From chemistry-request@server.ccl.net Fri Aug 30 04:25:57 2002 Received: from ns1.tudelft.nl ([130.161.180.1]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g7U8Pvr07108 for ; Fri, 30 Aug 2002 04:25:57 -0400 Received: from CONVERSION-DAEMON.mailhost2.tudelft.nl by mailhost2.tudelft.nl (PMDF V6.1-1 #40925) id <0H1N00101E2YJ9@mailhost2.tudelft.nl> for chemistry@ccl.net; Fri, 30 Aug 2002 10:25:48 +0200 (MEST) Received: from listserv.tudelft.nl (listserv.tudelft.nl [130.161.180.33]) by mailhost2.tudelft.nl (PMDF V6.1-1 #40925) with ESMTP id <0H1N008MAE2YRS@mailhost2.tudelft.nl> for chemistry@ccl.net; Fri, 30 Aug 2002 10:25:46 +0200 (MEST) Received: from stm-ltc2.dct.tudelft.nl (stm-ltc2.dct.tudelft.nl [130.161.196.198]) by listserv.tudelft.nl (8.12.5/8.12.5) with ESMTP id g7U8Pkp2002345 for ; Fri, 30 Aug 2002 10:25:46 +0200 (MEST) Received: from STM-LTC2/SpoolDir by stm-ltc2.dct.tudelft.nl (Mercury 1.47) ; Fri, 30 Aug 2002 10:25:46 +0000 (MET-1MEST) Received: from SpoolDir by STM-LTC2 (Mercury 1.47); Fri, 30 Aug 2002 10:25:40 +0000 (MET-1MEST) Date: Fri, 30 Aug 2002 10:25:39 +0200 From: Martijn Zwijnenburg Subject: G98 and SCRF To: chemistry@ccl.net Message-id: <3D6F481F.23899.E229C836@localhost> MIME-version: 1.0 X-Mailer: Pegasus Mail for Win32 (v3.12c) Content-type: text/plain; charset=US-ASCII Content-transfer-encoding: 7BIT Priority: normal Hi, I'm trying to optimize the structure of a simple silica compund (H3SiOH) in THF solvent by means of SCRF calculation in Gaussian 98. When I run the calculation with opt=(loose) and SCRF=(cpcm,solvent=THF) the calculation converges in a couple of steps. However, when I run the calculation with the standard convergence criteria (or tighter) the calculation does never converge. The energy remains oscilating (typically in the second decimal), as does the force and displacements, and the calculation typically exits with a L9999 error. Increasing the maximum number of steps only causes the calculation to stop after more steps and not the job to converge. In both job files G98 warnes that sometimes some elements are discarded. However, only in the tighter criteria run there are warning that a certain electronic charge (in this case charge 144) has positive or a negative charge ("Electronic charge 144 has a negative value: -0.349460"). Could this screw up convergence or are there other important details wich are important to insure convergence in such SCRF calculations. Cheers, Martijn ------------------------------------------------------------------------- Martijn Zwijnenburg Lab. of Applied Organic Chemistry and Catalysis Delft University of Technology Julianalaan 136 2628 BL Delft The Netherlands Tel: 0031-(0)152782691 Fax: 0031-(0)152784700 e-mail: M.A.Zwijnenburg@tnw.tudelft.nl web page: http://come.to/tock From chemistry-request@server.ccl.net Fri Aug 30 06:38:16 2002 Received: from ws0e.pc.chemie.tu-darmstadt.de ([130.83.242.14]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g7UAcFr09663 for ; Fri, 30 Aug 2002 06:38:15 -0400 Received: from localhost (hatice@localhost) by ws0e.pc.chemie.tu-darmstadt.de (SGI-8.9.3/8.9.3) with ESMTP id MAA24575 for ; Fri, 30 Aug 2002 12:38:15 +0200 (CDT) Date: Fri, 30 Aug 2002 12:38:14 +0200 From: "Dr. Hatice Can" To: chemistry@ccl.net Subject: CASSCF Convergence Problem Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear All, I have tried to do CASSCF calculation for S1 state of a cation. The active space orbitals do not actually cover all pi electrons in the molecule. I used SCF= tight and VShift options for converge the wave function. But it could not converged. I also observed the large orbital rotations.How may I prevent it? If I use all pi electrons in the active space, it will be too large. And then it will cause again a problem. What may I do to solve these problems? All the suggestions and helps will be