From chemistry-request@server.ccl.net Wed Sep 20 02:37:56 2000 Received: from fjohn.Stanford.EDU (fjohn.Stanford.EDU [171.64.38.72]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id CAA27639 for ; Wed, 20 Sep 2000 02:37:56 -0400 Received: from localhost (greg@localhost) by fjohn.Stanford.EDU (8.9.3/8.9.3) with ESMTP id XAA01596 for ; Tue, 19 Sep 2000 23:37:48 -0700 Date: Tue, 19 Sep 2000 23:37:48 -0700 (PDT) From: Greg Lakatos To: chemistry@ccl.net Subject: Electromagnetic waves within CHARMm Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hello, Does anyone know if it is possible to have CHARMm simulate the effects of an EM wave interacting with a macromolecule? In particular, is there a way to get CHARMm to compute the Lorentz force acting on an atom given the wavevector, polarization, amplitude, and frequency of the wave? Thanks very much for the help. - Greg Lakatos (glakatos@fjohn.stanford.edu) From chemistry-request@server.ccl.net Wed Sep 20 04:10:36 2000 Received: from alice.phy.tcd.ie (alice.phy.tcd.ie [134.226.69.20]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id EAA28228 for ; Wed, 20 Sep 2000 04:10:35 -0400 Received: (from jhayes@localhost) by alice.phy.tcd.ie (8.9.1/8.9.1) id JAA25231 for chemistry@ccl.net; Wed, 20 Sep 2000 09:08:09 +0100 (BST) From: Joe Hayes Message-Id: <200009200808.JAA25231@alice.phy.tcd.ie> Subject: ESFF forcefield To: chemistry@ccl.net Date: Wed, 20 Sep 2000 9:08:09 BST X-Mailer: Elm [revision: 212.4] Hi, I'm looking for information re. the ESFF forcefield. It was originally supplied by Bisoym with their Discover/Insight II software, but I can't seem to get a literature reference. All references I have found state that the paper was in preparation. To my knowledge, ESFF is no longer available and being used. But could someone please let me know (1) if there is a ESFF reference ? (2) what has happened to ESFF? (3) if there is a direct descendant of ESFF, i.e. new forcefield based on ESFF but under another name. Thanks J.H. From chemistry-request@server.ccl.net Wed Sep 20 05:10:22 2000 Received: from cheviot3.ncl.ac.uk (root@cheviot.ncl.ac.uk [128.240.233.51]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id FAA28484 for ; Wed, 20 Sep 2000 05:10:21 -0400 Received: from aidan.ncl.ac.uk (nbwt@aidan.ncl.ac.uk [128.240.233.1]) by cheviot3.ncl.ac.uk (8.10.1/8.10.1) with ESMTP id e8K9A7Z15509 for ; Wed, 20 Sep 2000 10:10:09 +0100 (BST) Received: from localhost (nbwt@localhost) by aidan.ncl.ac.uk (8.9.3+Sun/8.9.0) with ESMTP id KAA24828 for ; Wed, 20 Sep 2000 10:10:01 +0100 (BST) X-Authentication-Warning: aidan.ncl.ac.uk: nbwt owned process doing -bs Date: Wed, 20 Sep 2000 10:10:01 +0100 (GMT) From: "Bruce. Tattershall" To: Computational Chemistry List Subject: Babel Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-Filter-Version: 1.8 (cheviot3) The recent correspondence about Babel seems to reveal a bit of a web jungle. As far as I can see, the Open Eyes site yields a very old unix version, which is pre- g94. Version 1.6, which I have found very useful for reading g94 output, seems to be still available via http://www.chem.ohiou.edu/~dolata/babel.html What seems desperately missing is a unix version (which for me needs to be usable on a Sun) which can read g98 output. Is this available anywhere? Bruce Tattershall Dept. of Chemistry, Univ. of Newcastle, England Bruce.Tattershall@newcastle.ac.uk From chemistry-request@server.ccl.net Wed Sep 20 00:26:13 2000 Received: from cheetah.it.wsu.edu (root@cheetah.it.wsu.edu [134.121.1.8]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id AAA27199 for ; Wed, 20 Sep 2000 00:26:13 -0400 Received: from ucis (ucis.chem.wsu.edu [134.121.41.180]) by cheetah.it.wsu.edu (8.9.3/8.9.3) with SMTP id VAA02418; Tue, 19 Sep 2000 21:25:58 -0700 (PDT) Message-ID: <000f01c022ba$dfe126b0$b4297986@chem.wsu.edu> From: "Phillip Matz" To: "Sidney Ramos" , "CCL List" References: <39C80C69.86220B4F@dqfex.ufpe.br> Subject: Re: CCL:What is mean? Date: Tue, 19 Sep 2000 21:25:58 -0700 MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 5.50.4133.2400 X-MimeOLE: Produced By Microsoft MimeOLE V5.50.4133.2400 Hello Sydney! If your input is EXACTLY as you included in your CCL email then you need to remove one of the empty lines between the charge/multiplicity line and the cube filename line (you currently indicate 2, you need only one). Let me know if that solves the problem! Respectfully, Phillip Matz matz@wsunix.wsu.edu ----- Original Message ----- From: "Sidney Ramos" To: "CCL List" Sent: Tuesday, September 19, 2000 6:01 PM Subject: CCL:What is mean? > Dear CCL Users, > > I did try perform a calculation of electronic density in the > Gaussian 98 but it stop and write the error message below: > > open: [2] No such file or directory > logical unit 31, named '' > > This is my input file: > > %chk=1Phoh_b3lyp.chk > # B3LYP/6-31G* Pop=NBO Density=Current Cube=Density Geom=Check > Guess=Read > > 1Phoh > > 0 1 > > > 1Phoh_b3lyp.cube > > and the checkpoint file is in the directory of input. > Thanks for any help! > Best Regards! > > Sidney Ramos > DQF - CCEN - UFPE > > > -= 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 Wed Sep 20 05:19:32 2000 Received: from lrz.uni-muenchen.de (root@f-215-6.cvx.ipdial.viaginterkom.de [62.180.215.6]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id FAA28550 for ; Wed, 20 Sep 2000 05:19:30 -0400 Received: (from eugene.leitl@localhost) by lrz.uni-muenchen.de (8.8.8/8.8.8) id BAA10943; Wed, 20 Sep 2000 01:15:54 -0700 From: Eugene Leitl MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Message-ID: <14792.29241.292506.656476@lrz.uni-muenchen.de> Date: Wed, 20 Sep 2000 01:15:53 -0700 (PDT) To: Greg Lakatos Cc: chemistry@ccl.net Subject: CCL:Electromagnetic waves within CHARMm In-Reply-To: References: X-Mailer: VM 6.71 under 21.1 (patch 4) "Arches" XEmacs Lucid Greg Lakatos writes: > Does anyone know if it is possible to have CHARMm simulate the effects of > an EM wave interacting with a macromolecule? In particular, is > there a way to get CHARMm to compute the Lorentz force acting on an atom > given the wavevector, polarization, amplitude, and frequency of the wave? I'm also interested in an answer to this, with an angle on NEMS (nano electro mechanical systems) utilizing optics and generally operating in a high energy density dissipation regime. From chemistry-request@server.ccl.net Wed Sep 20 06:42:34 2000 Received: from mel.ruc.dk (mel.ruc.dk [130.225.220.27]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id GAA28853 for ; Wed, 20 Sep 2000 06:42:34 -0400 Received: from smtprelay.ruc.dk (smtprelay.ruc.dk [130.225.220.22]) by mel.ruc.dk (8.9.3/8.9.1) with ESMTP id MAA08632 for ; Wed, 20 Sep 2000 12:42:23 +0200 (MET DST) Received: from virgil.ruc.dk (virgil.ruc.dk [130.225.220.110]) by smtprelay.ruc.dk (8.9.3+Sun/8.9.3) with ESMTP id MAA24450 for ; Wed, 20 Sep 2000 12:32:32 +0200 (MEST) Received: from VIRGIL/SpoolDir by virgil.ruc.dk (Mercury 1.44); 20 Sep 00 12:42:23 +0100 Received: from SpoolDir by VIRGIL (Mercury 1.44); 20 Sep 00 12:42:18 +0100 From: "Jens Spanget-Larsen" Organization: Roskilde Universitetscenter To: CHEMISTRY@ccl.net Date: Wed, 20 Sep 2000 12:42:17 +0100 Subject: CCL: Aromaticity, pi and sigma? (summary) Priority: normal X-mailer: Pegasus Mail for Windows (v2.23) Message-ID: Dear CCL, thank you to all of you who helped me with my search for literature on the relative roles of sigma and pi systems in "aromaticity": > I saw some time ago a paper with a theoretical analysis of the origin of > "aromaticity" in benzene (and possibly other species), concluding that the > so-called aromatic stability originated from the sigma-system rather than the > pi-system. However, I cannot trace the original reference. Anybody knows it? > Have additional work been published in this field? Below is a list of the suggested literature references. Yours, Jens >--< S.S. Shaik, P.C. Hiberty: J. Amer. Chem. Soc. 107, 3089 (1985). S.S. Shaik et al.: J. Org. Chem. 50, 4657 (1985). P.C. Hiberty, S.S. Shaik, G. Ohanessian, J.-M. Lefour: J. Org. Chem. 51, 3908 (1986). S.S. Shaik, P.C. Hiberty, J.-M. Lefour and G. Ohanessian: J. Am. Chem. Soc. 109, 363 (1987). G. Ohanessian, P.C. Hiberty, J.-M. Lefour, J.-P. Flament, S.S. Shaik: Inorg. Chem. 27, 2219 (1988). K. Jug, A. Koester: J. Am. Chem. Soc. 112, 6772 (1990). J. Schuett, M.C. Boehm: J. Am. Chem. Soc. 114, 7252 (1992). E.D. Glendening, R. Faust, A. Streitwieser, K.P.C. Vollhardt, F. Weinhold: J. Amer. Chem. Soc. 115, 10952 (1993). P.C. Hiberty, G. Ohanessian G, S.S. Shaik, J.P. Flament JP: Pure & Appl. Chem. 65, 35 (1993). P.C. Hiberty, D. Danovich, A. Shurki, S. Shaik: J. Am. Chem. Soc. 117, 7760 (1995). A. Gobbi, Y. Yamaguchi, G. Frenking, H.F. Schaefer III: Chem. Phys. Lett. 244, 27 (1995). F. Bernardi, P. Celani, M. Olivucci, M.A. Robb, G. Suzzivalli: J. Amer. Chem. Soc. 117, 10531 (1995). M.J. Bearpark, F. Bernardi, S. Clifford, M. Olivucci, M.A. Robb, T. Vreven: Mol. Phys. 89, 37 (1996). M.J. Bearpark, F. Bernardi, M. Olivucci, M.A. Robb: Int. J. Quantum Chem. 60, 505 (1996). S. Clifford, M.J. Bearpark, F. Bernardi, M. Olivucci, M.A. Robb, B.R. Smith: J. Amer. Chem. Soc. 118, 7353 (1996). S. Shaik, S. Zilberg, Y. Haas: Accts. Chem. Res. 29, 211 (1996). S. Shaik, A. Shurki, D. Danovich, P.C. Hiberty: J. Mol. Struct. (Theochem) 398-399, 155 (1997). M. Sola, J. Mestres and M. Duran: J. Phys. Chem. 1995, 99, 10752. J.M. Galbraith, E. Blank, S. Shaik, P.C. Hiberty: Chemistry - A European Journal 6, 2425 (2000). M.C. Boehm, C. Saal: Int. J. Quantum Chem. 79, 125 (2000). =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= JENS SPANGET-LARSEN Phone: +45 4674 2000 (RUC) Department of Chemistry +45 4674 2710 (direct) Roskilde University (RUC) Fax: +45 4674 3011 P.O.Box 260 E-Mail: JSL@virgil.ruc.dk DK-4000 Roskilde, Denmark http://www.rub.ruc.dk/dis/chem/psos/ =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= From chemistry-request@server.ccl.net Wed Sep 20 08:33:42 2000 Received: from judy.ic.ac.uk (judy.ic.ac.uk [155.198.5.28]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id IAA30407 for ; Wed, 20 Sep 2000 08:33:41 -0400 Received: from juliet.ic.ac.uk ([155.198.5.4]) by judy.ic.ac.uk with esmtp (Exim 2.12 #1) id 13bj45-0006jn-00 for chemistry@ccl.net; Wed, 20 Sep 2000 13:33:29 +0100 Received: from sg1.cc.ic.ac.uk ([155.198.63.8] helo=cscmgb.cc.ic.ac.uk) by juliet.ic.ac.uk with esmtp (Exim 2.12 #1) id 13bj4F-0000Y5-00 for chemistry@ccl.net; Wed, 20 Sep 2000 13:33:39 +0100 Received: from [155.198.234.86] by cscmgb.cc.ic.ac.uk (980427.SGI.8.8.8/4.0) id NAA11781; Wed, 20 Sep 2000 13:33:23 +0100 (bst) Mime-Version: 1.0 X-Sender: rzepa@argon.ch.ic.ac.uk Message-Id: In-Reply-To: References: Date: Wed, 20 Sep 2000 13:30:42 +0100 To: chemistry@ccl.net From: "Rzepa, Henry" Subject: A Babel of Babels Cc: chemistry@ccl.net Content-Type: text/plain; charset="us-ascii" >The recent correspondence about Babel seems to reveal a bit of a web jungle. >As far as I can see, the Open Eyes site yields a very old unix version, which >is pre- g94. Version 1.6, which I have found very useful for reading >g94 output, seems to be still available via > http://www.chem.ohiou.edu/~dolata/babel.html > >What seems desperately missing is a unix version (which for me needs to be >usable on a Sun) which can read g98 output. > >Is this available anywhere? There are of course many Babel-like programs often lurking inside other programs as input/output filters. One good for G94/98 outputs is JMol (which, being Java, is more or less cross platform, and will certainly work on Sun). http://www.openscience.org/jmol/index.html There have been occasions, when I have had to use 2-3 file conversion programs in series in order to achieve a lossy but reliable conversion of one format to another Old timers will sense Deja-vu, but for a different approach to file transformations, see http://www.xml-cml.org/ which has been rejuvenated (!) and contains much information about this sort of thing under the Chimeral heading. The promised land of course is one where every program outputs in XML, and Babel is replaced by XSLT transform collections.. Chimeral is an illustration of this, using a Browser (IE5) as the transform engine. -- Henry Rzepa. +44 (0)20 7594 5774 (Office) +44 (0)20 7594 5804 (Fax) Dept. Chemistry, Imperial College, London, SW7 2AY, UK. http://www.ch.ic.ac.uk/rzepa/ From chemistry-request@server.ccl.net Wed Sep 20 09:35:07 2000 Received: from silver.ch.unito.it (silver.ch.unito.it [130.192.118.1]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id JAA30700 for ; Wed, 20 Sep 2000 09:35:06 -0400 Received: (from milanesi@localhost) by silver.ch.unito.it (8.9.3/8.9.3) id PAA18666; Wed, 20 Sep 2000 15:48:55 +0200 (MET DST) Date: Wed, 20 Sep 2000 15:48:54 +0200 (MET DST) From: Marco Milanesio To: Chan Kyung Kim cc: CHEMISTRY@ccl.net Subject: Re: CCL:How to obtain NBO4.0 In-Reply-To: <001801c01fbb$6624b140$4d9af6a5@inha.ac.kr> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear Chan, I think that you can request NBO4.0 from the author: Professor Frank Weinhold Department of Chemistry, Room 8309A University of Wisconsin-Madison 1101 University Ave. Madison, WI 53706 USA Voice: (608) 262-0263 or 262-1511 E-Mail: weinhold@chem.wisc.edu or search the University of Winsconsin web site: http://www.chem.wisc.edu/main/research/ Marco Milanesio