From chemistry-request@server.ccl.net Fri Oct 11 08:42:22 2002 Received: from resu1.ulb.ac.be ([164.15.59.200]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g9BCgMJ22917 for ; Fri, 11 Oct 2002 08:42:22 -0400 Received: from mach.vub.ac.be (mach.ulb.ac.be [164.15.128.3]) by resu1.ulb.ac.be (8.8.8/3.17.1.ap (resu)) id OAA26812; Fri, 11 Oct 2002 14:39:58 +0200 (MEST) for Received: from resu1.ulb.ac.be (resu1.ulb.ac.be [164.15.59.200]) by mach.vub.ac.be (8.9.3/3.13.3.ap (mach)) id OAA05560; Fri, 11 Oct 2002 14:42:03 +0200 (MET DST) for chemistry@ccl.net Date: Fri, 11 Oct 2002 14:42:03 +0200 (MET DST) Message-Id: <200210111242.OAA05560@mach.vub.ac.be> From: Pierre Mignon To: chemistry@ccl.net Subject: amber param ... X-Mailer: Webmail ULB v2.1 Hello, I am using amber since a few weeks and i am getting in troubles with two problems: _The paraterization of the calcium atom. What I did since now, is to create a frcmod file with the mass and non bonded parameters. I created also a prep file to specify the type of the calcium atom : C0. But when I saved the topology-parm file and when I look to it, I can't find the non-bonded parameters. My question is : is it necessary to do this in that way since the parameters of Calcium are present in the parm99.dat file. _I am trying to calculate the Gibbs free energy change within the mutation of a amino-acid with the FEP method. The problem is how to define parameters for dummy atoms, these are not specified in standard parmxx.dat files. All responses appreciated. Thank you in advance. Pierre Mignon. From chemistry-request@server.ccl.net Fri Oct 11 09:42:31 2002 Received: from sandmail01.sd.accelrys.com ([64.165.22.62]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g9BDgVJ24222 for ; Fri, 11 Oct 2002 09:42:31 -0400 To: chemistry@ccl.net Cc: elizabethc@accelrys.com, peili@accelrys.com, tweissbrod@accelrys.com Subject: Accelrys Customer Training in December MIME-Version: 1.0 X-Mailer: Lotus Notes Release 5.0.9a January 7, 2002 Message-ID: From: jnauss@accelrys.com Date: Fri, 11 Oct 2002 06:42:23 -0700 X-MIMETrack: Serialize by Router on sandmail01/Server/Accelrys(Release 5.0.9 |November 16, 2001) at 10/11/2002 06:42:32 AM, Serialize complete at 10/11/2002 06:42:32 AM Content-Type: text/plain; charset="us-ascii" Accelrys Inc. are holding the following training workshops at locations in the US and Europe during December. These events are designed to help you get more value from your Accelrys software, helping you to better accomplish your research goals. Costs are $600 per day for commercial, $450 per day for government and $330 per day for academic. Bioinformatics: Wisconsin Package and SeqLab 9th-10th December in San Diego, CA SeqWeb 11th December in San Diego, CA DS Gene Workshop 12th-13th December in San Diego, CA For course details and registration see: http://www.accelrys.com/training/bioinf/schedule.html Macromolecular Modeling: Introduction to Life Science Modeling with InsightII 17th-18th December in New Brunswick, NJ Homology-Based Protein Design 19th-20th December in New Brunswick, NJ For course details and registration see: http://www.accelrys.com/training/macro/schedule.html Cheminformatics: Accord for Access 2nd December in Cambridge, UK Accord for Excel 3rd December in Cambridge, UK Accord Database Explorer 5th December in Cambridge, UK Accord Developer Studio 2nd-3rd December in Burlington, MA Accord Chemistry Cartridge 4th December in Burlington, MA Accord Grid Control 5th December in Burlington, MA Accord CombiChem Addon 6th December in Burlington, MA RS3 HTS Client 9th December in Burlington,MA RS3 Inventory 10th December in Burlington, MA OMMM 11th December in Burlington, MA RS3 for Excel 12th December in Burlington, MA DIVA 13th December in Burlington, MA RS3 HTS Database Administration 16th-17th December in Burlington, MA For course details and registration see: http://www.accelrys.com/training/cheminf/schedule.html -- Jeffrey L. Nauss, Ph.D. Manager, Discovery Studio Training Accelrys Inc. 9685 Scranton Road San Diego, CA 92121-3752 Phone: 