appriciated. Many thanks and regards, Hatice ***************************************************************************** Dr. Hatice Can Darmstadt University of Technology Chemistry Department Physical Chemistry I Petersenstrase 20 64287 Darmstadt Germany Phone: (+49) 6151 16 5397 Fax: (+49) 6151 16 4298 E-mail: hatice@pc.chemie.tu-darmstadt.de WWW: http://www.pc.chemie.tu-darmstadt.de/staff/hatice/ ***************************************************************************** From chemistry-request@server.ccl.net Fri Aug 30 11:21:45 2002 Received: from radon.pc.helsinki.fi (postfix@[128.214.14.200]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g7UFLjr19172 for ; Fri, 30 Aug 2002 11:21:45 -0400 Received: by radon.pc.helsinki.fi (Postfix, from userid 522) id 5016A1E694; Fri, 30 Aug 2002 18:21:40 +0300 (EEST) Date: Fri, 30 Aug 2002 18:21:40 +0300 To: chemistry@ccl.net Subject: HOW TO PLOT NLMO's FROM G98? Message-ID: <20020830152140.GA8599@chem.helsinki.fi> Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Disposition: inline User-Agent: Mutt/1.3.25i From: straka@chem.helsinki.fi (Michal Straka) Dear CCL'ers, is there a simple way how to plot the NLMO (or NBO) orbitals calculated by NBO module in Gaussian98? Michal -- I----------------------------------------------------------------------------I I Michal Straka Telephone: 358-9-191 50173 I I Department of Chemistry Secretary: 358-9-191 50170 I I P.O.B. 55 (A.I. Virtasen aukio 1) FAX: 358-9-191 50169 I I FIN-00014 Helsinki E-mail: straka@chem.helsinki.fi I I Finland http://www.chem.helsinki.fi/~straka I I----------------------------------------------------------------------------I From chemistry-request@server.ccl.net Fri Aug 30 12:19:47 2002 Received: from chem.wisc.edu ([128.104.68.11]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g7UGJlr22699 for ; Fri, 30 Aug 2002 12:19:47 -0400 Received: from localhost (xdzhang@localhost) by chem.wisc.edu (8.11.2/8.11.2) with ESMTP id g7UGJfo18512; Fri, 30 Aug 2002 11:19:41 -0500 Date: Fri, 30 Aug 2002 11:19:41 -0500 (CDT) From: Zhang Xiaodong To: Martijn Zwijnenburg cc: Subject: about convertion format In-Reply-To: <3D6F481F.23899.E229C836@localhost> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII hi, guys IN my mind, there is a summary about the convertion of format form PDB or sth to mol2 for docking process, but it is pity that I have not this message. If you happen to SAVE this one, please send to me. THNAK YOU VERY MUCH!!! HAPPY HOLIDAY. From chemistry-request@server.ccl.net Fri Aug 30 14:35:25 2002 Received: from mr0.wpafb.af.mil ([198.97.67.50]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g7UIZPr27689 for ; Fri, 30 Aug 2002 14:35:25 -0400 Received: from mvs1.wpafb.af.mil (mvs1.wpafb.af.mil [198.97.67.122]) by mr0.wpafb.af.mil (8.11.6/8.11.6) with ESMTP id g7UIZMl24303 for ; Fri, 30 Aug 2002 14:35:22 -0400 (EDT) Received: from mvs1.wpafb.af.mil (localhost [127.0.0.1]) by mvs1.wpafb.af.mil (8.11.6/8.11.6) with ESMTP id g7UIZLB22522 for ; Fri, 30 Aug 2002 14:35:21 -0400 (EDT) Received: from fszhtv02.wpafb.af.mil (fszhtv02.wpafb.af.mil [129.48.28.35]) by mvs1.wpafb.af.mil (8.11.6/8.11.6) with ESMTP id g7UIZLR22516 for ; Fri, 30 Aug 2002 14:35:21 -0400 (EDT) Received: by fszhtv02.wpafb.af.mil with Internet Mail Service (5.5.2653.19) id ; Fri, 30 Aug 2002 14:32:31 -0400 Message-ID: <53A10F824E50D511820800508BDF3F22034A12AC@fszhtv12.wpafb.af.mil> From: Trohalaki Steven Contr AFRL/MLPJ To: chemistry@ccl.net Subject: An award for Jan? Date: Fri, 30 Aug 2002 14:32:30 -0400 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2653.19) Content-Type: text/plain; charset="iso-8859-1" The complete announcement of the Patterson-Crane Award can be found at: http://membership.acs.org/C/Colu/welcome.html, but I'll include the parts that I think are particularly pertinent to nominating Jan (caps added for