From chemistry-request@server.ccl.net Tue Apr 9 01:50:17 2002 Received: from hotmail.com ([64.4.8.132]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g395oHp14405 for ; Tue, 9 Apr 2002 01:50:17 -0400 Received: from mail pickup service by hotmail.com with Microsoft SMTPSVC; Mon, 8 Apr 2002 22:50:06 -0700 Received: from 63.184.81.225 by lw9fd.law9.hotmail.msn.com with HTTP; Tue, 09 Apr 2002 05:50:06 GMT X-Originating-IP: [63.184.81.225] From: "Fernando De La Vega" To: CHEMISTRY@ccl.net Subject: Ionization Potential: Summary of Answers Date: Mon, 08 Apr 2002 22:50:06 -0700 Mime-Version: 1.0 Content-Type: text/plain; format=flowed Message-ID: X-OriginalArrivalTime: 09 Apr 2002 05:50:06.0752 (UTC) FILETIME=[66DFFA00:01C1DF8A] Hello, I would like to thank Li Zhenhua, Brian Salter-Duke, Alan Shusterman, Jens Spanget-Larsen, N.O.J. Malcolm, Marcin Makowski, Ulrike Salzner, Pascal Boulet, Teodorico Ramalho, E. Lewars, David Shobe, Pierre Vitorge and, Robert Ponec for their response to my inquiry. I reproduce below my original questions and their answers. Thanks again. My question: 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. Answers: ---------------------------------------------- Li Zhenhua: The usual procedure is to optimize the geometry of the cation and calculate the energy difference. -------------------------------------- Brian Salter-Duke: It depends whether you want the Vertical Ionization Energy as measured say by Photoelectron spectroscopy, in which case you want the cation to be at the same geometry as the neutral molecule, or whether you want the adiapatic ionization energy where both the neutral and the cation should be at a geometric minimum energy. -------------------------------------- Alan Shusterman: The correct choice depends on what use you intend to make of your result. If you leave the geometry the same, you can estimate the vertical IP. If you optimize the cation's geometry, you can estimate the adiabatic IP. --------------------------------------- JENS SPANGET-LARSEN: if you use the neutral groundstate molecular geometry in the calculation for the cation, you end up with so-called vertical ionization energies (according to the Franck-Condon principle). These ionization energies generally correspond to the maximum, or the center of gravity, of the photoelectron (PE) band. If you optimize the geometries of the cationic states, you obtain the so-called adiabatic ionization energies that would correspond to the onset op the PE bands. --------------------------------- Dr. N.O.J. Malcolm: It really depends what you want to know, if you use teh neutral system geometry for teh cation then you will have calculated a vertical IP (VIP) otherwise using the optimised cation geometry you will have teh adiabatic IP (AIP). Both the VIP and AIP can be determined via experiments so check what you want/have. By the way you may want to have a look at Greens function methods for calculating IPs as these are generally a bit more accurate than energy difference approximations. --------------------------------- Marcin Makowski: 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). --------------------------------- Ulrike Salzner: if you use the geometry of the neutral, you get the verticel ionization energy, if you re-optimize, you get the adiabatic ionization energy. Now you have to decide what you need. In experiment, the vertical IP isusually determined, because the nuclear motion is slow compared to the movement of the electrons (Franck-Condon principle). -------------------------------------- Pascal Boulet: There is an alternative way to calculate vertical ionization potential : use the geometry of the neutral molecule, put half an electron on the HOMO and perform a single point calculation. The energy of the HOMO should give you a good idea of the IP. It's working well within the DFT formalism. I've not tried for ab initio methods. ------------------------------------------------------ Teodorico Ramalho: Computing energy of the cation at the same geometry will give you vertical IP, Experimentaaly, the IP vertical is most difultof