From chemistry-request@server.ccl.net Mon Apr 8 00:40:44 2002 Received: from hotmail.com ([64.4.43.101]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g384eip28601 for ; Mon, 8 Apr 2002 00:40:44 -0400 Received: from mail pickup service by hotmail.com with Microsoft SMTPSVC; Sun, 7 Apr 2002 21:40:33 -0700 Received: from 63.191.53.201 by www.hotmail.msn.com with HTTP; Mon, 08 Apr 2002 04:40:33 GMT X-Originating-IP: [63.191.53.201] From: "Fernando De La Vega" To: CHEMISTRY@ccl.net Subject: Ionization Potentials Date: Sun, 07 Apr 2002 21:40:33 -0700 Mime-Version: 1.0 Content-Type: text/plain; format=flowed Message-ID: X-OriginalArrivalTime: 08 Apr 2002 04:40:33.0871 (UTC) FILETIME=[853B1DF0:01C1DEB7] Dear All, I want to calculate the Ionization Potential (IP) for a particular system. I know I can get an approximate value through Koopman's theorem but I would like to be more exact. I understand that I can calculate the IP from the energy difference between the molecule and its +1 cation. However, what I am not sure about is whether I should calculate the energy for the +1 cation using the geometry of the of the neutral molecule or whether I should optimize the geometry of the cation and then calculate the difference. Your comments on the subject are really appreciated. I will summarize if there are any responses. Thanks. Fernando De La Vega _________________________________________________________________ Send and receive Hotmail on your mobile device: http://mobile.msn.com From chemistry-request@server.ccl.net Mon Apr 8 00:55:47 2002 Received: from mcmail.cis.mcmaster.ca (mattacf@[130.113.64.66]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g384tlp29153 for ; Mon, 8 Apr 2002 00:55:47 -0400 Received: from localhost (mattacf@localhost) by mcmail.cis.mcmaster.ca with ESMTP id AAA07162; Mon, 8 Apr 2002 00:55:35 -0400 (EDT) Date: Mon, 8 Apr 2002 00:55:34 -0400 (EDT) From: "C.F. Matta" To: "H. Martin Gillis" cc: CCL Net Subject: Re: CCL:Altona Equation In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=X-UNKNOWN Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from QUOTED-PRINTABLE to 8bit by server.ccl.net id g384tlp29154 Dear Dr. Martin Gillis, I am not familiar with the Altona equation, however this is what I know: The coupling constant J(AB) can be either positive or negative. It is positive when the antiparallel arrangement of nuclear spins is energetically favoured, and it is negative when the parallel arrangement has a lower energy. Hope this helps. Cheers, Cherif ---------------------------------- Chérif F. Matta, Theoretical/Computational Chemist, Polanyi Research Group, Lash Miller Chemical Laboratories, Chemistry Department, University of Toronto, 80 St. George Street (Room 261), Toronto, Ontario, Canada M5S 1A1 .................................. Telephone: (416) 978 - 3625 Cellular: (416) 996 - 2444 Fax: (416) 978 - 7580 E-mail: matta@chem.utoronto.ca ---------------------------------- On Sun, 7 Apr 2002, H. Martin Gillis wrote: > Hi all, > > Just wondering if anyone is familiar with using the Altona equation for > predicting vicinal J couplings. I have recently attempted to use this but I > noticed that the curves I generated give me negative J values. Does anyone > know how to interpret this??? > > Thanks in advance, > > -Martin > > > > -- > H. Martin Gillis > > 1105-101 Cumberland Ave., S. > Saskatoon, SK > S7N 1L5 > > (306) 652-7797 - Home > (306) 966-4690 - Work > > From chemistry-request@server.ccl.net Mon Apr 8 04:28:33 2002 Received: from myamlak.ch.uj.edu.pl ([149.156.71.18]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g388SWp04097 for ; Mon, 8 Apr 2002 04:28:32 -0400 Received: from localhost (makowskm@localhost) by myamlak.ch.uj.edu.pl (8.9.3/8.9.3) with ESMTP id KAA12937; Mon, 8 Apr 2002 10:24:48 +0200 (MET DST) Date: Mon, 8 Apr 2002 10:24:48 +0200 (MET DST) From: Marcin Makowski X-Sender: makowskm@myamlak.ch.uj.edu.pl To: Fernando De La Vega cc: CHEMISTRY@ccl.net Subject: Re: CCL:Ionization Potentials In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Computing energy of the cation at the same geometry will give you vertical IP, while relaxing geometry will result in adiabatic IP. I dont know which of these you are interested in, because both of them might be measured in experiment (but different type). Yours sincerely, Marcin Makowski Ph.D. - student in Theoretical Chemistry makowskm@chemia.uj.edu.pl From chemistry-request@server.ccl.net Mon Apr 8 05:06:36 2002 Received: from chemde5.LeidenUniv.nl ([132.229.119.141]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g3896Zp05088 for ; Mon, 8 Apr 2002 05:06:36 -0400 Received: (from aldert@localhost) by chemde5.LeidenUniv.nl (8.9.3/8.9.3) id LAA12255; Mon, 8 Apr 2002 11:02:06 +0200 (METDST) Date: Mon, 8 Apr 2002 11:02:06 +0200 (METDST) From: Aldert Westra Hoekzema Message-Id: <200204080902.LAA12255@chemde5.LeidenUniv.nl> To: CCL Net , "H. Martin Gillis" Subject: Re: CCL:Altona Equation Reply-To: a.whoekzema@chem.LeidenUniv.nl Hi Martin, I'm not the expert on J couplings of the Altona group but hopefully can give you some clues. First of all, most of the equations for predicting vicinal J couplings published by the Altona group are valid only for 3J(HH) and some for 3J(13CH) and 3J(19FH) couplings. All are valid only when the coupling nuclei are bound to aliphatic carbon atoms. Furthermore it is essential that the correct electronegativity values for the other substituents of these carbon atoms are entered into the equation. Several schemes to obtain electronegativity parameters have been used and a specific set of parameters is valid only in combination with a specific equation. Negative values of 3J(HH) couplings can occur for torsion angles around 90 and 270 degrees for compounds with multiple substituents that have large electronegativity parameters, like 1,2-difluoroethane. Our research was meant to describe the curves in order to use them for conformational analysis, so an interpretation must not go beyond the observation that the substituents are strongly electronegative. Aldert -- A.J.A. Westra Hoekzema Leiden Institute of Chemistry The Netherlands > From: "H. Martin Gillis" > > Hi all, > > Just wondering if anyone is familiar with using the Altona equation > for predicting vicinal J couplings. I have recently attempted to > use this but I noticed that the curves I generated give me negative > J values. Does anyone know how to interpret this??? > > Thanks in advance, > > -Martin > > -- > H. Martin Gillis > > 1105-101 Cumberland Ave., S. > Saskatoon, SK > S7N 1L5 > > (306) 652-7797 - Home > (306) 966-4690 - Work > > -= 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 Mon Apr 8 06:45:06 2002 Received: from smtp.csc.fi ([193.166.0.99]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g38Aj5p07284 for ; Mon, 8 Apr 2002 06:45:05 -0400 Received: from cedar-f.csc.fi (cedar.csc.fi [128.214.248.26]) by smtp.csc.fi (8.9.3/8.9.3/CSC) with ESMTP id NAA23916 for ; Mon, 8 Apr 2002 13:44:59 +0300 Date: Mon, 8 Apr 2002 13:44:59 +0300 From: Maija Lahtela To: chemistry@ccl.net Subject: Program for converting sdf file for molecular structure ? Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear All, I would appreciate your help in this file format problem. Do you know if there are available a program (cheap or free) which could convert file in sdf format to molecular structure ? Thanks in advance! Regards, Maija Lahtela-Kakkonen ***************************************************** Maija Lahtela-Kakkonen, Research Scientist Department of Pharmaceutical Chemistry University of Kuopio P.O.Box 1627, FIN-70210 Kuopio, FINLAND tel: +358-(0)17-162462, fax:+358-(0)17-162456 e-mail: mlahtela@csc.fi **************************************************** From chemistry-request@server.ccl.net Mon Apr 8 08:07:23 2002 Received: from cuces.unisi.it ([193.205.4.2]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g38C7Mp09736 for ; Mon, 8 Apr 2002 08:07:22 -0400 Received: from unisi.it (sgio2.ctf.unisi.it [172.16.3.81]) by unisi.it (PMDF V6.0-24 #43309) with ESMTPA id <01KGBNRFXA360009SS@unisi.it> for chemistry@ccl.net; Mon, 08 Apr 2002 14:07:14 +0100 (MET) Date: Mon, 08 Apr 2002 14:07:06 -0700 From: Stefano Forli Subject: Re: CCL:Program for converting sdf file for molecular structure ? Sender: stefano@unisi.it To: Maija Lahtela Cc: chemistry@ccl.net Message-id: <3CB2067A.CAA4F02C@unisi.it> MIME-version: 1.0 X-Mailer: Mozilla 4.5 [en] (X11; I; IRIX 6.3 IP32) Content-type: text/plain; charset=RESERVED Content-transfer-encoding: 7BIT X-Accept-Language: en References: You can try to download a version of BABEL for your platform. Check the following address http://smog.com/chem/babel/ or look for other links from a search engine (i.e. Google) It's free, and it's avalable for most used platforms (Irix,Linux,Unix,Mac,Ms-Dos) Enjoy Stefano Maija Lahtela wrote: > > Dear All, > > I would appreciate your help in this file format problem. > Do you know if there are available a program (cheap or free) which could > convert file in sdf format to molecular structure ? > > Thanks in advance! > > Regards, > Maija Lahtela-Kakkonen > > ***************************************************** > Maija Lahtela-Kakkonen, > Research Scientist > Department of Pharmaceutical Chemistry > University of Kuopio > P.O.Box 1627, FIN-70210 Kuopio, FINLAND > tel: ?(0)17-162462, fax:?