On Sat, 16 Sep 2000, Chan Kyung Kim wrote: > > Dear Computational Chemists: > > I think this question was already on the list on August 26, 1999. > But I could not find the answer from CCL. I also could not get reply > >from the original sender. So, please forgive me for duplicate question. > > Where can I get NBO 4.0 (to implement on Gaussian 98 or GAMESS)? > From chemistry-request@server.ccl.net Wed Sep 20 10:16:29 2000 Received: from lulu.it.northwestern.edu (lulu.acns.nwu.edu [129.105.16.54]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id KAA30930 for ; Wed, 20 Sep 2000 10:16:29 -0400 Received: (from mailnull@localhost) by lulu.it.northwestern.edu (8.8.7/8.8.7) id JAA04138 for ; Wed, 20 Sep 2000 09:16:17 -0500 (CDT) Received: from ficus (ficus.at.nwu.edu [129.105.233.95]) by lulu.acns.nwu.edu via smap (V2.0) id xma003601; Wed, 20 Sep 00 09:14:59 -0500 Message-Id: <4.2.2.20000920091410.00ac5c20@lulu.acns.nwu.edu> X-Sender: far482@lulu.acns.nwu.edu X-Mailer: QUALCOMM Windows Eudora Pro Version 4.2.2 Date: Wed, 20 Sep 2000 09:17:36 -0500 To: chemistry@ccl.net From: "Frederick P. Arnold, Jr." Subject: Re: CCL:A Babel of Babels In-Reply-To: References: Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii"; format=flowed Depending what format you need the output in, you could always use gOpenMol or Molden to read your G98 output file, and then write it back out in something (generally xyz, but in the case of Molden from the zmat editor, a host of zmats (gamess, g9x, mopac) that you can use. Molden will also write cml, but I'm not sure what that gets you at this point in time, except forward compatibility. (I have great hopes for CML, but I seem to remember that HDF was going to cure some of these problems as well) -Fred Frederick P. Arnold, Jr. NUIT Northwestern University, Evanston, IL. USA f-arnold@northwestern.edu From chemistry-request@server.ccl.net Wed Sep 20 10:26:46 2000 Received: from gandalf.cber.nih.gov (gandalf.cber.nih.gov [128.231.52.5]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id KAA30988 for ; Wed, 20 Sep 2000 10:26:46 -0400 Received: from localhost (rvenable@localhost) by gandalf.cber.nih.gov (980427.SGI.8.8.8/980728.SGI.AUTOCF) via ESMTP id KAA89450; Wed, 20 Sep 2000 10:29:56 -0400 (EDT) Date: Wed, 20 Sep 2000 10:29:56 -0400 From: Rick Venable To: Eugene Leitl cc: Greg Lakatos , chemistry@ccl.net Subject: Re: CCL:Electromagnetic waves within CHARMm In-Reply-To: <14792.29241.292506.656476@lrz.uni-muenchen.de> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Greg Lakatos writes: > Does anyone know if it is possible to have CHARMm simulate the > effects of an EM wave interacting with a macromolecule? In > particular, is there a way to get CHARMm to compute the Lorentz > force acting on an atom given the wavevector, polarization, > amplitude, and frequency of the wave? On Wed, 20 Sep 2000, Eugene Leitl wrote: > I'm also interested in an answer to this, with an angle on NEMS (nano > electro mechanical systems) utilizing optics and generally operating > in a high energy density dissipation regime. There is an addition to CHARMM (academic), but perhaps not in CHARMMm (commercial) yet, named PULL described in cons.doc as follows: [SYNTAX External Forces] PULL { FORCe } XDIR YDIR ZDIR [PERIod ] { EFIEld } { OFF } { LIST } [WEIGht] atom-selection A force will be applied in the specified direction on the selected atoms either as a constant: FORCe specified in picoNewtons (pN) or oscillating in time: FORCe*COS(TWOPI*TIME/PERIod), FORCe PERIod time is counted from the start of the dynamcis run. The force due to an electrical EFIEld (V/m) (possibly also oscillating) may also be specified, in which case partial charges are taken from the psf and used to calculate the force. If WEIGht is specified the forces are multiplied by the wmain array. Each invocation of this command adds a set of forces to the previously defined set. PULL OFF turns off all these forces. PULL LIST produces a listing. NB! Forces defined by PULL will move atoms in the specified direction, which is opposite to that listed by the forces from the COOR FORCE command. -- Rick Venable =====\ |=| "Eschew Obfuscation" FDA/CBER Biophysics Lab |____/ |=| Bethesda, MD U.S.A. | \ / |=| ( Not an official statement or Rick_Venable@nih.gov | \ / |=| position of the FDA; for that, rvenable@speakeasy.org \/ |=| see http://www.fda.gov ) From chemistry-request@server.ccl.net Wed Sep 20 07:30:04 2000 Received: from