emphasis). ~~~~~ The Columbus and Dayton, Ohio Sections of the American Chemical Society sponsor the Patterson-Crane Award for contributions to CHEMICAL INFORMATION. The biennial award consists of a $2,000 honorarium and a personalized commendation. Nominees should demonstrate outstanding achievement in the field of chemical information science. Contributions of International significance may relate to design, development, production, or management of chemical information systems or services; electronic access to and retrieval of chemical information; critically evaluated data compilations; information technology applications in chemistry; or other significant chemical documentation, including production of original works, editorial work, or chemical library work. A nominee does not have to be an ACS member. Nominations must be in writing and should include the nominee's contributions to the field and an evaluation of his or her accomplishments. A biography and bibliography of publications and presentations relevant to the award and supporting the nomination should be enclosed. Seconding letters are required. Nominations and seconding letters may be submitted via email. The Award Committee must receive one copy of the nomination materials by January 31, 2003. Send nominations to Ed King at eking@cas.org or: The Patterson-Crane Award Committee Ed King, Chair P.O. Box 3012 2540 Olentangy River Rd. Columbus, OH 43210-0012 ~~~~~~~ Obviously, the Dayton and Columbus Sections of the ACS stand to save lots of travel $ if Jan wins but that's not why I think he should be nominated. I'm sure there are many CCLers who would write a better nomination for Jan than me but I'm certainly willing to do it. If Jan is willing to be nominated, that is. Sincerely, Steve Trohalaki From chemistry-request@server.ccl.net Fri Aug 30 06:23:21 2002 Received: from roche.bath.ac.uk (IDENT:isc4kfbwfyqal5sxm70r@[138.38.32.21]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g7UANLr09323 for ; Fri, 30 Aug 2002 06:23:21 -0400 Received: from mmdf by roche.bath.ac.uk with pleasure id 17kivw-00086N-02 for chemistry@ccl.net; Fri, 30 Aug 2002 11:23:20 +0100 Received: from midge.bath.ac.uk ([138.38.32.34] ident=mmdf) by roche.bath.ac.uk with smtp id 17kivv-0008Gp-02; Fri, 30 Aug 2002 11:23:19 +0100 Received: from prpcn144 ( prpc-n144.bath.ac.uk [138.38.128.144] ) by bath.ac.uk id aa06759 ; 30 Aug 2002 11:23 +0100 From: James Robinson To: Martijn Zwijnenburg , chemistry@ccl.net Subject: RE: G98 and SCRF Date: Fri, 30 Aug 2002 11:24:49 +0100 Message-ID: MIME-Version: 1.0 Content-Type: text/plain; charset="Windows-1252" X-Priority: 3 (Normal) X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook IMO, Build 9.0.2416 (9.0.2911.0) Importance: Normal X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2600.0000 In-Reply-To: <3D6F481F.23899.E229C836@localhost> Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id g7UANLr09324 It may help to alter the number of tesserae that are use to construct the PCM solvent cavity that surrounds the molecule. I think the default in G98 is around 60-70, but it can be increased to 100. If the PCM method is having problems then some other solvent treatment may do the job, say SCI-PCM or CPCM ( cf. to Cosmo). Using SCF=tight or SCF=verytight has also help difficult cases. I have experienced these problems myself. I did find that relaxing some symmetry constraints from the z-matrix allowed the jobs to finish in quicker time too. However changing the number of tesserae only worked for a few instances. James -----Original Message----- From: Computational Chemistry List [mailto:chemistry-request@ccl.net]On Behalf Of Martijn Zwijnenburg Sent: 30 August 2002 09:26 To: chemistry@ccl.net Subject: CCL:G98 and SCRF Hi, I'm trying to optimize the structure of a simple silica compund (H3SiOH) in THF solvent by means of