(0)17-162456 > e-mail: mlahtela@csc.fi > **************************************************** > > -= 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 -- *********************************** Forli Stefano Dip. Farmaco Chimico Tecnologico Universita' degli Studi di Siena Via Aldo Moro I-53100 Siena, Italy Phone: ++39 0577 234307 Fax: ++39 0577 234333 *********************************** From chemistry-request@server.ccl.net Mon Apr 8 09:12:33 2002 Received: from c2bapps1.btconnect.com ([193.113.209.21]) by server.ccl.net (8.11.6/8.11.0) with SMTP id g38DCXp11611 for ; Mon, 8 Apr 2002 09:12:33 -0400 Received: from patriot (actually host host213-123-40-16.in-addr.btopenworld.com) by c2bapps1 with SMTP (XT-PP); Mon, 8 Apr 2002 14:12:18 +0100 From: "Roma Oakes" To: "ccl" Subject: RE: CCL:Dear netters, Date: Mon, 8 Apr 2002 14:11:58 +0100 Message-ID: MIME-Version: 1.0 Content-Type: text/plain; charset="US-ASCII" Content-Transfer-Encoding: 7bit X-Priority: 3 (Normal) X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook IMO, Build 9.0.2416 (9.0.2911.0) Importance: Normal X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2600.0000 In-Reply-To: Hi Pete Ermm.....it wasn't me who asked the question :-)) it was Sscrates Dantas. Regards Roma > -----Original Message----- > From: Peter Gannett [mailto:pgannett@hsc.wvu.edu] > Sent: 08 April 2002 14:08 > To: r.e.oakes@btconnect.com > Subject: Re: CCL:Dear netters, > > > Roma: > > It also depends on what computer equipment you have. If you are > running on an SGI you can use one of the media tools to make a > movie. Basically, you start the imagemkr, then run you dynamics > simulation, with the imagemkr running to capture what is > displayed on screen. If you need more details, let me know, I > know this is a bit sketchy. > > Pete > > >>> "Roma Oakes" 04/07/02 11:49AM >>> > This site may help to answer your question. > > http://hackberry.chem.trinity.edu/IJC/Text/example5.html > > Regards Roma > > > -----Original Message----- > > From: Computational Chemistry List [mailto:chemistry-request@ccl.net]On > > Behalf Of Socrates de Oliveira Dantas > > Sent: 04 April 2002 20:40 > > To: chemistry@ccl.net; dantas@fisica.ufjf.br > > Subject: CCL:Dear netters, > > > > > > Dear netters, > > > > We need an advice on how to create a movie from > > xyz files (generated by moledular dynamics simulation). > > We have a thousand xyz files. Is there a script or another > > automated tool could help us to generate an AVI > > movie suitable to our needs? Could you help us with > > this problem? (an open or freeware software would be > > better) > > > > Thanks in advance. > > > > Sscrates Dantas. > > > > dantas@fisica.ufjf.br > > > > > > > > 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 > > > > > > From chemistry-request@server.ccl.net Mon Apr 8 11:18:47 2002 Received: from addu.axelero.hu ([195.228.240.77]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g38FIlp15541 for ; Mon, 8 Apr 2002 11:18:47 -0400 Received: from chemaxon.com (user164.obuda.axelero.hu [195.228.88.164]) by mail02.axelero.hu (iPlanet Messaging Server 5.1 (built Jan 30 2002)) with ESMTP id <0GU900CF2929A3@mail02.axelero.hu> for chemistry@ccl.net; Mon, 08 Apr 2002 17:15:45 +0200 (MEST) Date: Mon, 08 Apr 2002 17:15:27 +0200 From: Ferenc Csizmadia Subject: Re: CCL:Program for converting sdf file for molecular structure ? To: Maija Lahtela Cc: chemistry@ccl.net Message-id: <3CB1B40F.3080105@chemaxon.com> Organization: ChemAxon MIME-version: 1.0 Content-type: text/plain; charset=us-ascii; format=flowed Content-transfer-encoding: 7BIT X-Accept-Language: en-us, hu User-Agent: Mozilla/5.0 (Windows; U; Windows NT 5.1; en-US; rv:0.9.9) Gecko/20020311 References: Hi, Maija Lahtela wrote: >I would appreciate your help in this file format problem. >Do you know if there are available a program (cheap or free) which could >convert file in sdf format to molecular structure ? > It is not clear what you would like to do with the structure. Using MarvinView (available as applet, JavaBean, or application), you can display structures coming from an SDfile, or other structure formats like SMILES, Molfile, .... The usage of the application is described at http://www.chemaxon.com/marvin/doc/mview.html (The application is free for academic/home users, the Java applet is free for free web sites) The Molconverter application (part of the Marvin Beans package) allows you to convert the structures to other formats or picture files (JPG, PNG, SVG, ...) http://www.chemaxon.com/marvin/doc/molconvert.html All these software pieces are in Java, so they can be run under all OS-s. The software can be downloaded at http://www.chemaxon.com/products.html. Please let me know if you have any question. Best regards, Ferenc -- Dr. Ferenc Csizmadia ChemAxon Ltd. http://www.chemaxon.com From chemistry-request@server.ccl.net Mon Apr 8 12:18:46 2002 Received: from ivory.trentu.ca ([192.75.12.103]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g38GIkp17242 for ; Mon, 8 Apr 2002 12:18:46 -0400 Received: from trentu.ca ([206.248.117.30]) by trentu.ca (PMDF V5.2-32 #37862) with ESMTP id <01KGBJWKHA90008T9O@trentu.ca> for chemistry@ccl.net; Mon, 