risc1.gfq.uff.br (risc1.gfq.uff.br [200.20.3.195]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id HAA29972 for ; Wed, 20 Sep 2000 07:29:59 -0400 Received: from abulafia (abulafia.quimica.uff.br [200.20.3.52]) by risc1.gfq.uff.br (AIX4.3/UCB 8.8.8/8.8.8) with SMTP id IAA05670 for ; Wed, 20 Sep 2000 08:23:38 -0300 Message-ID: <002a01bcc101$000cd3e0$340314c8@quim.uff.br> From: "Alex Gutterres Taranto" To: Subject: Babel ? Date: Sun, 14 Sep 1997 08:26:08 -0300 Hello !!! Can babel tranform the output of G98W (BUT THE OPTIMIZED GEOMETRY) to = input to mopac ? Thanks, Alex From chemistry-request@server.ccl.net Wed Sep 20 08:39:31 2000 Received: from www3.pobox.sk (www3.pobox.sk [212.5.216.13]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id IAA30451 for ; Wed, 20 Sep 2000 08:39:31 -0400 Received: from localhost (localhost [127.0.0.1]) by www3.pobox.sk (POBOX server v.III/1.2) with SMTP id OAA03197 for ; Wed, 20 Sep 2000 14:54:22 +0200 Date: Wed, 20 Sep 2000 14:54:22 +0200 Message-Id: <200009201254.OAA03197@www3.pobox.sk> From: Shotgun Reply-To: Shotgun To: chemistry@ccl.net MIME-Version: 1.0 Content-Type: TEXT/plain; charset=iso-8859-2 X-Pobox-Id: 672187806 X-User-Agent: Mozilla/4.0 (compatible; MSIE 5.5; Windows 98) X-Mailer: POBOX (mico's engine 5.0/3.0.1) Content-Transfer-Encoding: 8bit I am a student of Faculty of Natural Sciences of UPJS and I am trying to compute ( using programme GAMESS ) the general reaction path of addition of ammonia to NCS group. But there is a problem with one IRC calculation. I have found a transition state,hessian computed at this transition geometry has one and only one imaginatory frequency ( value about 2060 ), so ti seems to be OK.I have also tried different methods of finding TS and all resulted to the same structure and same value of imaginatory frequency.But an IRC calculation stops after computing the first point,because the energy of this point is higher than the energy of TS. Please send me some advices,how to solve this problem.My address is maverick@pobox.sk Thank you. From chemistry-request@server.ccl.net Wed Sep 20 09:15:02 2000 Received: from web220.mail.yahoo.com (web220.mail.yahoo.com [128.11.68.120]) by server.ccl.net (8.8.7/8.8.7) with SMTP id JAA30609 for ; Wed, 20 Sep 2000 09:15:02 -0400 Message-ID: <20000920131447.2737.rocketmail@web220.mail.yahoo.com> Received: from [194.249.15.130] by web220.mail.yahoo.com; Wed, 20 Sep 2000 06:14:47 PDT Date: Wed, 20 Sep 2000 06:14:47 -0700 (PDT) From: Irena Bonin Subject: solvation energies To: chemistry@ccl.net MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Dear CCLers Can someone help me to find a good program for calculating solvation energies (for enzyme-substrate systems)and for the evaluation of the solvent-accessible surface. Thanks. __________________________________________________ Do You Yahoo!? Send instant messages & get email alerts with Yahoo! Messenger. http://im.yahoo.com/ From chemistry-request@server.ccl.net Wed Sep 20 09:49:57 2000 Received: from ccl.net (atlantis.ccl.net [192.148.249.4]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id JAA30800 for ; Wed, 20 Sep 2000 09:49:57 -0400 Received: from hscmg02.hou.ucarb.com (hscmg02.hou.ucarb.com [144.68.4.25]) by ccl.net (8.9.3/8.9.3/OSC 2.0) with ESMTP id JAA11554 for ; Wed, 20 Sep 2000 09:49:43 -0400 (EDT) Received: by hscmg02.hou.ucarb.com with Internet Mail Service (5.5.2650.10) id ; Wed, 20 Sep 2000 08:50:09 -0500 Message-ID: <47F7EAA0389AD011840500805FEAB9C6043C934C@sctms01.sct.ucarb.com> From: "Fulton CR (Charles)" To: "'Bruce. Tattershall'" Cc: "'CCL'" Subject: RE: Babel Date: Wed, 20 Sep 2000 08:50:06 -0500 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2650.10) Content-Type: text/plain > What seems desperately missing is a unix version (which for me needs to be > usable on a Sun) which can read g98 output. > I have written a few gaussian98 extracting programs in perl, if your interested. One of which does a simple (xyz coordinates) conversion to cml. Another perl program that will read in a large number of g98 outputs extract the data and dump into a nice tab delimited data file. I took some time a few months back to look at the babel code for reading gaussian94 input, I believe it would be pretty trivial for a real programmer (tm) to modify that code to read gaussian98 outputs. The biggest change from g94 -> g98 (as far as just getting the xyz coordinates) is in the "Standard orientation" section. The number