasus Mail for Windows (v2.23) Message-ID: <1040F4390488@virgil.ruc.dk> X-Spam-Status: No, hits=-3.2 required=5.0 tests=QUOTED_EMAIL_TEXT version=2.50 X-Spam-Level: X-Spam-Checker-Version: SpamAssassin 2.50 (1.173-2003-02-20-exp) Dear Ian: > I am using GaussianW98 > I am trying to solvate a molecule in a liquid other than the ones > described in the manual with the following input line > > # opt=tight hf/sto-3g* scrf=(pcm,dielectric=34.9) geom=connectivity > > It seem to ignore the dielectric value and reverts to water. Iam > doing something wrong here I know but I cant see it. > . . . . Yeah, this is annoying! I never succeeded in making this work with G98 (it was no problem with G94). I gave up and switched to IPCM. This is a somewhat more sophisticated SCRF-model where the solute/solvent boundary is defined as an electronic isodensity surface, allowed to relax in the solvent field. A job like the following, specifying, say, dielectric constant = 10 and isodensity = 0.001, will work. You may adjust the isodensity value to suit your problem. ---------------------------------------------------------- %chk=chryzrad #t B3LYP/EPR-II IPCM SCF=Tight Guess=Read Geom=Check test Chrysazin Radical Anion (eps=10, IsoDensity=0.001) -1 2 10 0.001 ---------------------------------------------------------- Yours, Jens >--< =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= JENS SPANGET-LARSEN Office: +45 4674 2710 Department of Chemistry Fax: +45 4674 3011 Roskilde University (RUC) Mobile: +45 2320 6246 P.O.Box 260 E-Mail: spanget@ruc.dk DK-4000 Roskilde, Denmark http://virgil.ruc.dk/~spanget =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= From chemistry-request@server.ccl.net Fri Mar 14 19:08:33 2003 Received: from nature.Berkeley.EDU ([128.32.175.19]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h2F08X515652 for ; Fri, 14 Mar 2003 19:08:33 -0500 Received: from localhost (localhost [127.0.0.1]) by nature.Berkeley.EDU (Postfix) with ESMTP id BFD96261365 for ; Fri, 14 Mar 2003 16:08:32 -0800 (PST) Received: from nature.Berkeley.EDU ([127.0.0.1]) by localhost (nature.Berkeley.EDU [127.0.0.1:10024]) (amavisd-new) with ESMTP id 02636-04 for ; Fri, 14 Mar 2003 16:08:32 -0800 (PST) Received: from nature.berkeley.edu (localhost [127.0.0.1]) by nature.Berkeley.EDU (Postfix) with SMTP id 04CE226135B for ; Fri, 14 Mar 2003 16:08:32 -0800 (PST) Received: from 128.32.27.14 (SquirrelMail authenticated user moconnor) by nature.Berkeley.EDU with HTTP; Fri, 14 Mar 2003 16:08:32 -0800 (PST) Message-ID: <2411.128.32.27.14.1047686912.squirrel@nature.Berkeley.EDU> Date: Fri, 14 Mar 2003 16:08:32 -0800 (PST) Subject: EXAFS From: "Dr. Mary V. O'Connor" To: "computational chemistry" X-Priority: 3 Importance: Normal X-Mailer: SquirrelMail (version 1.2.11) MIME-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit X-Virus-Scanned: by amavisd-new Dear CCL: Is there any way to turn EXAFS data for a unit cell into fractional co-ordinates suitable for building a lattice? Any help will be welcome (even an 'it can't be done', because then I will stop beating my head against a wall). Thanks as always, Mary Mary V. O'Connor, Ph.D. Berkeley, CA 94704 From chemistry-request@server.ccl.net Fri Mar 14 19:10:01 2003 Received: from mx3.ust.hk ([143.89.13.11]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h2F0A0515669 for ; Fri, 14 Mar 2003 19:10:01 -0500 Received: from ust.hk (sqmail2.ust.hk [143.89.13.12]) by mx3.ust.hk (8.12.8/8.12.8) with SMTP id h2F09uOc066659 for ; Sat, 15 Mar 2003 08:09:57 +0800 (HKT) Received: from 143.89.53.94 (SquirrelMail authenticated user chgy) by sqmail.ust.hk with HTTP; Sat, 15 Mar 2003 08:09:57 +0800 (HKT) Message-ID: <1300.143.89.53.94.1047686997.squirrel@sqmail.ust.hk> Date: Sat, 15 Mar 2003 08:09:57 +0800 (HKT) Subject: RE:Summary of gibbs free energy From: "GAO Yi" To: X-Priority: 3 Importance: Normal X-Mailer: SquirrelMail (version 1.2.8) MIME-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit Dear Everyone, Thank you for your help.Below are the summary of the response for my questions. Gao Yi Dear Gao, I have not much experience in the field of computational chemistry, but maybe I can be of help. The FREQ keyword in G98 yields gibbs corrections, that are only