8 Apr 2002 12:16:50 EDT Date: Mon, 08 Apr 2002 12:19:01 -0400 From: elewars Subject: Re: CCL:Ionization Potentials To: chemistry@ccl.net Cc: mparnis@trentu.ca Message-id: <3CB1C2F5.DB636253@trentu.ca> MIME-version: 1.0 X-Mailer: Mozilla 4.7 [en] (WinNT; I) Content-type: text/plain; charset=us-ascii Content-transfer-encoding: 7bit X-Accept-Language: en References: Hello, Fernando De La Vega asked about ionization energies. Whether you use for your calculation (1) the cation at the geometry of the neutral or (2) the optimized geometry of the cation, depends on which ionization energy (ionization potential) you want: (1) gives the _vertical_ ionization energy, (2) gives the _adiabatic_ IE The adiabatic values seem to be of more interest to chemists, since they represent the energy difference between two "stable" species (potential energy surface relative minima), but compilations of IE do not always state clearly whether their listed IEs are vertical or adiabatic; an exception is R. D. levin and S. G. Lias, "Ionization Potential and and Appearance Potential Measurements, 1971-1981", National Bureau of Standards, Washington DC, 1982. Vertical IEs seem to be slightly (up to 0.2 eV) higher than adiabatic (e.g. experimental CH3OH, 11.0 and 10.9 eV). Koopman' IEs are about 1.0 eV too high (CH3OH 12.06 by HF/6-31G*, 12.12 by MP2(fc)/6-31G*, HOMO energy). The difference of the calculated cation and neutral energies can give accurate IEs if post-HF calculations are used; for CH3OH (eV): vertical HF/6-31G* 9.66, MP2(fc)/6-31G* 10.82 adiabatic HF/6-31G* 9.38, MP2(fc)/6-31G* 10.6 Note that experimental and calculated vertical IEs are for electronically but not geometrically relaxed cations; adiabatic IEs are for completely relaxed cations; and Koopman' IEs refer to cations that are neither electronically nor geometrically relaxed. E. Lewars ================ Fernando De La Vega wrote: > Dear All, > I want to calculate the Ionization Potential (IP) for a particular system. > I know I can get an approximate value through Koopman's theorem but I would > like to be more exact. I understand that I can calculate the IP from the > energy difference between the molecule and its +1 cation. However, what I am > not sure about is whether I should calculate the energy for the +1 cation > using the geometry of the of the neutral molecule or whether I should > optimize the geometry of the cation and then calculate the difference. Your > comments on the subject are really appreciated. I will summarize if there > are any responses. Thanks. > > Fernando De La Vega > > _________________________________________________________________ > Send and receive Hotmail on your mobile device: http://mobile.msn.com > > -= This is automatically added to each message by mailing script =- > CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins > MAILSERV@ccl.net -- HELP CHEMISTRY or HELP SEARCH > CHEMISTRY-SEARCH@ccl.net -- archive search | Gopher: gopher.ccl.net 70 > Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net From chemistry-request@server.ccl.net Mon Apr 8 11:48:10 2002 Received: from igc.phys.chem.ethz.ch ([129.132.218.130]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g38Fm9p16319 for ; Mon, 8 Apr 2002 11:48:10 -0400 Received: from humagne.ethz.ch (humagne [129.132.218.162]) by igc.phys.chem.ethz.ch (8.11.4/8.11.4) with ESMTP id g38Fm4x28886 for ; Mon, 8 Apr 2002 17:48:04 +0200 (MEST) Received: (from portmann@localhost) by humagne.ethz.ch (8.11.4/8.11.4) id g38Fm4626924 for chemistry@ccl.net; Mon, 8 Apr 2002 17:48:04 +0200 (MEST) Date: Mon, 8 Apr 2002 17:48:04 +0200 (MEST) From: Message-Id: <200204081548.g38Fm4626924@humagne.ethz.ch> X-Authentication-Warning: humagne.ethz.ch: portmann set sender to chem-support@cscs.ch using -r To: chemistry@ccl.net Subject: MOLEKEL: New Release Dear Computational Chemists CSCS (http://www.cscs.ch) is proud to announce the release of MOLEKEL version 4.2. Improvements compared to version 4.1 are: - bugs fixed as far as reported to date - automatic H-bond detection implemented. - color coded slices through grid data at any position (not just perpendicular to the axis as before) added. - legend of color map in texture mode added. - display of coordinate system added. - MOLDEN file format support added. - command line options added: reading data files on start up. MOLEKEL is an interactive molecular graphics program to visualize molecular and electronic structure data from a number of electronic structure program outputs (Gaussian, Gamess, ADF...) as well as from XYZ and PDB files. MOLEKEL is able to render the molecular structure in different styles, display orbitals, electron densities, map and color code properties on any surface, display and animate vibrational normal modes, animate a sequence of coordinates and produces great graphics... Look and see! More