SCRF calculation in Gaussian 98. When I run the calculation with opt=(loose) and SCRF=(cpcm,solvent=THF) the calculation converges in a couple of steps. However, when I run the calculation with the standard convergence criteria (or tighter) the calculation does never converge. The energy remains oscilating (typically in the second decimal), as does the force and displacements, and the calculation typically exits with a L9999 error. Increasing the maximum number of steps only causes the calculation to stop after more steps and not the job to converge. In both job files G98 warnes that sometimes some elements are discarded. However, only in the tighter criteria run there are warning that a certain electronic charge (in this case charge 144) has positive or a negative charge ("Electronic charge 144 has a negative value: -0.349460"). Could this screw up convergence or are there other important details wich are important to insure convergence in such SCRF calculations. Cheers, Martijn ------------------------------------------------------------------------- Martijn Zwijnenburg Lab. of Applied Organic Chemistry and Catalysis Delft University of Technology Julianalaan 136 2628 BL Delft The Netherlands Tel: 0031-(0)152782691 Fax: 0031-(0)152784700 e-mail: M.A.Zwijnenburg@tnw.tudelft.nl web page: http://come.to/tock -= 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 From chemistry-request@server.ccl.net Fri Aug 30 09:56:47 2002 Received: from postmark.nist.gov ([129.6.16.93]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g7UDulr14653 for ; Fri, 30 Aug 2002 09:56:47 -0400 Received: from BRATSCHE.nist.gov (bratsche.nist.gov [129.6.194.154]) by postmark.nist.gov (8.12.5/8.12.5) with ESMTP id g7UDul8I020971 for ; Fri, 30 Aug 2002 09:56:47 -0400 (EDT) Message-Id: <5.0.0.25.2.20020830093151.00c22d90@mailserver3.nist.gov> X-Sender: irikura@mailserver3.nist.gov X-Mailer: QUALCOMM Windows Eudora Version 5.0 Date: Fri, 30 Aug 2002 09:41:50 -0400 To: chemistry@ccl.net From: Karl Irikura Subject: Re: CCL:Summary: Thermal corrections at T .ne. 298 K In-Reply-To: <004001c216df$0b2223a0$fcdcf143@anick000> References: Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii"; format=flowed Dear CCL folks, Several people have asked for this script. I've now posted it on the web at http://www.nist.gov/compchem/irikura/prog/thermo.html All comments will be appreciated! In particular, if you find the script helpful, please send a quick email--it will help me to justify working on such utilities. Best wishes, Karl >To All, > >Heartfelt thanks to the many of you who responded to my >query regarding computation of thermal corrections at >temperatures other than 298 K. The original query is >repeated here, followed by summary of responses. >While all responses are useful, Karl Irikura's perl script >was the quickest and easiest way to solve my problem, >and I recommend it to anyone else faced with the >same situation. > >David Anick >David.Anick@gte.net >======================================== >Dear CCLers, > >Having completed a Gaussian98 frequencies/ZPE calculation >at an optimized geometry, I now find that I would like to know >the thermal corrections to energy, enthalpy and Gibbs free >energy at a different temperature (77 K) than the one that >Gaussian98 automatically calculated (298 K). > >I don't want to re-run the calculation if possible because >it took nearly a week. > >Can anyone tell me the formula(s) that Gaussian98 uses >to compute these data? If it involves integrating Cp or >Cp/T, how do I obtain Cp as a function of temperature? > >Thank you in advance, > >David Anick MD PhD >David.Anick@gte.net ---------------------------------------------- Dr. Karl K. Irikura National Institute of Standards and Technology 100 Bureau Drive, Stop 8380 Gaithersburg, MD 20899-8380 voice: 301-975-2510 fax: 301-869-4020 e-mail: karl.irikura@nist.gov http://www.nist.gov/compchem/ ---------------------------------------------- From chemistry-request@server.ccl.net Fri Aug 30 02:42:53 2002 Received: from smtp2.ruc.dk ([130.225.220.70]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g7U6gMr05118 for ; Fri, 30 Aug 2002 02:42:53 -0400 Received: by smtp2.ruc.dk (Postfix, from userid 504) id 8D810456C5F; Fri, 30 Aug 2002 08:41:51 +0200 (CEST) Received: from virgil.ruc.dk (virgil.ruc.dk [130.225.220.110]) by smtp2.ruc.dk (Postfix) with ESMTP id 95528456C5C for ; Fri, 30 Aug 2002 08:41:50 +0200 (CEST) Received: from VIRGIL/SpoolDir by virgil.ruc.dk (Mercury 1.47); 30 Aug 02 08:41:50 +0100 Received: from SpoolDir by VIRGIL (Mercury 1.47); 30 Aug 02 08:41:44 +0100 From: "Jens Spanget-Larsen" Organization: Roskilde Universitetscenter To: chemistry@ccl.net Date: Fri, 30 Aug 2002 08:41:26 +0100 Subject: CCL: Max Planck and Philipp von Jolly Reply-To: spanget@ruc.dk Priority: normal X-mailer: Pegasus Mail for Windows (v2.23) Message-ID: <435133E10BB@virgil.ruc.dk> Dear CCL, thanks a lot to all of you who contributed to my 'history question'. The story of Philipp von Jolly discouraging the young Max Planck from entering the field of Physics can be found on numerous www-pages. Below just a few quotations. Yours, Jens >--< ------------------------------------------------------------------ http://www-groups.dcs.st-and.ac.uk/~history/Mathematicians/Planck.html In 1874, at the age of 16, he entered the University of Munich. Before he began his studies he discussed the prospects of research in physics with Philipp von Jolly, the professor of physics there, and was told that physics was essentially a complete science with little prospect of further developments. Fortunately Planck decided to study physics despite the bleak future for research that was presented to him. ------------------------------------------------------------------ http://www.psicounsel.com/end.html "When I began my physical studies [in Munich in 1874] and sought advice from my venerable teacher Philipp von Jolly... he portrayed to me physics as a highly developed, almost fully matured science... Possibly in one or another nook there would perhaps be a dust particle or a small bubble to be examined and classified, but the system as a whole stood there fairly secured, and theoretical physics approached visibly that degree of perfection which, for example, geometry has had already for centuries." - from a 1924 lecture by Max Planck (Sci. Am, Feb 1996 p.10) ------------------------------------------------------------------ http://www.astronomiepur.de/mthemen/mtapril01.html Als er sich bei Philipp von Jolly nach den Aussichten eines Physikstudiums erkundigte, riet dieser dringend ab: In der Physik sei im wesentlichen schon alles erforscht, und es gaebe nur noch einige Luecken auszufuellen. AEhnlich betrachtete damals Emil Du Bois-Reymond die theoretische Mechanik mit dem Energieprinzip an der Spitze als Hoehepunkt und endgueltigen Schlussstein der Physik: Ende des 19. Jahrhunderts und um die Jahrhundertwende war fuer das Buergertum in Europa eine konservative Einstellung typisch. Sowohl die staatliche Ordnung wie die Wissenschaft wurden als gefestigt angesehen; nach einer stuermischen Aufbauphase glaubte man an die Erhaltung des Bestehenden. In diesem "Denkklima" haben sich die Auffassungen Plancks von der Wissenschaft und vom Staate geformt, und schon deshalb hat es eines ungeheuren inneren Kampfes bedurft, dass er diese UEberzeugungen spaeter durch andere Ansichten zu ersetzen vermochte. ------------------------------------------------------------------ http://www.uni-potsdam.de/u/putz/dez00/plancki.htm Er solle lieber nicht Physik studieren, hatte ihm vor ueber 100 Jahren der Physikprofessor Philipp von Jolly geraten. In diesem Fach, so die Begruendung, sei bereits alles weitgehend