be obtained. Thi is, generally, obtained by spectroscopic studies. There is one option in Gaussian98 to calculation vertical IP, the keyword is OVGF. If you relax geometry will result in adiabatic IP. This is IP, generaly, obtained to electrochemistry studies. ------------------------------------------------ E. Lewars: 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. ------------------------------------------------- David Shobe: 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. ----------------------------------------------------------------------- Pierre Vitorge: optimize the geometry of the cation and then calculate the difference ------------------------------------------------------------------------ Robert Ponec: you can calculate both, the IP calculated for the geometry of +1 ion with the fixed geometry of the neutral molecule is the so-called "vertical IP", the other possibility is to relax the geometry of +1 ion to its optimum, in this case the IP is called "adiabatic", both values can be in principle determined fron experiment. _________________________________________________________________ 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 Tue Apr 9 03:37:56 2002 Received: from tigris.klte.hu ([193.6.138.33]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g397btp20143 for ; Tue, 9 Apr 2002 03:37:55 -0400 Received: from cthulhu (193.6.133.59) by tigris.klte.hu (MX V5.1-A Vn6f) with SMTP; Tue, 9 Apr 2002 09:38:11 +0200 Message-ID: <001701c1df99$51c3a090$3b8506c1@cthulhu> From: "Tamas E. Gunda" To: "Maija Lahtela" CC: References: Subject: Re: CCL:Program for converting sdf file for molecular structure ? Date: Tue, 9 Apr 2002 09:36:53 +0200 MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 5.50.4522.1200 X-MIMEOLE: Produced By Microsoft MimeOLE V5.50.4522.1200 Mol2Mol can do it. You can browse the structure or convert it to several molfile formats in one or in sliced form. See http://www.compuchem.com/mol2mol.htm or http://www.klte.hu/~gundat/mol2mola.htm Best regards Tamas ------------------------ Dr. Tamas E. Gunda Research Group for Antibiotics Hungarian Academy of Sciences University of Debrecen, POBox 36 H-4010 Debrecen, Hungary tamasgunda@tigris.klte.hu ----- Original Message ----- From: "Maija Lahtela" To: Sent: Monday, April 08, 2002 12:44 Subject: CCL:Program for converting sdf file for molecular structure ? > 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 > **************************************************** > > > -= 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 Tue Apr 9 05:42:38 2002 Received: from vytautas.vdu.lt ([193.219.38.33]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g399gbp24758 for ; Tue, 9 Apr 2002 05:42:38 -0400 Received: from vaidila.vdu.lt ([193.219.38.52] ident=mail) by vytautas.vdu.lt with esmtp for chemistry@ccl.net id 16us8x-0006LI-00; Tue, 09 Apr 2002 11:42:27 +0200 Received: from vejas.vdu.lt ([193.219.38.82] helo=TYREX) by vaidila.vdu.lt with esmtp for chemistry@ccl.net id 16us9b-00036O-00; Tue, 09 Apr 2002 11:43:07 +0200 Date: Tue, 9 Apr 2002 11:42:39 +0300 From: a3arzi X-Mailer: The Bat! (v1.44) UNREG / CD5BF9353B3B7091 Reply-To: "Art'" X-Priority: 3 (Normal) Message-ID: <327784543.20020409114239@vaidila.vdu.lt> To: chemistry@ccl.net Subject: CCL: LJ potentials for metals Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hello CCL'ers, I tried search CCL archive, but without significant success. I wander about where could I find LJ parameters of various metals (Cu Zn, Mg, ... ) for docking (AutoDock). -- Best regards and thank you in advance, Arturas Z. mailto:a3arzi@vaidila.vdu.lt http://biologija.vdu.lt/person/ziemar/index.html From chemistry-request@server.ccl.net Tue Apr 9 06:21:39 2002 Received: from post.webmailer.de ([192.67.198.65]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g39ALcp27144 for ; Tue, 9 Apr 2002 06:21:38 -0400 Received: from fepa.biop.ox.ac.uk (fepa.biop.ox.ac.uk [163.1.16.72]) by post.webmailer.de (8.9.3/8.8.7) with ESMTP id MAA17082; Tue, 9 Apr 2002 12:21:28 +0200 (MET DST) Message-Id: <200204091021.MAA17082@post.webmailer.de> X-Mailer: exmh version 2.3.1 01/18/2001 (debian 2.3.1-1) with nmh-1.0.2 To: a3arzi cc: chemistry@ccl.net Subject: Re: CCL:LJ potentials for metals In-reply-to: Your message of "Tue, 09 Apr 2002 11:42:39 +0300." <327784543.20020409114239@vaidila.vdu.lt> X-image-url: http://crypt.u-strasbg.fr/marc/m-baaden.gif X-url: X-face: -Nz&SN]%I8g9WFR#/!fe9se!