information, a precompiled binary for SGI, SUN, LINUX systems and WINDOWS PC's and detailed documentation is available from http://www.cscs.ch/molekel/. Best regards Stefan Portmann From chemistry-request@server.ccl.net Mon Apr 8 11:31:11 2002 Received: from mail.UTB.edu (IDENT:20211A85@[192.150.93.2]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g38FVAp15953 for ; Mon, 8 Apr 2002 11:31:11 -0400 Received: from utb1.utb.edu ("port 18302"@[206.254.3.83]) by mail.UTB.edu (PMDF V6.0-025 #39593) with ESMTPA id <01KGBG85K6OS8WXI98@mail.UTB.edu> for chemistry@ccl.net; Mon, 08 Apr 2002 10:30:51 -0500 (CDT) Date: Mon, 08 Apr 2002 16:09:56 -0500 From: "Dr. Bill Davis" Subject: parallel quantum solutions Sender: bdavis@UTB.edu To: chemistry@ccl.net Message-id: <3CB20723.87CE9126@utb1.utb.edu> Organization: University of Texas MIME-version: 1.0 X-Mailer: Mozilla 4.61C-SGI [en] (X11; I; IRIX 6.5 IP32) Content-type: multipart/alternative; boundary="Boundary_(ID_kohTZ4owp8/50kCBphB4Bg)" X-Accept-Language: en --Boundary_(ID_kohTZ4owp8/50kCBphB4Bg) Content-type: text/plain; charset=us-ascii Content-transfer-encoding: 7BIT Hi! Does anyone have any experience with the PQS hardware/software combination, more specifically the QS4-1800S? Any comments on ease of use, support and any other important points would be greatly appreciated...Thanks! Bill -- ********************************** Dr. William M. Davis Assistant Professor of Chemistry/ Phi Theta Kappa Advisor Dept. of Chemistry and Environmental Science University of Texas at Brownsville 80 Fort Brown Brownsville, TX 78520 Phone: (956) 574-6646 Fax: (956) 574-6692 WWW: unix.utb.edu/~bdavis ********************************** --Boundary_(ID_kohTZ4owp8/50kCBphB4Bg) Content-type: text/html; charset=us-ascii Content-transfer-encoding: 7BIT Hi!

Does anyone have any experience with the PQS hardware/software combination, more specifically the QS4-1800S?  Any comments on ease of use, support and any other important points would be greatly appreciated...Thanks!

Bill
  

-- 
**********************************
Dr. William M. Davis
Assistant Professor of Chemistry/
Phi Theta Kappa Advisor
Dept. of Chemistry and Environmental Science
University of Texas at Brownsville
80 Fort Brown
Brownsville, TX 78520
Phone: (956) 574-6646
Fax: (956) 574-6692
WWW: unix.utb.edu/~bdavis
**********************************
  --Boundary_(ID_kohTZ4owp8/50kCBphB4Bg)-- From chemistry-request@server.ccl.net Mon Apr 8 14:02:37 2002 Received: from ucidoor.unitedcatalysts.com ([208.23.162.2]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g38I2bp19524 for ; Mon, 8 Apr 2002 14:02:37 -0400 Received: by ucidoor.unitedcatalysts.com; (8.8.8/1.3/10May95) id OAA24113; Mon, 8 Apr 2002 14:02:28 -0400 (EDT) Received: from 10.1.0.50 by ucismtp02.unitedcatalysts.com (InterScan E-Mail VirusWall NT); Mon, 08 Apr 2002 13:59:35 -0400 (Eastern Daylight Time) Received: from lvlxch01.unitedcatalysts.com ([10.16.100.88]) by lvlmail.unitedcatalysts.com (PMDF V6.0-24 #41777) with ESMTP id <0GU900FB1GIJ4P@lvlmail.unitedcatalysts.com>; Mon, 08 Apr 2002 13:56:43 -0400 (EDT) Received: by lvlxch01.unitedcatalysts.com with Internet Mail Service (5.5.2650.21) id ; Mon, 08 Apr 2002 14:00:26 -0400 Content-return: allowed Date: Mon, 08 Apr 2002 14:00:26 -0400 From: "Shobe, Dave" Subject: RE: Ionization Potentials To: "'elewars'" , chemistry@ccl.net Cc: mparnis@trentu.ca Message-id: <157A51F55AAAD3119CD70008C7B1629D01C15B74@lvlxch01.unitedcatalysts.com> MIME-version: 1.0 X-Mailer: Internet Mail Service (5.5.2650.21) Content-type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id g38I2bp19525 E. Lewars wrote: >Vertical IEs seem to be slightly (up to 0.2 eV) higher than adiabatic (e.g. >experimental CH3OH, 11.0 and 10.9 eV). There's a reason for IE-vert being > IE-adia. Actually it's implicit in the rest of E. Lewars' message, but it's worth stating explicitly: 1. The IE-vert is the energy required to go from neutral at its geometric energy minimum to cation at the *neutral's* geometric energy minimum; 2. whereas the IE-adia is the energy required to go from neutral at its geometric energy minimum to the *cation's* geometric energy minimum. Note that the starting point is in both cases the same: the neutral at the neutral's geometric minimum. 