bekannt. Es war wohl ein Gluecksfall, dass Max Planck sich von diesem Rat nicht beeindrucken liess und mit dem Studium der Physik begann. Vor genau 100 Jahren, am 14. Dezember 1900, hielt er in Berlin einen Vortrag, der als der Beginn der Quantenphysik in die Geschichte eingehen sollte. ------------------------------------------------------------------ http://www.gwu.edu/~physics/newslet/news6.htm "Physics in our Future" Scott Crawford, GW Graduate Student Dramatic developments in physics are often completely unexpected. Consider, for instance, the account given by Max Planck of his own experience before beginning his studies at the University of Munich. Professor Philipp von Jolly told him that physics was essentially a complete science with little prospect for further developments*. Given subsequent theoretical insight and technological advances, such as the transistor and the development of the integrated circuit, the laser, superconductivity, microwave devices, jets, chemical rockets and ion propulsion, and nuclear energy, it is difficult to imagine an intelligent person supposing that physics was essentially complete a little more than hundred years ago! Fortunately, Max Planck was not dissuaded, and he went on to revolutionize classical physics in 1900 by introducing the theory of the quantum of energy. The point, in fact, is that we cannot know when the next innovation might occur, nor do we know where it might eventually lead. Conceivably, an innovation in any one of the specialties of physics can each lead to a whole new epoch. My personal aspiration is to study physics so that I may fully appreciate and, perchance, contribute to this now much anticipated revolution in science. While I realize that we cannot foresee when a sea change will occur, I remain confident that our best insights are yet to come. * In this regard the following remarks, made a few years earlier, are of interest: "_the opinion seems to have got abroad, that in a few years all the great physical constants will have been approximately estimated, and that the only occupation that will be left to men of science will be to carry on these measurements to another place of decimals_ But we have no right to think thus of the unsearchable riches of creation, or of the untried fertility of those fresh minds into which these riches will be poured." James Clerk Maxwell, Inaugural Lecture as first Cavendish Professor in Cambridge, 25 October, 1871 ------------------------------------------------------------------ http://www.rzuser.uni-heidelberg.de/~q61/qm100.html Max Planck Fuer die von ihm ausgeloeste Revolution war der 1858 als Sohn eines Jura-Professors an der Universitaet Kiel geborene Max Planck (Bild 1) keineswegs praedestiniert. Als Schueler auf dem Maximiliansgymnasium in Muenchen war seine herausragende physikalische Begabung jedenfalls noch nicht sehr deutlich in Erscheinung getreten, wenngleich sein Lehrer Hermann Mueller sein mathematisches und physikalisches Interesse weckte, und er auch auf allen anderen Gebieten ein sehr guter Schueler war. 1874 begann er das Physikstudium an der Universitaet Muenchen - fand dort aber wenig Ermutigung durch seinen Professor Philipp von Jolly, der ihm riet, besser etwas anderes als Physik zu studieren, da alle fundamentalen Gesetze bereits bekannt seien und die Physiker sich deshalb nur noch mit unwesentlichen Details abgeben muessten. ------------------------------------------------------------------ NB! Please note new mail address: =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= 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 Thu Aug 29 23:23:24 2002 Received: from relay2.softcomca.com ([168.144.1.68]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g7U3NOr01574 for ; Thu, 29 Aug 2002 23:23:24 -0400 Received: from M2W068.mail2web.com ([168.144.108.68]) by relay2.softcomca.com