_G_OndNloj@t+6jrGsoZ"z)?an0n P!Nls~*o?u7fy:]1N|^^(KX*uE>Nk{bHaCJ)(hXF~E#5)j.k0n4hgfIzpmn,[VY'\7X:;VOZ\CItIq G!2f8,k2`VLrkXQ:<.3LxEQ'E-;d:A)V# Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Date: Tue, 09 Apr 2002 11:21:19 +0100 From: Marc Baaden Dear Arturas, you might want to check out the forcefields that come with Gromacs. As far as I know they contain LJ parameters for a number of metal ions (eg Zn, Mg, ..). All relevant information should be available from www.gromacs.org a3arzi@vaidila.vdu.lt said: >> I tried search CCL archive, but without significant success. I wander >> about where could I find LJ parameters of various metals (Cu Zn, Mg, >> ... ) for docking (AutoDock). Marc -- Dr. Marc Baaden - Laboratory of Molecular Biophysics, Oxford University mailto:baaden@smplinux.de - ICQ# 11466242 - http://www.marc-baaden.de FAX/Voice +49 697912 39550 - Tel: +44 1865 275380 or +33 609 843217 From chemistry-request@server.ccl.net Tue Apr 9 04:03:07 2002 Received: from pat.ccc.nottingham.ac.uk ([128.243.40.194]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g39836p20933 for ; Tue, 9 Apr 2002 04:03:06 -0400 Received: from granby.ccc.nottingham.ac.uk ([128.243.40.43]) by pat.ccc.nottingham.ac.uk with esmtp (Exim 3.34 #1) id 16uqah-00027O-00; Tue, 09 Apr 2002 09:02:59 +0100 Received: from ppcrjw0.nottingham.ac.uk ([128.243.121.89] helo=ppcrw1) by granby.ccc.nottingham.ac.uk with smtp (Exim 3.34 #1) id 16uqaC-00076B-00; Tue, 09 Apr 2002 09:02:28 +0100 Message-Id: <3.0.6.32.20020409091153.00bbee60@unix.ccc.nottingham.ac.uk> X-Sender: pczrjw@unix.ccc.nottingham.ac.uk X-Mailer: QUALCOMM Windows Eudora Light Version 3.0.6 (32) Date: Tue, 09 Apr 2002 09:11:53 +0100 To: elewars , chemistry@ccl.net From: Richard Wheatley Subject: Re: CCL:Universities, Computational chemistry In-Reply-To: <3CB220A5.D9D27398@trentu.ca> Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" X-MailScanner: No virus detected The University of Nottingham, UK, has three and four year courses in Chemistry with Computational Chemistry. http://www.nottingham.ac.uk/chemistry/student-opportunities/undergraduate/co mpchem.html http://www.nottingham.ac.uk/chemistry/teaching/undergraduate/handbooks/compu tational_chemistry/index.html Best wishes, Richard Wheatley. At 06:58 PM 4/8/02 -0400, elewars wrote: >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 >====================== > > >-= 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 > > > > > > Richard Wheatley, School of Chemistry, University of Nottingham "Exploring Modern Computational Chemistry" University of Nottingham, July 31 - Aug 2, 2002 http://www.nottingham.ac.uk/chemistry/emc2 From chemistry-request@server.ccl.net Tue Apr 9 04:05:34 2002 Received: from web12802.mail.yahoo.com ([216.136.174.37]) by server.ccl.net (8.11.6/8.11.0) with SMTP id g3985Yp20970 for ; Tue, 9 Apr 2002 04:05:34 -0400 Message-ID: <20020409080524.43446.qmail@web12802.mail.yahoo.com> Received: from [203.87.132.164] by web12802.mail.yahoo.com via HTTP; Tue, 09 Apr 2002 01:05:24 PDT Date: Tue, 9 Apr 2002 01:05:24 -0700 (PDT) From: amor san juan Subject: Bugs in Awk programs: Share bin of AutoDock3 To: chemistry@ccl.net MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Fellows: I followed Scotney's command in fixing nawk bugs. cd ${SRC} perl -pi -e "s,nawk,awk," ${SRC}/dist_3.0/share/* The comment i get is: "Substitution pattern not terminated at -e line 1". **************************************************** I'm stocked up in executing deftors, mkgpf3,mkdpf3 programs. As i issue the command "mkgpf3" at share bin the application is aborted because the reply is "mkgpf3gen cant be found either as file or directory". The end effect ligand.dpf nor macro.gpf cant be written. Hoping for your