3. And by definition, the cation's energy will be lower at *its* geometric minimum than at any other geometry, including the neutral's geometric energy minimum. QED. --David Shobe Süd-Chemie Inc. phone (502) 634-7409 fax (502) 634-7724 email dshobe@sud-chemieinc.com Don't bother flaming me: I'm behind a firewall. -----Original Message----- From: elewars [mailto:elewars@trentu.ca] Sent: Monday, April 08, 2002 12:19 PM To: chemistry@ccl.net Cc: mparnis@trentu.ca Subject: CCL:Ionization Potentials Hello, Fernando De La Vega asked about ionization energies. Whether you use for your calculation (1) the cation at the geometry of the neutral or (2) the optimized geometry of the cation, depends on which ionization energy (ionization potential) you want: (1) gives the _vertical_ ionization energy, (2) gives the _adiabatic_ IE The adiabatic values seem to be of more interest to chemists, since they represent the energy difference between two "stable" species (potential energy surface relative minima), but compilations of IE do not always state clearly whether their listed IEs are vertical or adiabatic; an exception is R. D. levin and S. G. Lias, "Ionization Potential and and Appearance Potential Measurements, 1971-1981", National Bureau of Standards, Washington DC, 1982. Vertical IEs seem to be slightly (up to 0.2 eV) higher than adiabatic (e.g. experimental CH3OH, 11.0 and 10.9 eV). Koopman' IEs are about 1.0 eV too high (CH3OH 12.06 by HF/6-31G*, 12.12 by MP2(fc)/6-31G*, HOMO energy). The difference of the calculated cation and neutral energies can give accurate IEs if post-HF calculations are used; for CH3OH (eV): vertical HF/6-31G* 9.66, MP2(fc)/6-31G* 10.82 adiabatic HF/6-31G* 9.38, MP2(fc)/6-31G* 10.6 Note that experimental and calculated vertical IEs are for electronically but not geometrically relaxed cations; adiabatic IEs are for completely relaxed cations; and Koopman' IEs refer to cations that are neither electronically nor geometrically relaxed. E. Lewars ================ Fernando De La Vega wrote: > Dear All, > I want to calculate the Ionization Potential (IP) for a particular system. > I know I can get an approximate value through Koopman's theorem but I would > like to be more exact. I understand that I can calculate the IP from the > energy difference between the molecule and its +1 cation. However, what I am > not sure about is whether I should calculate the energy for the +1 cation > using the geometry of the of the neutral molecule or whether I should > optimize the geometry of the cation and then calculate the difference. Your > comments on the subject are really appreciated. I will summarize if there > are any responses. Thanks. > > Fernando De La Vega > > _________________________________________________________________ > Send and receive Hotmail on your mobile device: http://mobile.msn.com > -= This is automatically added to each message by mailing script =- CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins MAILSERV@ccl.net -- HELP CHEMISTRY or HELP SEARCH CHEMISTRY-SEARCH@ccl.net -- archive search | Gopher: gopher.ccl.net 70 Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net From chemistry-request@server.ccl.net Mon Apr 8 05:59:24 2002 Received: from suncom.rz.hu-berlin.de ([141.20.1.31]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g389xNp06282 for ; Mon, 8 Apr 2002 05:59:24 -0400 Received: from Debug (webmania.rz.hu-berlin.de [141.20.1.45]) by suncom.rz.hu-berlin.de (8.9.3/8.9.3) with SMTP id LAA19698; Mon, 8 Apr 2002 11:59:15 +0200 (MET DST) Message-Id: <200204080959.LAA19698@suncom.rz.hu-berlin.de> To: Krzysztof Radacki Cc: CCL From: h38052kq@rz.hu-berlin.de Reply-To: ah@chemie.hu-berlin.de Subject: Date: Mon, 8 Apr 2002 11:59:15 MET X-Mailer: Endymion MailMan Standard Edition v3.0.33 Hi Krzysztof, it's the underscore problem. It always arises, if you mix C and FORTRAN Code. So You have to search your man pages for proper handling of mixing both languages. By the way, MOPAC 5 is stone edge. Fujitsu is claiming, that even the last free MOPAC Versions (as I remember V7) are containing a lot of bugs ... Hth Alex --- Dr. Alexander Hofmann Humboldt-Universitaet zu Berlin Institut fuer Chemie Arbeitsgruppe Quantenchemie Brook-Taylor-Strasse 2 ah@chemie.hu-berlin.de Tel.: +49-30-2093-7138 Fax.: +49-30-2093-7136 http://www.chemie.hu-berlin.de/ag_sauer/index.html From chemistry-request@server.ccl.net Mon Apr 8 02:42:32 2002 Received: from web12806.mail.yahoo.com ([216.136.174.41]) by server.ccl.net (8.11.6/8.11.0) with SMTP id g386gWp00588 for ; Mon, 8 Apr 2002 02:42:32 -0400 Message-ID: <20020408064219.1129.qmail@web12806.mail.yahoo.com> Received: from [203.87.132.164] by web12806.mail.yahoo.com via HTTP; Sun, 07 Apr 2002 23:42:19 PDT Date: Sun, 7 Apr 2002 23:42:19 -0700 (PDT) From: amor san juan Subject: docket where GPF & DPF can be executed To: chemistry@ccl.net MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Fellow dockers; I'm using AutoDock3.0, would anyone please lead me where programs of AutoDock3.0 I will launch the conversion of ligand.pdbq to dpf (for ligand preparation) & macro.pdbqs to gpf (for protein prep) prior using AutoGrid editings. I believe that there will be someone who will give me time to help me out there. Please do, I will greatly appreciate it. Working hard, Amor San Juan University of the Philippines-Diliman __________________________________________________ Do You Yahoo!? Yahoo! Tax