858-799-5555 Fax: 858-799-5100 E-mail: jnauss@accelrys.com http://www.accelrys.com/training From chemistry-request@server.ccl.net Thu Oct 10 19:43:22 2002 Received: from ned1.sims.nrc.ca ([132.246.108.2]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g9ANhLJ03640 for ; Thu, 10 Oct 2002 19:43:21 -0400 Received: from localhost (ps@localhost) by ned1.sims.nrc.ca (8.8.8/8.8.8) with ESMTP id TAA18967; Thu, 10 Oct 2002 19:43:12 -0400 (EDT) Date: Thu, 10 Oct 2002 19:43:12 -0400 From: Serguei Patchkovskii Reply-To: Serguei.Patchkovskii@nrc.ca To: "Stephen P. Molnar, Ph.D." , Chemistry@ccl.net Subject: Re: CCL:GAMESS on a Laptop In-Reply-To: <5.1.1.2.2.20021010063915.00a00ec0@mail.jadeinc.com> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII On Thu, 10 Oct 2002, Stephen P. Molnar, Ph.D. wrote: > Connect to kickoff socket by process 0 has failed, error 101 > ddikick: Trapped SIGCHLD: Unexpected termination of a child process. > What is an error 101? How is it corrected? If you look at the source code of ddikick, you'll sse that this error message is issued if the following system call fails: connect( sock, (struct sockaddr *) &netsoc, sizeof(netsoc) ) The error code is simply the errno value, returned by the operating system. Now, if you look up this errno value in /usr/include/asm/errno.h, you'll find it's meaning: #define ENETUNREACH 101 /* Network is unreachable */ Now, on your laptop, issue the command: ping `hostname` My $2 bet is that ping will respond with "Network unreachable". The most likely reason for this is that the host name of your laptop (returned by "hostname") is associated with an IP address assigned either to a PCMCIA network card, or to a dialup interface. When these are not available (i.e. when you are not connected to the Internet), this IP address becomes unreachable. There are two solutions - the quick one, and the right one. The quick solution is to go into rungms script, search for all instances of the string `hostname` (don't forget the backticks!), and replace it with "localhost". The right solution is to make sure that the default host name of your laptop is always associated with valid, reachable IP address. One way of doing this is to keep a dummy ethernet interface (implemented by network driver "dummy") loaded, when you are not connected to the Internet. If you are not certain on how to proceed with this, look up your resident Linux wizard. Hope this helps, Serguei --- Tel: +1-(613)-991-2719 Fax: +1-(613)-947-2838 E-mail: Serguei.Patchkovskii@nrc.ca Coordinator of Modelling Software Theory and Computation Group Steacie Institute for Molecular Sciences National Research Council Canada Room 2006/8, 100 Sussex Drive Ottawa, Ontario K1A 0R6 Canada From chemistry-request@server.ccl.net Fri Oct 11 11:51:22 2002 Received: (from root@localhost) by server.ccl.net (8.11.6/8.11.0) id g9BFpMq27073 for chemistry@ccl.net; Fri, 11 Oct 2002 11:51:22 -0400 Message-ID: <20021011061539.95334.qmail@web20415.mail.yahoo.com> Date: Thu, 10 Oct 2002 23:15:39 -0700 (PDT) From: Juraina Jamil Subject: autodock again To: chemistry@ccl.net MIME-Version: 1.0 Hi all, I'm currently preparing files to run docking on autodock. Tried making a dpf file using the mkdpf3 autodock. Tried making a dpf file using the mkdpf3 command but it said that it could not find the dpf3gen command. How is that possible when the script is right there in the same directory. FYI I'm running autodock on Redhat 6.2. I think the dpf3gen script calls for the dpf3gen.awk program and I had to fix the bug by typing perl -pi -e "awk" * Pls help. Juraina University Malaya Kuala Lumpur Malaysia __________________________________________________ Do you Yahoo!? Faith Hill - Exclusive Performances, Videos & More http://faith.yahoo.com From chemistry-request@server.ccl.net Fri Oct 11 04:52:23 2002 Received: from roche.bath.ac.uk (IDENT:cqc6rrxjw4jdzmuw26lv@[138.38.32.21]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g9B8qNJ19420 for ; Fri, 11 Oct 2002 04:52:23 -0400 Received: from mmdf by roche.bath.ac.uk with pleasure id 