ideas & guidance please. Amor San Juan University of the Philippines-Diliman __________________________________________________ Do You Yahoo!? Yahoo! Tax Center - online filing with TurboTax http://taxes.yahoo.com/ From chemistry-request@server.ccl.net Tue Apr 9 07:30:05 2002 Received: from srv2.resnet.ohio-state.edu ([164.107.3.56]) by server.ccl.net (8.11.6/8.11.0) with SMTP id g39BU5p29726 for ; Tue, 9 Apr 2002 07:30:05 -0400 Received: (qmail 89435 invoked by uid 1011); 9 Apr 2002 11:56:53 -0000 Received: from kiniu@mps.ohio-state.edu by srv2.resnet.ohio-state.edu with qmail-scanner-0.96 (. Clean. Processed in 0.014124 secs); 09 Apr 2002 11:56:53 -0000 Received: from rjot-84-232.resnet.ohio-state.edu (HELO kiniu) (164.107.84.232) by srv2.resnet.ohio-state.edu with SMTP; 9 Apr 2002 11:56:53 -0000 Message-ID: <007501c1dfb9$e2976140$e8546ba4@kiniu> From: "Kiniu WONG \(Kin-Yiu\)" To: Subject: Reduce the size of Freq analysis (GAUSSIAN) Date: Tue, 9 Apr 2002 07:30:00 -0400 Organization: Physics, OSU MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 6.00.2600.0000 X-MIMEOLE: Produced By Microsoft MimeOLE V6.00.2600.0000 Hi everybody, Frequency analysis ("Freq") in GAUSSIAN is computationally VERY expensive. In fact, there is too much information obtained by this keyword "Freq" since I just would like to know whether the stationary point found is a saddle point (transition state) or the minimum point (ground state). From the GAUSSIAN's manual, I know that the computational time can be reduced by the option Freq(NoRaman). But my question is: Does anybody know that what I should do to further reduce the computational time for the purpose to get information of the nature of the stationary point only?? Thanks a bunch in advance! Wishes, Kiniu ---- Kiniu WONG (Kin-Yiu) Graduate Student Department of Physics The Ohio State University USA Primary Email: kiniu@mps.ohio-state.edu Permanent Email: kiniu@alumni.cuhk.net From chemistry-request@server.ccl.net Tue Apr 9 09:00:11 2002 Received: from ouveze.ujf-grenoble.fr ([193.54.238.117]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g39D0Ap00451 for ; Tue, 9 Apr 2002 09:00:10 -0400 Received: from athi.ujf-grenoble.fr (athi.ujf-grenoble.fr [193.48.255.131]) by ouveze.ujf-grenoble.fr (Switch-2.1.4/Switch-2.1.0/Configured by JE 06 12 2001) with ESMTP id g39Cxqw19364 for ; Tue, 9 Apr 2002 14:59:57 +0200 (MEST) Received: from pop-sante.ujf-grenoble.fr (localhost.ujf-grenoble.fr [127.0.0.1]) by athi.ujf-grenoble.fr (8.9.3/8.9.3) with SMTP id PAA16722 for chemistry@ccl.net; Tue, 9 Apr 2002 15:07:14 +0200 (CEST) (envelope-from afortune@niger.ujf-grenoble.fr) Message-Id: <200204091307.PAA16722@athi.ujf-grenoble.fr> Date: Tue, 9 Apr 2002 13:07:14 -0000 To: chemistry@ccl.net Subject: CCL: Autodock - diff between sources code and binaries ?? From: FORTUNE X-Mailer: TWIG 2.3.1 X-Client-IP: 195.83.29.81 Hi all, I hope this is not in CCL's archives (didn't find) ... I would like to use autodock3, LGA method, with big ligands (polysaccharide) so I need to modify some parameters like MAX_NONBONDS, MAX_TORS, LINE_LEN and so to recompile (autodock, autogrid, autotors). I notice some differences between the results given by that new compiled binary and thoses from the binaries coming with the distribution (sgi4D.IRIX64_6.5_R10000). The main trouble is that the energy of the docked ligand kept after LGA reseach do not correspond with the lowest energie found during the search. That energie can be very (very !) higher and the structure be false (valences and connectivity not respected). Anyone already noticed that and have an explanation ? I also noticed differences between results from precompiled binaries (sgi4D.IRIX64_6.5_R10000) and binaries compiled for Linux PC with standard parameters. Is there some known differences between binaries and the source code of the distributed package ? Thank's in advance. I will summarize your answers. -- Antoine FORTUNE Dept Pharmacochimie Moleculaire Universite Grenoble 1 FRANCE From chemistry-request@server.ccl.net Tue Apr 9 09:50:50 2002 Received: from dqf.ufpe.br ([150.161.5.2]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g39Doip02104 for ; Tue, 9 Apr 2002 09:50:48 -0400 Received: from npd.ufpe.br ([150.161.5.215]) by dqf.ufpe.br (8.11.4/8.11.4) with ESMTP id g39D8XU18483 for ; Tue, 9 Apr 2002 10:08:36 -0300 Message-ID: <3CB2F2C9.51015C38@npd.ufpe.br> Date: Tue, 09 Apr 2002 10:55:21 -0300 From: Bosco X-Mailer: Mozilla 4.7 [en] (Win98; I) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net Subject: How to define the cartesian axes in G98 ? Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit Dear colleague When a z-matrix is constructed in G98 the program creates/defines his ower cartesian system. However I need to define at least one of the cartesian axes to coincide with a chemical bond in my molecule (in particular the C-H bond in pyrazine). How to do that? Please suggestions are welcome! Thanks in advance, Bosco -- Prof. João Bosco Paraiso da Silva e-mail: paraiso@npd.ufpe.br Bosco´s Homepage: www.dqf.ufpe.br/Professores/Bosco/Bosco.html Departamento de Química Fundamental Universidade Federal de Pernambuco 50740.250 - Recife (PE) - Brazil DQF´s Homepage: www.dqf.ufpe.br Phone: +55 81 3271-8441 ext. 5009 Fax: +55 81 271-8442 From chemistry-request@server.ccl.net Tue Apr 9 10:21:19 2002 Received: from unlserve.unl.edu ([129.93.1.130]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g39ELJp03264 for ; Tue, 9 Apr 2002 10:21:19 -0400 Received: from localhost (jmazlo@localhost) by unlserve.unl.edu (AIX4.3/8.9.3/8.9.2) with SMTP id JAA38012 for ; Tue, 9 Apr 2002 09:21:13 -0500 Date: Tue, 9 Apr 2002 09:21:13 -0500 (CDT) From: Johanna Mazlo To: chemistry@ccl.net Subject: antibody-antigen docking Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear CCLers, I am currently trying to dock an antibody and antigen. I have been trying to find information about this area of docking and was wondering if anyone knew of other labs or experts that also work this particular area of docking. Thank you, Johanna Mazlo From chemistry-request@server.ccl.net Tue Apr 9 11:47:56 2002 Received: from mail.rochester.edu (root@[128.151.224.31]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g39Flup06238 for ; Tue, 9 Apr 2002 11:47:56 -0400 Received: from there (ice.chem.rochester.edu [128.151.195.5]) by mail.rochester.edu (8.12.1/8.12.1) with SMTP id g39FlP6C15770578; Tue, 9 Apr 2002 11:47:29 -0400 (EDT) Message-Id: <200204091547.g39FlP6C15770578@mail.rochester.edu> Content-Type: text/plain; charset="us-ascii" From: weizhuang Reply-To: weiz@mail.rochester.edu To: help@schrodinger.com Subject: help in Macromodel Date: Tue, 9 Apr 2002 12:01:29 -0400 X-Mailer: KMail [version 1.3.1] Cc: CHEMISTRY@ccl.net, weiz@mail.rochester.edu MIME-Version: 1.0 Content-Transfer-Encoding: 8bit Hi, in Macromodel Version 7.0, while I run the "dynamics", I choose the solvent as "CHCL3", then I need to choose dielectric constant, is it the dielectric constant of chcl3 or the dielectric constant needed in the running of Delphi? or is it something else? another thing is, also in the dynamics, I choose "distence constraint", I want to know are the two atoms I chosed be constraint by a high potential well or are they just simply connected by a spring? regards From chemistry-request@server.ccl.net Tue Apr 9 12:36:57 2002 Received: from juliet.schrodinger.com ([192.156.98.102]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g39Gavp07247 for ; Tue, 9 Apr 2002 12:36:57 -0400 Received: from localhost (jshelley@localhost) by juliet.schrodinger.com (8.9.3/8.9.3) with ESMTP id JAA18143; Tue, 9 Apr 2002 09:36:34 -0700 X-Authentication-Warning: juliet.schrodinger.com: jshelley owned process doing -bs Date: Tue, 9 Apr 2002 09:36:34 -0700 (PDT) From: John Shelley To: weizhuang , CHEMISTRY@ccl.net, Macromodel account #1 Subject: Re: CCL:help in Macromodel In-Reply-To: <200204091547.g39FlP6C15770578@mail.rochester.edu> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi, On Tue, 9 Apr 2002, weizhuang wrote: > Hi, > > in Macromodel Version 7.0, while I run the "dynamics", I choose the solvent > as "CHCL3", then I need to choose dielectric constant, is it the