of fields is different. You should definitely take a look at both the cml site and Jmol. -charlie > ------------------------------------------------------------------------ > "Open your source and they will come" - various. > > Charles Fulton > Catalyst Skill Center > Union Carbide Corporation > S. Charleston, WV. phone: (304) 747-3175 email: fultoncr@ucarb.com > > From chemistry-request@server.ccl.net Wed Sep 20 13:00:38 2000 Received: from cheetah.it.wsu.edu (root@cheetah.it.wsu.edu [134.121.1.8]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id NAA31975 for ; Wed, 20 Sep 2000 13:00:37 -0400 Received: from ucis (ucis.chem.wsu.edu [134.121.41.180]) by cheetah.it.wsu.edu (8.9.3/8.9.3) with SMTP id KAA18165; Wed, 20 Sep 2000 10:00:20 -0700 (PDT) Message-ID: <000d01c02324$420fa410$b4297986@chem.wsu.edu> From: "Phillip Matz" To: "Shotgun" , References: <200009201254.OAA03197@www3.pobox.sk> Subject: Re: No Subject Given By The Author Date: Wed, 20 Sep 2000 10:00:19 -0700 MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-2" Content-Transfer-Encoding: 7bit X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 5.50.4133.2400 X-MimeOLE: Produced By Microsoft MimeOLE V5.50.4133.2400 Hello! It sounds like the IRC is following a reaction path which is leading to a saddle point instead of a the standard "reactants go to products" IRC you would like to see with your TS. Just a thought... If the above is true then your options/problems have increased tenfold - you can try to characterize the system better by searching for a 2nd order saddle point (an option for the OPT keyword), or you can try and force the IRC to follow the reaction coordinate which would give you a standard reaction path. To do this try the PHASE switch for the IRC keyword. Hope that helps a little! Respectfully, Phillip Matz matz@wsunix.wsu.edu ----- Original Message ----- From: "Shotgun" To: Sent: Wednesday, September 20, 2000 5:54 AM Subject: No Subject Given By The Author > > I am a student of Faculty of Natural Sciences of UPJS and I am trying to > compute ( using programme GAMESS ) the general reaction path of addition of > ammonia to NCS group. > > But there is a problem with one IRC calculation. > I have found a transition state,hessian computed at this transition geometry > has one and only one imaginatory frequency ( value about 2060 ), so ti seems > to be OK.I have also tried different methods of finding TS and all resulted > to the same structure and same value of imaginatory frequency.But an IRC > calculation stops after computing the first point,because the energy of > this point is higher than the energy of TS. > > Please send me some advices,how to solve this problem.My address is > maverick@pobox.sk > Thank you. > > > > > > -= 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 Wed Sep 20 14:09:22 2000 Received: from mailgw.cc.uga.edu (mailgw.cc.uga.edu [128.192.1.101]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id OAA32376 for ; Wed, 20 Sep 2000 14:09:22 -0400 Received: from zopyros.ccqc.uga.edu by mailgw.cc.uga.edu (LSMTP for Windows NT v1.1b) with SMTP id <0.024F63ED@mailgw.cc.uga.edu>; Wed, 20 Sep 2000 14:07:37 -0400 Received: from localhost (zxwang@localhost) by zopyros.ccqc.uga.edu (8.9.1/8.9.1) with SMTP id OAA29839 for ; Wed, 20 Sep 2000 14:09:07 -0400 Date: Wed, 20 Sep 2000 14:09:06 -0400 (EDT) From: Zhi-Xiang Wang To: chemistry@ccl.net Subject: global minimum Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear CClers I'm interesting in locating global minima for clusers or molecules with atom numbers larger than 20. I would like to know some suggestions from you. Thank you very much. Sincerely Zhixiang From chemistry-request@server.ccl.net Wed Sep 20 11:53:18 2000 Received: from mailhost.msi.com (fire.msi.com [146.202.0.242]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id LAA31557 for ; Wed, 20 Sep 2000 11:53:17 -0400 Received: (from daemon@localhost) by mailhost.msi.com (980427.SGI.8.8.8/970903.SGI.AUTOCF) id IAA06680; Wed, 20 Sep 2000 08:47:41 -0700 (PDT) Received: from osman-pc.msi.com(146.202.7.202) by mailhost.msi.com via smap (V2.0) id xma006651; Wed, 20 Sep 00 08:47:11 -0700 Message-Id: <5.0.0.25.0.20000920083737.01f0bd50@146.202.6.217> X-Sender: osman@146.202.6.217 X-Mailer: QUALCOMM Windows Eudora Version 5.0 Date: Wed, 20 Sep 2000 08:52:44 -0500 To: chemistry@server.ccl.net, CHMINF-L@LISTSERV.INDIANA.EDU, qsar_society@unil.ch From: "Osman F. Guner" Subject: Call for