17zvWw-0006n2-02 for chemistry@ccl.net; Fri, 11 Oct 2002 09:52:22 +0100 Received: from amos.bath.ac.uk ([138.38.32.36] ident=mmdf) by roche.bath.ac.uk with smtp id 17zvWv-0007F6-02; Fri, 11 Oct 2002 09:52:21 +0100 Received: from prpcn144 ( prpc-n144.bath.ac.uk [138.38.128.144] ) by solaris.bath.ac.uk id aa18573 ; 11 Oct 2002 09:52 +0100 From: James Robinson To: "Pradyumna S. Singh" , Chemistry Subject: RE: SCIPCM Date: Fri, 11 Oct 2002 09:54:14 +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) X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2600.0000 Importance: Normal In-Reply-To: Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id g9B8qNJ19421 One can alter the number of tesserae used make up the cavity, use SCRF=(Scipcm,solvent=oooooo, read) and SCF=tight (or even verytight). After the Z-matrix and a blank line, add TSNUM=100. This will cause the solvent cavity to be made up of more components. Mr James J Robinson MRSC Molecular Modeller Pharmacy and Pharmacology Dept. University of Bath Claverton Down Bath, Somerset, UK. BA2 7AY. J.J.Robinson@bath.ac.uk http://www.bath.ac.uk tel +44(0) 1225 384723 -----Original Message----- From: Computational Chemistry List [mailto:chemistry-request@ccl.net]On Behalf Of Pradyumna S. Singh Sent: 10 October 2002 21:56 To: Chemistry@ccl.net Subject: CCL:SCIPCM Hi, I have been trying (unsuccessfully !) to do some ab initio studies on trans-2,3-dinitro butene in solution. Typically I've employed DFT level of theory with 6-31G basis set, and the SCIPCM model; Gaussian98.A11 However it has been impossible to optimise the structure in solution (using the SCIPCM). What I usually end up with is the following : ----------------------------------------------------------------------------- E=-0.111166749562117D+04 DIIS: error= 3.26D-01 at cycle 1. Fock symm off for IB=2 I1= 3 I= 113 J= 83 Cut=1.00D-04 Err=2.02D-04 Fock matrix is not symmetric: symmetry in diagonalization turned off. T= 2927. Gap= 0.012 NK=0 IS= 1 IE= 220 NO(<0.9)= 1 NV(>0.1)= 1 38.63e < EF 0.37e >EF Err=5.6D-11 RMSDP=2.01D+00 MaxDP=1.14D+02 Density matrix breaks symmetry, PCut= 1.00D-04 Density matrix has no symmetry -- integrals replicated. Cycle 2 Pass 1 IDiag 1: RMSU= 1.92D+00 CP: 3.00D+00 Compute SCI-PCM surface. WARNING! Serious error in surface integrals. It is probable that some of the solute is outside the cavity and/or parts of the cavity surface cannot be reached from the origin. Try more integration points or a different set of integration origins. Surface Problems in SciFoc ------------------------------------------------------------------------------- Could someone kindly point out what the problem here is, and what could be changed to make it work ? Any help/leads in the matter would be much appreciated. Thanks, Pradyumna -= 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 Oct 11 12:23:24 2002 Received: from staff2.cso.uiuc.edu (root@[128.174.5.53]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g9BGNOB27953 for ; Fri, 11 Oct 2002 12:23:24 -0400 Received: from epr4.scs.uiuc.edu (epr4.scs.uiuc.edu [130.126.225.114]) by staff2.cso.uiuc.edu (8.11.0/8.11.0) with ESMTP id g9BGNIH25048; Fri, 11 Oct 2002 11:23:18 -0500 (CDT) Message-ID: X-Mailer: XFMail 1.5.2 on Linux X-Priority: 3 (Normal) Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit MIME-Version: 1.0 In-Reply-To: <20021011061539.95334.qmail@web20415.mail.yahoo.com> Date: Fri, 11 Oct 2002 11:24:03 -0500 (CDT) Sender: aborel@epr4.scs.uiuc.edu From: Alain Borel To: Juraina Jamil Subject: RE: CCL:autodock again Cc: chemistry@ccl.net On 11-Oct-2002 Juraina Jamil wrote: > I'm currently preparing files to run docking on > autodock. Tried making a dpf file using the mkdpf3 > autodock. Tried making a dpf file using the mkdpf3 > command but it said that it could not find the dpf3gen > command. How is that possible when the script is right > there in the same directory. > > FYI I'm running autodock on Redhat 6.2. I think the > dpf3gen script calls for the dpf3gen.awk program and I > had to fix the bug by typing > > perl -pi -e "awk" * In most Linux distributions, the current directory (.) is left out of the PATH for security reasons. That's why the script can't find a command in the same directrory. Adding it at the end of a normal user's PATH should be harmless enough, though. Hope this helps! Alain Borel University of Illinois -- E-Mail: Alain Borel Date: 11-Oct-2002 Time: 11:21:23 From chemistry-request@server.ccl.net Fri Oct 11 12:39:41 2002 Received: from cornell.edu ([132.236.56.6]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g9BGdfB28412 for ; Fri, 11 Oct 2002 12:39:41 -0400 Received: from cornell.edu (lock.lassp.cornell.edu [128.84.241.198]) by cornell.edu (8.9.3/8.9.3) with ESMTP id MAA13022 for ; Fri, 11 Oct 2002 12:39:40 -0400 (EDT) Sender: cc236@cornell.edu Message-ID: <3DA6FECD.AC86BAFB@cornell.edu> Date: Fri, 11 Oct 2002 12:39:41 -0400 From: Connie Chang X-Mailer: Mozilla 4.77 [en] (X11; U; Linux 2.2.19-6.2.16smp i686) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net Subject: Guassian98 w/ PM3 error message? Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi -- I'm trying to run a C140 complex with Gaussian using PM3. But I'm getting this error message I don't understand. It says that I have insufficient memory for my task, but I used Windows task manager to monitor the memory usage during the calculation, but it seemed fine. HAs anyone had this kind of error before and what can I do to fix it? The error message is: Leave Link 202 at Tue Oct 08 12:15:06 2002, MaxMem= 6291456 cpu: 0.0 (Enter C:\G98W\l301.exe) Standard basis: VSTO-3G (5D, 7F) Integral buffers will be 262144 words long. Raffenetti 1 integral format. Two-electron integral symmetry is turned off. 560 basis functions 1680 primitive gaussians 280 alpha electrons 280 beta electrons nuclear repulsion energy 13722.0528113451 Hartrees. Leave Link 301 at Tue Oct 08 12:15:07 2002, MaxMem= 6291456 cpu: 0.0 (Enter C:\G98W\l401.exe) Simple Huckel Guess. Leave Link 401 at Tue Oct 08 12:15:36 2002, MaxMem= 6291456 cpu: 29.0 (Enter C:\G98W\l402.exe) RHF-PM3 calculation of energy and first derivatives. MO and density RWFs will be updated. Closed-shell calculation: 280 occupied levels. NNHCO= 0. References: C: (PM3): J. J. P. STEWART, J. COMP. CHEM. 10, 209 (1989). Insufficient memory for Iter: NGot= 495796. Error termination via Lnk1e in C:\G98W\l402.exe. Job cpu time: 0 days 0 hours 0 minutes 40.0 seconds. File lengths (MBytes): RWF= 48 Int= 0 D2E= 0 Chk= 1 Scr= 1 Thanks, Connie Chang cc236@cornell.edu From chemistry-request@server.ccl.net Fri Oct 11 14:36:38 2002 Received: from rutchem.rutgers.edu ([128.6.1.216]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g9BIacB32235 for ; Fri, 11 Oct 2002 14:36:38 -0400 Received: from rutchem.rutgers.edu (chem-77-80.rutgers.edu [128.6.77.80]) by rutchem.rutgers.edu (8.9.3/8.9.3) with ESMTP id OAA2306671 for ; Fri, 11 Oct 2002 14:36:37 -0400 (EDT) Message-ID: <3DA71ACF.B9B31A41@rutchem.rutgers.edu> Date: Fri, 11 Oct 2002 14:42:35 -0400 From: "Ronald R. Sauers" X-Mailer: Mozilla 4.61 (Macintosh; U; PPC) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net Subject: electrostatic potential surfaces with Gaussview Content-Type: text/plain; charset=us-ascii; x-mac-type="54455854"; x-mac-creator="4D4F5353" Content-Transfer-Encoding: 7bit Dear Folks: I am trying to to use Gaussview 2.03 to generate color graphics of electrostatic potential surfaces. Cube files were prepared with the following commands: cube=(potential,40). We expected to see a rainbow of colors indicating variable charge distribution. In face, on (Gauss)viewing, only two colors (red and yellow) were seen for various molecules at several isodensity levels. Can anyone comment on what can be done to rectify this situation? Thanks in advance. RRSauers -- ************************************************************************ Ronald R. Sauers 732-445-2626 (office) Professor Emeritus of Chemistry 732-445-2618 (dept) Department of Chemistry 732-445-5312 (FAX) Rutgers, The State University of New Jersey 610 Taylor Road Piscataway, New Jersey 