with Microsoft SMTPSVC(5.0.2195.5329); Thu, 29 Aug 2002 23:23:23 -0400 Message-ID: <57050-2200285303232363@M2W068.mail2web.com> X-EM-Version: 6, 0, 0, 3 X-EM-Registration: #00E0641810D91B008120 X-Priority: 3 Reply-To: rowyna@vplaces.net X-Originating-IP: 202.185.72.215 X-URL: http://mail2web.com/ From: "nepenthes@vplaces.net" To: chemistry@ccl.net Subject: RMSD in Autodock Date: Thu, 29 Aug 2002 23:23:23 -0400 MIME-Version: 1.0 Content-type: text/plain; charset=iso-8859-1 X-OriginalArrivalTime: 30 Aug 2002 03:23:23.0251 (UTC) FILETIME=[98A69430:01C24FD4] Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id g7U3NOr01575 Hi CCLers, Does anybody know how the RMSD is calculated in Autodock3? I haven't been able to find out as of now. My initial thought was the heavy atoms of the docked conformations and reference structure were used. But when I use other programs like InsightII or VMD to calculate the RMSD, the values are quite different. Can I find out from the source code? I looked through but wasn't sure. Any suggestions/feedback would be appreciated. Thank you for your time. Sincerely, Rowyna -------------------------------------------------------------------- mail2web - Check your email from the web at http://mail2web.com/ . From chemistry-request@server.ccl.net Thu Aug 29 17:03:03 2002 Received: from hotmail.com ([207.68.165.59]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g7TL33r13658 for ; Thu, 29 Aug 2002 17:03:03 -0400 Received: from mail pickup service by hotmail.com with Microsoft SMTPSVC; Thu, 29 Aug 2002 14:02:58 -0700 Received: from 141.218.90.234 by sea2fd.sea2.hotmail.msn.com with HTTP; Thu, 29 Aug 2002 21:02:57 GMT X-Originating-IP: [141.218.90.234] From: "Jan Kim" To: chemistry@ccl.net Subject: Compilers for computational chemistry softwares Date: Thu, 29 Aug 2002 17:02:57 -0400 Mime-Version: 1.0 Content-Type: text/plain; format=flowed Message-ID: X-OriginalArrivalTime: 29 Aug 2002 21:02:58.0117 (UTC) FILETIME=[73CF8750:01C24F9F] Dear CCLers: Recently I got a used SGI Origin2000 with 4 CPU's which I am going to use it to do computational chemistry studies. Unfortunately there is no compiler in this machine. As the whole package with C, C++, F77, F90, MP Tool kit etc > from SGI is too expensive for me, I am thinking to purchase one or two compilers only. My question is, which compiler(s) I should pick up to compile CHARMM, Gaussian, and GAMESS(US)? Another question, can the freeware GNU compilers accomplish the same jobs? Many thanks, Jan Kim _________________________________________________________________ MSN Photos is the easiest way to share and print your photos: http://photos.msn.com/support/worldwide.aspx From chemistry-request@server.ccl.net Fri Aug 30 14:45:08 2002 Received: from ccl.net ([192.148.249.4]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g7UIj8r28335 for ; Fri, 30 Aug 2002 14:45:08 -0400 Received: from krakow.ccl.net (krakow.ccl.net [192.148.249.195]) by ccl.net (8.11.6+Sun/8.11.6/OSC 2.1) with ESMTP id g7UIj9m00196 for ; Fri, 30 Aug 2002 14:45:09 -0400 (EDT) Date: Fri, 30 Aug 2002 14:45:07 -0400 (EDT) From: Jan Labanowski To: chemistry@ccl.net Subject: 02.09.20 Vanderbilt Biomolecular Modeling Symposium (fwd) Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII ---------- Forwarded message ---------- Date: Fri, 30 Aug 2002 13:00:40 -0500 (CDT) From: Jarrod Smith To: amber@heimdal.compchem.ucsf.edu Subject: Vanderbilt Biomolecular Modeling Symposium I'd like to invite AMBER list members to the Vanderbilt Biomolecular Modeling Symposium hosted by the Center for Structural Biology. The symposium will be held at Vanderbilt University on September 20-21, 2002. There will be a poster session/competition on Friday night, with the symposium to follow on Saturday. Please see below for a quick listing of the talks. The symposium is free, but registration