papers: Advances in 3D Searching and Pharmacophores Mime-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1"; format=flowed Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id LAA31560 ADVANCES IN 3D SEARCHING AND PHARMACOPHORES At Spring ACS meeting in San Diego (April 1-5, 2001) Sponsored by the Chemical Information Division (CINF) Co-sponsored by Division of Medicinal Chemistry (MEDI) and Computers in Chemistry (COMP) The symposium will be on recent advances in 3D searching and pharmacophore development technologies as well as successes in using these technologies in drug discovery and design. Please use the OASys to submit your abstract. You can access the CINF symposia at OASys via http://oasys.acs.org/acs/221nm/cinf/papers/index.cgi. The deadline for submitting abstracts is November 30th. --- Osman F. Güner, Ph.D. Director, Lead Identification & Optimization Molecular Simulations Inc. (858) 799-5341 osman@msi.com http://www.msi.com From chemistry-request@server.ccl.net Wed Sep 20 14:01:49 2000 Received: from usc.edu (root@usc.edu [128.125.253.136]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id OAA32344 for ; Wed, 20 Sep 2000 14:01:49 -0400 Received: from chem1.usc.edu (chem1.usc.edu [128.125.8.55]) by usc.edu (8.9.3.1/8.9.3/usc) with ESMTP id LAA24017; Wed, 20 Sep 2000 11:01:33 -0700 (PDT) Received: from usc.edu (IDENT:jorgevil@futura.usc.edu [128.125.14.59]) by chem1.usc.edu (8.9.3.1/8.9.3/usc) with ESMTP id LAA32500; Wed, 20 Sep 2000 11:01:33 -0700 Sender: jorgevil@chem1.usc.edu Message-ID: <39C8FBBE.617C8C49@usc.edu> Date: Wed, 20 Sep 2000 11:02:38 -0700 From: Jordi Villa X-Mailer: Mozilla 4.61 [en] (X11; I; Linux 2.2.12-20 i686) X-Accept-Language: en MIME-Version: 1.0 CC: Shotgun , chemistry@ccl.net Subject: Re: CCL:No Subject Given By The Author References: <200009201254.OAA03197@www3.pobox.sk> <000d01c02324$420fa410$b4297986@chem.wsu.edu> Content-Type: multipart/alternative; boundary="------------7078A7B38B86F02C54BA93E7" --------------7078A7B38B86F02C54BA93E7 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit I would use a smaller stepsize. Probably the first step in your calculation is so large that you are not in the "valley" anymore. > > > > I am a student of Faculty of Natural Sciences of UPJS and I am trying to > > compute ( using programme GAMESS ) the general reaction path of addition > of > > ammonia to NCS group. > > > > But there is a problem with one IRC calculation. > > I have found a transition state,hessian computed at this transition > geometry > > has one and only one imaginatory frequency ( value about 2060 ), so ti > seems > > to be OK.I have also tried different methods of finding TS and all > resulted > > to the same structure and same value of imaginatory frequency.But an IRC > > calculation stops after computing the first point,because the energy of > > this point is higher than the energy of TS. > > > > Please send me some advices,how to solve this problem.My address is > > maverick@pobox.sk > > Thank you. > > > > > > > > > > > > CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To > Admins > > 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 > > > > > > > > > > > > -= 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 -- Jordi Villa i Freixa jorgevil@usc.edu http://laetro.usc.edu/wgroup/people/jorgevil Department of Chemistry, University of Southern California Los Angeles, CA, USA, 90089-1062 Tlf: 1-(213)-740 7671 Fax: 1-(213)-740 2701 --------------7078A7B38B86F02C54BA93E7 Content-Type: text/html; charset=us-ascii Content-Transfer-Encoding: 7bit I would use a smaller stepsize. Probably the first step in your calculation is so large that you are not in the "valley" anymore.
>
> I am a student of Faculty of Natural Sciences of UPJS and I am trying to
> compute ( using programme GAMESS ) the general reaction path of addition
of
> ammonia to NCS group.
>
> But there is a problem with one IRC calculation.
> I have found a transition state,hessian computed at this transition
geometry
> has one and only one imaginatory frequency ( value about 2060 ), so ti
seems
> to be OK.I have also tried different methods of finding TS and all
resulted
> to the same structure and same value of imaginatory frequency.But an IRC
> calculation stops after computing the first point,because the energy of
> this point is higher than the energy of TS.
>
> Please send me some advices,how to solve this problem.My address is
> maverick@pobox.sk
> Thank you.