Center - online filing with TurboTax http://taxes.yahoo.com/ From chemistry-request@server.ccl.net Mon Apr 8 18:57:48 2002 Received: from ivory.trentu.ca ([192.75.12.103]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g38Mvlp27003 for ; Mon, 8 Apr 2002 18:57:48 -0400 Received: from trentu.ca ([206.248.117.30]) by trentu.ca (PMDF V5.2-32 #37862) with ESMTP id <01KGBXV634FW002AU8@trentu.ca> for chemistry@ccl.net; Mon, 8 Apr 2002 18:56:33 EDT Date: Mon, 08 Apr 2002 18:58:45 -0400 From: elewars Subject: Universities, Computational chemistry To: chemistry@ccl.net Message-id: <3CB220A5.D9D27398@trentu.ca> MIME-version: 1.0 X-Mailer: Mozilla 4.7 [en] (WinNT; I) Content-type: text/plain; charset=us-ascii Content-transfer-encoding: 7bit X-Accept-Language: en 2002 April 8 Hello, If anyone knows approximately, or even has just a rough idea, how many universities in North America (or anywhere else, if you know) offer a course in computational chemistry, I would very much appreciate this information. Even an educated guess could be useful. Thank you. E. Lewars ====================== From chemistry-request@server.ccl.net Mon Apr 8 17:15:56 2002 Received: from web13407.mail.yahoo.com ([216.136.175.65]) by server.ccl.net (8.11.6/8.11.0) with SMTP id g38LFtp24095 for ; Mon, 8 Apr 2002 17:15:56 -0400 Message-ID: <20020408211549.12726.qmail@web13407.mail.yahoo.com> Received: from [169.232.140.249] by web13407.mail.yahoo.com via HTTP; Mon, 08 Apr 2002 14:15:49 PDT Date: Mon, 8 Apr 2002 14:15:49 -0700 (PDT) From: eric hu Subject: amber force field parameters To: chemistry@ccl.net MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Dear all, I need the parameters for bond(SH-O2), angle(CB-CB-SH,CB-SH-O2),torsion(CB-CB-SH-O2). Can anybody point out those parameters or where I can find the sulfer related force field parameters. Thanks a lot! Eric __________________________________________________ Do You Yahoo!? Yahoo! Tax Center - online filing with TurboTax http://taxes.yahoo.com/ From chemistry-request@server.ccl.net Mon Apr 8 14:54:15 2002 Received: from zephyr.meteo.McGill.CA ([132.206.43.13]) by server.ccl.net (8.11.6/8.11.0) with SMTP id g38IsEp21120 for ; Mon, 8 Apr 2002 14:54:15 -0400 Received: from kinetic.Meteo.McGill.CA by zephyr.meteo.McGill.CA (AIX 4.1/UCB 5.64/4.03) id AA19260; Mon, 8 Apr 2002 14:47:40 -0400 Date: Mon, 8 Apr 2002 14:54:08 -0400 From: Andrew Ryzhkov X-Mailer: The Bat! (v1.53d) Reply-To: Andrew Ryzhkov Organization: Dep. of Atm. & Oc. Sci. McGill Univ. X-Priority: 3 (Normal) Message-Id: <193179969101.20020408145408@zephyr.meteo.mcgill.ca> To: h38052kq@rz.hu-berlin.de Cc: CCL , Krzysztof Radacki Subject: Re: CCL:Date: Mon, 8 Apr 2002 11:59:15 MET In-Reply-To: <200204080959.LAA19698@suncom.rz.hu-berlin.de> References: <200204080959.LAA19698@suncom.rz.hu-berlin.de> Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hello, hrhbd> By the way, MOPAC 5 is stone edge. Fujitsu is claiming, that even the last free hrhbd> MOPAC Versions (as I remember V7) are containing a lot of bugs ... I think, Fujitsu wish that people have to buy the Fujitsu MOPAC instead using a free version of this one. So, you should take into consideration this moment. Of course, MOPAC 7 is not ideal and has some bugs, but actually it is working well. If you would not like to buy new MOPAC or have not enough money, I recommend use GAMESS. It has included MOPAC code which is working good and faster that one in original MOPAC. Best regards, Andrew Dr. Andrei Ryjkov Departments of Chemistry, and Atmospheric and Oceanic Sciences, McGill University, 805 Sherbrooke St. West #808 Montreal, Quebec, CANADA, H3A 2K6. ---------------------------------------------------------------- E-mail: Andrew@Zephyr.Meteo.McGill.Ca Internet: http://RedAndr.tripod.com From chemistry-request@server.ccl.net Mon Apr 8 15:24:01 2002 Received: from so.sd.lionbioscience.com ([209.68.255.43]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g38JO0p21882 for ; Mon, 8 Apr 2002 15:24:00 -0400 Received: from tempest.sd.lionbioscience.com (tempest.sd.lionbioscience.com [10.8.0.8]) by so.sd.lionbioscience.com (8.11.3/8.11.3) with ESMTP id g38JNTV21930; Mon, 8 Apr 2002 12:23:29 -0700 (PDT) Received: by tempest.sd.lionbioscience.com with Internet Mail Service (5.5.2653.19) id ; Mon, 8 Apr 2002 12:23:07 -0700 Message-ID: From: Stephen Bowlus To: "'h38052kq@rz.hu-berlin.de'" , Krzysztof Radacki Cc: CCL Subject: RE: Date: Mon, 8 Apr 2002 11:59:15 MET Date: Mon, 8 Apr 2002 12:23:01 -0700 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2653.19) Content-Type: multipart/alternative; boundary="----_=_NextPart_001_01C1DF32.CC53FE20" This message is in MIME format. Since your mail reader does not understand this format, some or all of this message may not be legible. ------_=_NextPart_001_01C1DF32.CC53FE20 Content-Type: text/plain; charset="iso-8859-1" Mopac6 was the last, free public version intended for production use. For many (most?) common uses, it is remarkably stable. In addition to bug-fixes, Mopac6 has a major improvement over Mopac5 through the incorporation of eigenvector following as a minimizer option. I've never had to use the more exotic features of the program, so I can't comment on its suitability for these. Mopac7 was the public access version of post-Mopac6 improvements which did not contain the proprietary (?) features which were included in Mopac93 (which is subject to license). Mopac7 was _never_ touted as stable production code, but was intended for "developers" use ... and as a way to get around the outcry at the "privatization" of the "publicly funded development" of the Mopac package. The Fujitsu funded development of Mopac has certainly led to enormous improvements in algorithms (and invention of some new ones!) and parameterization. But they do have a vested interest in encouraging adoption of the latest bells and whistles. For the common uses, I am not aware that Mopac6 (specifically) suffers from serious bugs that would not have been discussed in the Mopac7/Mopac93 documentation. If you want to upgrade to Mopac6, all of the "public" versions of Mopac (and Mopac93) are available from QCPE. Cheers, Steve > -----Original Message----- > From: h38052kq@rz.hu-berlin.de [mailto:h38052kq@rz.hu-berlin.de] > Sent: Monday, April 08, 2002 2:59 AM > To: Krzysztof Radacki > Cc: CCL > Subject: CCL:Date: Mon, 8 Apr 2002 11:59:15 MET > > > Hi Krzysztof, > > it's the underscore problem. It always arises, if you mix C > and FORTRAN Code. > So You have to search your man pages for proper handling of > mixing both > languages. > > By the way, MOPAC 5 is stone edge. Fujitsu is claiming, that > even the last free > MOPAC Versions (as I remember V7) are containing a lot of bugs ... > > Hth > > Alex > > > > --- > > Dr. Alexander Hofmann > > Humboldt-Universitaet zu Berlin > Institut fuer Chemie > Arbeitsgruppe Quantenchemie > > Brook-Taylor-Strasse 2 > > ah@chemie.hu-berlin.de > > Tel.: +49-30-2093-7138 > Fax.: +49-30-2093-7136 > > http://www.chemie.hu-berlin.de/ag_sauer/index.html > > > > > > > > -= 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 > > > > > ------_=_NextPart_001_01C1DF32.CC53FE20 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable RE: Date: Mon, 8 Apr 2002 11:59:15 MET

Mopac6 was the last, free public version intended for = production use.  For many (most?) common uses, it is remarkably = stable.  In addition to bug-fixes, Mopac6 has a major improvement = over Mopac5 through the incorporation of eigenvector following as a = minimizer option.  I've never had to use the more exotic features = of the program, so I can't comment on its suitability for these.  =

Mopac7 was the public access version of post-Mopac6 = improvements which did not contain the proprietary (?) features which = were included in Mopac93 (which is subject to license).  Mopac7 = was _never_ touted as stable production code, but was intended for = "developers" use ... and as a way to get around the outcry at = the "privatization" of the "publicly funded = development" of the Mopac package.

The Fujitsu funded development of Mopac has certainly = led to enormous improvements in algorithms (and invention of some new = ones!) and parameterization.  But they do have a vested interest = in encouraging adoption of the latest bells and whistles.  For the = common uses, I am not aware that Mopac6 (specifically) suffers from = serious bugs that would not have been discussed in the Mopac7/Mopac93 = documentation.

If you want to upgrade to Mopac6, all of the = "public" versions of Mopac (and Mopac93) are available from = QCPE.

Cheers,
Steve

> -----Original Message-----
> From: h38052kq@rz.hu-berlin.de [mailto:h38052kq@rz.hu-berlin.de= ]
> Sent: Monday, April 08, 2002 2:59 AM
> To: Krzysztof Radacki
> Cc: CCL
> Subject: CCL:Date: Mon, 8 Apr 2002 11:59:15 = MET
>
>
> Hi Krzysztof,
>
> it's the underscore problem. It always arises, = if you mix C
> and FORTRAN Code.
> So You have to search your man pages for proper = handling of
> mixing both
> languages.
>
> By the way, MOPAC 5 is stone edge. Fujitsu is = claiming, that
> even the last free
> MOPAC Versions (as I remember V7) are = containing a lot of bugs ...
>
> Hth
>
> Alex
>
>
>
> ---
>
> Dr. Alexander Hofmann
>
> Humboldt-Universitaet zu Berlin
> Institut fuer Chemie
> Arbeitsgruppe Quantenchemie
>
> Brook-Taylor-Strasse 2
>
> ah@chemie.hu-berlin.de
>
> Tel.: +49-30-2093-7138
> Fax.: +49-30-2093-7136
>
> http://www.chemie.hu-berlin.de/ag_sauer/index.html=
>
>
>
>
>
>
>
> -=3D This is automatically added to each = message by mailing script =3D-
> 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
>
>
>
>
>

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