accurate as long as: -the normal modes you are considering are quite harmonic (otherwise, the partition function for this mode is not going to be very good) -the normal modes have a frequency high enough, that doesn't require a hindered rotor treatment. (I'm suposing here that the "non-local minimum" you are speaking of is the variational transition state theory minimum, sorry if I am mistaken and this answer is out of the point). Anyway, there is on the net (I don't remember where I printed this from) a paper called "Thermochemistry in Gaussian", that might be interesting. Regards, Olalla Nieto Faza Dpto. Qu¨ªmica Org¨¢nica Universidade de Vigo Lagoas-Marcosende 36200 Vigo faza@uvigo.es On Tue, 11 Mar 2003, GAO Yi wrote: > Dear CClers, > > I'm now calculating the gibbs energy via Gaussian98. I wonder whether I > can use the FREQ keyword to get the gibbs corrections for the non-local > minimum and whether these results are correct to represent the points of > the Gibbs free energy surface. > > Gao Yi > > > > -= This is automatically added to each message by mailing script =- > CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins > Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net Dear Gao, The calculation of frequencies in no-minimun-energy points is used, for example, when following the Minimum energy path (in order to sample the gibbs energy surface). The problem (of course) is that the first derivatives are not zero, so you have to project the frequencies that are not the frequency you are following (=the one that corresponds to the reaction coordinate) so that they are ortogonal to the gradient vector. This can be done with the GAMESS package (though I haven't used it), I don't know if G98 has this option implemented. (I think Truhlar has written about this kind of things if you need further reference; there are some programmes of his group Polyrate and Gaussrate that do this kind of variational studies, but here ends all my expertise in the subject). Regards Olalla Nieto Faza Dpto. Quimica Organica Universidade de Vigo Lagoas-Marcosende 36200 Vigo (Spain) e-mail: faza@uvigo.es No, but take a look at freq=projected for special cases, e.g. points on a carefully optimised reaction path, inflection points on surface... Hope this helps, J. ---------------------------------------------------------------------- Jeremy Greenwood jeremy@greenwood.net Department of Medicinal Chemistry bh +45 35306117 The Danish University of Pharmaceutical Sciences fx +45 35306040 Universitetsparken 2, DK-2100 Copenhagen, Denmark ah +45 32598030 ---------------------------------------------------------------------- The great thing about crummy software is the amount of employment it generates. If Moore's Law is upheld for another twenty or thirty years, there will not only be a vast amount of computation going on Planet Earth, but also the maintenance of that computation will consume the efforts of almost every living person. We're talking about a planet of helpdesks. -- Jaron Lanier ---------------------------------------------------------------------- Short answer is no. The thermodynamic corrections involve zero-point energies computed from the vibrational frequencies and temperature corrections from the partition functions. Both of these presume that the gradient is zero in the analysis which results in frequencies and at arbitrary points on the surface this is not true. There are special cases such as along a reaction path, where the forces can be projected out and the structure minimized wrt all other coordinates and the FREQ=Projected option can be used. But for arbitrary points, while the data is printed it is not rigorously correct. > > Dear CClers, > > I'm now calculating the gibbs energy via Gaussian98. I wonder whether I > can use the FREQ keyword to get the gibbs corrections for the non-local > minimum and whether these results are correct to represent the points of > the Gibbs free energy surface. > > Gao Yi > > > > -= This is automatically added to each message by mailing script =- > CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins > Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net > > > > > -- Douglas J. Fox Technical Support Gaussian, Inc. help@gaussian.com