08854-8087 USA E-mail:sauers@rutchem.rutgers.edu ************************************************************************ From chemistry-request@server.ccl.net Fri Oct 11 14:26:45 2002 Received: from ivory.trentu.ca ([192.75.12.103]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g9BIQjB31877 for ; Fri, 11 Oct 2002 14:26:45 -0400 Received: from trentu.ca ([206.248.117.30]) by trentu.ca (PMDF V5.2-32 #37862) with ESMTP id <01KNJ9OH03XG0001FP@trentu.ca> for chemistry@ccl.net; Fri, 11 Oct 2002 10:10:05 EDT Date: Fri, 11 Oct 2002 10:12:15 -0400 From: elewars Subject: reply, semiempirical methods To: chemistry@ccl.net Message-id: <3DA6DC3E.3C30FEE1@trentu.ca> MIME-version: 1.0 X-Mailer: Mozilla 4.79 [en] (WinNT; U) Content-type: text/plain; charset=us-ascii Content-transfer-encoding: 7bit X-Accept-Language: en 2002 Oct 11 Hello, Regarding your question about semiempirical methods: The tight binding method is what physicists call the simple Hueckel method (SHM), the simplest semiempirical method derived from the Schroedinger eqn (with the possible exception of the free-electron method, which doen't seem to be used now). The SHM, contrary to what some people think, still has its uses. The extended Hueckel method (EHM), popularized by Professor Roald Hoffmann, is a logical extension of the SHM which considers molecular geometry instead of just connectivity, uses all the valence orbitals on each atom, not just one (usually a p) orbital, and does not collapse the overlap matrix to a unit matrix. Neither Hueckel method will calculate frequencies (the EHM could in principle, but the results would not be very meaningful, I suspect). The most popular semiempirical methods today are simplifications of the rigorous ab initio approach (the SHM and by implication the EHM were developed in a different atmosphere); these originated with, or are offshoots of, the work of M. J. S. Dewar's group: the AM1 and PM3 (and the more recent SAM1 and PM5) methods. A good survey of SE methods, with references is: I. N. Levine, "Quantum Chemistry", Fourth Ed., Prentice Hall, 2000; chapters 16, 17 (15 is ab initio). I 'm surprised that AM1 ot PM3 can't give you useful vibrational modes (unless you have metal atoms for which parameters are unavailable). Maybe an STO-3G ab initio calculation would work and be of some value. E. Lewars ==== Connie Chang wrote: > Hi -- > > I am trying to find the vibrational modes of a 100 atom molecule that > includes elements such as carbon, nitrogen, hydrogen, and cobalt (just > one atom). I tried using commercial software such as Gaussian and > Hyperchem, but was having trouble getting "sensible" answers with their > semi-empirical methods and ab-initio methods proved to be too > computer-intensive. > > I'm trying to write my own code to calculate energies (so that I can > construct a hessian for the phonon spectra), but I'm not sure about the > methods out there. Is tight-binding the same as the semi-empirical > methods? I know that in tight binding, one needs to find the parameters > for the elements in the molecule and the parameters for the particular > atomic connectivity (so if my molecule has a carbon bonded to an oxygen, > I would need the parameters for a carbon-oxygen connectivity). Is this > how semi-empirical methods work as well? Or is there just a set of > parameters for each element without taking into account the > connectivity? Or is there some systematic way to derive parameters > between elements? > > Any advice about what method to use or resources that I can look at > would be much appreciated. > > -Connie Chang > > -= 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 Oct 11 14:26:46 2002 Received: from ivory.trentu.ca ([192.75.12.103]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g9BIQkB31883 for ; Fri, 11 Oct 2002 14:26:46 -0400 Received: from trentu.ca ([206.248.117.30]) by trentu.ca (PMDF V5.2-32 #37862) with ESMTP id <01KNJ9Y60J2Y0001FU@trentu.ca> for chemistry@ccl.net; Fri, 11 Oct 2002 10:18:07 EDT Date: Fri, 11 Oct 2002 10:20:02 -0400 From: elewars Subject: correction to reply, semiempirical To: chemistry@ccl.net Message-id: <3DA6DE12.30252792@trentu.ca> MIME-version: 1.0 X-Mailer: Mozilla 4.79 [en] (WinNT; U) Content-type: text/plain; charset=us-ascii Content-transfer-encoding: 7bit X-Accept-Language: en 2002 Oct 11 That should have been I. N. Levine, Fifth Ed. (not Fourth). EL ===== From chemistry-request@server.ccl.net Fri Oct 11 17:43:22 2002 Received: from trivial.uchicago.edu (IDENT:root@[128.135.160.75]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g9BLhJB03243 for ; Fri, 11 Oct 2002 17:43:22 -0400 Received: from localhost (cmtaylor@localhost) by trivial.uchicago.edu (8.9.3/8.9.3) with ESMTP id QAA26348 for ; Fri, 11 Oct 2002 16:43:19 -0500 Date: Fri, 11 Oct 2002 16:43:19 -0500 (CDT) From: Caroline Taylor To: CCL list Subject: MO visualization with OpenDX Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII I'd like to use OpenDX to look at the MO's for several calculations (generally from GAMESS, or a set of MO coefficients from another calculation), and I was hoping that somebody had already come up with a way for doing this that they might be willing to share. Thanks! -Caroline -- --------------------------------------------- Caroline M. Taylor Department of Chemistry University of Chicago, James Franck Institute 5640 S. Ellis Avenue Chicago, Illinois 60637 (773) 702-7223 http://home.uchicago.edu/~cmtaylor --------------------------------------------- From chemistry-request@server.ccl.net Fri Oct 11 19:34:21 2002 Received: from hotmail.com ([64.4.19.166]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g9BNYKB08796 for ; Fri, 11 Oct 2002 19:34:21 -0400 Received: from mail pickup service by hotmail.com with Microsoft SMTPSVC; Fri, 11 Oct 2002 16:34:15 -0700 Received: from 64.230.16.161 by lw12fd.law12.hotmail.msn.com with HTTP; Fri, 11 Oct 2002 23:34:09 GMT X-Originating-IP: [64.230.16.161] From: "kaci Tizi-Ouzou" To: chemistry@ccl.net Subject: Spectra matching algorithms/papers/source code Date: Fri, 11 Oct 2002 23:34:09 +0000 Mime-Version: 1.0 Content-Type: text/plain; format=flowed Message-ID: X-OriginalArrivalTime: 11 Oct 2002 23:34:15.0634 (UTC) FILETIME=[B631F320:01C2717E] Greetings all, Does anybody know about any algorithm/papers or source code to perform spectra matching. Basically, I'd like to automatize identification of chemical coumpounds for which I have the corresponding spectra. Thanks all, Kaci _________________________________________________________________ Join the world’s largest e-mail service with MSN Hotmail. http://www.hotmail.com From chemistry-request@server.ccl.net Fri Oct 11 18:24:05 2002 Received: from cornell.edu ([132.236.56.6]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g9BMO5B03944 for ; Fri, 11 Oct 2002 18:24:05 -0400 Received: from cornell.edu (dopey.lassp.cornell.edu [128.84.241.121]) by cornell.edu (8.9.3/8.9.3) with ESMTP id SAA03641 for ; Fri, 11 Oct 2002 18:24:05 -0400 (EDT) Message-ID: <3DA74F85.FCCDF7B7@cornell.edu> Date: Fri, 11 Oct 2002 18:24:05 -0400 From: Connie Chang X-Mailer: Mozilla 4.77 [en] (Windows NT 5.0; U) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net Subject: Another Gaussian error message... Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi -- I've received yet another error... My original error was due to the scratch read/write file getting too large and I tried to fix this following the suggestions on the Gaussian home page. This is my route heading: %rwf=Z:\C140\temp1,2000MW,Z:\C140\temp2,2000MW,Z:\C140\temp3,2000MW # HF/3-21G SCF=Tight Opt Freq Test No title specified 0 1 C C,1,R2 C,1,R3 And this is the error message: rust Radius=3.00D-01 FncErr=1.00D-07 GrdErr=1.00D-07 Number of steps in this run= 840 maximum allowed number of steps= 840. Optmz4 allocation failure: iend,mxcore= 9823595 6291456 Error termination via Lnk1e in C:\G98W\l103.exe. Job cpu time: 0 days 0 hours 0 minutes 4.0 seconds. File lengths (MBytes): RWF= 39 Int= 0 D2E= 0 Chk= 1 Scr= 1 Has anyone encountered this before and know what it means? Thanks, Connie Chang cc236@cornell.edu