>
>
>
>
>
> CHEMISTRY@ccl.net -- To Everybody    |   CHEMISTRY-REQUEST@ccl.net -- To
Admins
> 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
>
>
>
>
>

-= 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

-- 
Jordi Villa i Freixa                  
jorgevil@usc.edu   http://laetro.usc.edu/wgroup/people/jorgevil
Department of Chemistry, University of Southern California
Los Angeles, CA, USA, 90089-1062
Tlf: 1-(213)-740 7671 Fax: 1-(213)-740 2701
  --------------7078A7B38B86F02C54BA93E7-- From chemistry-request@server.ccl.net Wed Sep 20 14:41:46 2000 Received: from ucidoor.unitedcatalysts.com ([208.23.162.2]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id OAA32561 for ; Wed, 20 Sep 2000 14:41:46 -0400 Received: by ucidoor.unitedcatalysts.com; (8.8.8/1.3/10May95) id OAA20212; Wed, 20 Sep 2000 14:41:45 -0400 (EDT) Received: from 10.1.0.50 by ucismtp02.unitedcatalysts.com (InterScan E-Mail VirusWall NT); Wed, 20 Sep 2000 14:42:05 -0400 (Eastern Daylight Time) Received: from lvlxch01.unitedcatalysts.com ([10.1.0.88]) by lvlmail.unitedcatalysts.com (PMDF V6.0-24 #41777) with ESMTP id <0G1700C027S64M@lvlmail.unitedcatalysts.com>; Wed, 20 Sep 2000 14:38:30 -0400 (EDT) Received: by lvlxch01.unitedcatalysts.com with Internet Mail Service (5.5.2650.21) id ; Wed, 20 Sep 2000 14:38:59 -0400 Content-return: allowed Date: Wed, 20 Sep 2000 14:38:58 -0400 From: "Shobe, Dave" Subject: RE: No Subject Given By The Author To: "'Shotgun'" , chemistry@ccl.net Message-id: <157A51F55AAAD3119CD70008C7B1629D63858A@lvlxch01.unitedcatalysts.com> MIME-version: 1.0 X-Mailer: Internet Mail Service (5.5.2650.21) Content-type: text/plain; charset=iso-8859-2 Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id OAA32562 What comes to mind is that your calculation may have strayed from the reaction path. A smaller step size will help with that. --David Shobe Süd-Chemie Inc. phone (502) 634-7409 fax (502) 634-7724 email dshobe@sud-chemieinc.com Any opinions herein are not necessarily representative of Süd-Chemie. -----Original Message----- From: Shotgun [mailto:maverick@pobox.sk] Sent: Wednesday, September 20, 2000 8:54 AM To: chemistry@ccl.net Subject: No Subject Given By The Author I am a student of Faculty of Natural Sciences of UPJS and I am trying to compute ( using programme GAMESS ) the general reaction path of addition of ammonia to NCS group. But there is a problem with one IRC calculation. I have found a transition state,hessian computed at this transition geometry has one and only one imaginatory frequency ( value about 2060 ), so ti seems to be OK.I have also tried different methods of finding TS and all resulted to the same structure and same value of imaginatory frequency.But an IRC calculation stops after computing the first point,because the energy of this point is higher than the energy of TS. Please send me some advices,how to solve this problem.My address is maverick@pobox.sk Thank you. From chemistry-request@server.ccl.net Wed Sep 20 22:27:52 2000 Received: from mail2.ecc.u-tokyo.ac.jp (mail2.ecc.u-tokyo.ac.jp [130.69.250.23]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id WAA01660 for ; Wed, 20 Sep 2000 22:27:51 -0400 Received: from m.ecc.u-tokyo.ac.jp (m.ecc.u-tokyo.ac.jp [133.11.171.196]) by mail2.ecc.u-tokyo.ac.jp (8.9.3/3.7W) with ESMTP id LAA04897; Thu, 21 Sep 2000 11:27:46 +0900 (JST) Received: from sancho (dhcp-c213.chem.t.u-tokyo.ac.jp) by m.ecc.u-tokyo.ac.jp (Sun Internet Mail Server sims.3.5.1999.03.02.17.58.p5) with SMTP id <0G1700623TI9AF@m.ecc.u-tokyo.ac.jp>; Thu, 21 Sep 2000 11:27:45 +0900 (JST) Date: Thu, 21 Sep 2000 11:26:50 +0900 From: "N. Dragoe" Subject: Re: CCL:A Babel of Babels To: "Frederick P. Arnold, Jr." Cc: chemistry@ccl.net Message-id: <004b01c02373$664ce320$d5ae0b85@chem.t.utokyo.ac.jp> MIME-version: 1.0 X-Mailer: Microsoft Outlook Express 5.00.2615.200 Content-type: text/plain; charset="iso-8859-1" Content-transfer-encoding: 7bit X-MSMail-Priority: Normal X-MimeOLE: Produced By Microsoft MimeOLE V5.00.2615.200 References: <4.2.2.20000920091410.00ac5c20@lulu.acns.nwu.edu> X-Priority: 3 Hi, For other tools for graphic/conversions you can check Molda and Prax. See http://cssj.chem.sci.hiroshima-u.ac.jp/molda/molda.htm Cheers, N. Dragoe -- http://www.chem.t.u-tokyo.ac.jp/appchem/labs/kitazawa/dragoe/ ----- Original Message ----- From: Frederick P. Arnold, Jr. To: Sent: Wednesday, 20 September 2000 11:17 PM Subject: CCL:A Babel of Babels > Depending what format you need the output in, you could always use gOpenMol > or Molden to read your G98 output file, and then write it back out in > something (generally xyz, but in the case of Molden from the zmat editor, a > host of zmats (gamess, g9x, mopac) that you can use. Molden will also > write cml, but I'm not sure what that gets you at this point in time, > except forward compatibility.