is required. Details can be found at the symposium website: http://structbio.vanderbilt.edu/comp/symposium We hope to see some of you there! -------------------------------------------------------------------- Irwin D. Kuntz University of California, San Francisco "Molecular Recognition and Docking" Jeffrey M. Blaney Structural GenomiX, San Diego, CA "High-Throughput Docking for Lead Discovery" David A. Case The Scripps Research Institute "Using Continuum Solvent Models in Biomolecular Simulations" Bernard R. Brooks National Insitutes of Health (Talk title to be announced) Kim Sharp University of Pennsylvania "Back to Bjerrum: Calculation of Absolute Binding Free Energies" Terry P. Lybrand Vanderbilt University "Molecular Modeling of Protein-Ligand Interactions: Detailed Simulations of a Biotin-Streptavidin Complex" -------------------------------------------------------------------- -- Jarrod A. Smith, Ph.D. Asst. Director, Center for Structural Biology Research Asst. Professor, Biochemistry Vanderbilt University 162 processes: 125 sleeping, 37 running From chemistry-request@server.ccl.net Fri Aug 30 15:30:53 2002 Received: from hermes.csd.unb.ca (root@[131.202.3.20]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g7UJUrr30366 for ; Fri, 30 Aug 2002 15:30:53 -0400 Received: from mailserv2 (mailserv.unb.ca [131.202.3.23]) by hermes.csd.unb.ca (8.12.3/8.12.3) with SMTP id g7UJUrpT008271 for ; Fri, 30 Aug 2002 16:30:53 -0300 (ADT) Received: FROM pop.unb.ca BY mailserv2 ; Fri Aug 30 16:30:52 2002 -0300 Received: from webmail1 (webmail1.unb.ca [131.202.130.26]) by pop.unb.ca (8.9.3/8.9.3) with ESMTP id QAA25108; Fri, 30 Aug 2002 16:30:52 -0300 (ADT) X-WebMail-UserID: l72k6 Date: Fri, 30 Aug 2002 16:30:51 -0300 Sender: Robert Flight From: Robert Flight To: "nepenthes@vplaces.net" , Computational Chemistry List X-EXP32-SerialNo: 00003025, 00003442 Subject: RE: CCL:RMSD in Autodock Message-ID: <3D678870@webmail1> Mime-Version: 1.0 Content-Type: text/plain; charset="US-ASCII" Content-Transfer-Encoding: 7bit X-Mailer: WebMail (Hydra) SMTP v3.61.08 Hi Rowyna, I dont know how the RMSD is calculated in Autodock3 exactly, but I might know how to get values from a different program to match those give by Autodock (or at least come close). The program I use, MOE, assumes that all of the atoms are connected the same way and in the same order when doing the RMSD calculation. After all of the processing to the Autodock pdbq file, all of the connectivity was messed up from the original structure. I found if I took one of the docked results, and superposed the docked structure over the original reference structure, and then used the superposed structure from docking as your "new" reference; then I got RMSD values approaching those given by Autodock. They're not the exact same, but pretty close. This could be part of the problem you are haveing. Hope this helps, Robert >===== Original Message From "nepenthes@vplaces.net" ===== >Hi CCLers, > >Does anybody know how the RMSD is calculated in Autodock3? I haven't been >able to find out as of now. My initial thought was the heavy atoms of the >docked conformations and reference structure were used. But when I use >other programs like InsightII or VMD to calculate the RMSD, the values are >quite different. Can I find out from the source code? I looked through but >wasn't sure. > >Any suggestions/feedback would be appreciated. Thank you for your time. > >Sincerely, >Rowyna > > >-------------------------------------------------------------------- >mail2web - Check your email from the web at >http://mail2web.com/ . > > > > >-= 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 ******************************** Robert Flight Masters Student Department of Chemistry University of New Brunswick Fredericton, NB Canada E3B 6E2 e-mail: L72K6@unb.ca ********************************