dielectric > constant of chcl3 or the dielectric constant needed in the running of Delphi? > or is it something else? Specify a dielectric constant of 1. The dielectric constant for CHCL3 is built into the solvent model itself. > > another thing is, also in the dynamics, I choose "distence constraint", I > want to know are the two atoms I chosed be constraint by a high potential > well or are they just simply connected by a spring? It uses a spring. Regards, John C. Shelley Senior Scientist Schrodinger, Inc. From chemistry-request@server.ccl.net Tue Apr 9 10:20:30 2002 Received: from kodakr.kodak.com ([192.232.119.69]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g39EKUp03248 for ; Tue, 9 Apr 2002 10:20:30 -0400 Received: from acadia.image.kodak.com (acadia.image.kodak.com [150.220.67.56]) by kodakr.kodak.com (8.11.1/8.11.1) with ESMTP id g39EKY916737; Tue, 9 Apr 2002 10:20:34 -0400 (EDT) Received: from kodak.com (berlioz.rl.kodak.com [150.220.89.22]) by acadia.image.kodak.com (8.10.2+Sun/8.10.2) with ESMTP id g39EKJI11725; Tue, 9 Apr 2002 10:20:20 -0400 (EDT) Sender: david.giesen@kodak.com Message-ID: <3CB2F5BA.A9BBF405@kodak.com> Date: Tue, 09 Apr 2002 10:07:54 -0400 From: David J Giesen Organization: Eastman-Kodak X-Mailer: Mozilla 4.05C-SGI [en] (X11; I; IRIX64 6.5 IP25) MIME-Version: 1.0 To: "Dr. Bill Davis" , CHEMISTRY@ccl.net Subject: Re: CCL:parallel quantum solutions References: <3CB20723.87CE9126@utb1.utb.edu> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Bill - This is a long post, but I think vendors that do excellent jobs should get pats on the back. I am not a PQS employee nor do I receive new-customer kick-backs. Those not interested in a review of PQS products can hit delete now. I've been a very satisfied PQS customer since Aug. 2000. We purchased an 8-processor Linux cluster at that point, and several months later we were so pleased we bought a second. At the end of last year, we contracted with them to build a 34-processor cluster for general computational (not just chemistry) use. Hardware performance : The setup they use works well for running serial or parallel codes, and I have PQS, Jaguar and Gaussian (using LINDA) running in parallel on them. Based on timings against other machines/platforms, the PQS machines perform as well as could be expected. Our 1.2 GHz athlon PQS machine runs G98 slightly (~10%) faster than the latest-and-greatest-just-off-the-design-sheet Sun hardware, and 2-3 times faster than our SGI 194 MHz R10000. It is ~10% slower than a 1.5GHz P4. Both the Athlon and P4 machine used PIII optimized blas libraries... Software performance : the PQS software 'is what it is'. If you are interested in mainly HF, MP2 and DFT computations, it is very good. You can see its capabilities on their website. Speed-wise, it runs faster than other codes I use, although it is not faster than Jaguar's pseudo-spectral methods. The geometry optimizer is rock solid dependable as one would expect from code by Pulay and Baker. PQS uses PVM for parallel execution. Without getting into a debate about parallel paradigms, I'll say simply this: in our hands, I have never had a PVM job die because of inter-process communication problems while MPICH/MPI is very flaky and tends to die on about 10-25% of chemistry jobs (even more for systems using automount) independent of linux, sun or SGI. Because PQS uses PVM to set up the parallel system only once per job, there is less parallel overhead using PQS than with other codes that set up LINDA parallel systems at every SCF and geometry optimization step - although for large jobs, these both essentially go to zero. Support : PQS is a small company, and the support shows it. They have absolutely bent over backwards each time we have had an issue, and dealing with them is always a pleasure. We have not had a hardware or PQS software issue that they haven't resolved to our satisfaction. In fairness, you can't expect a 24-hour help line or technicians in suits to fly in and fix problems. You should be aware that they are not in the business of selling/supporting Linux or Gnu software, so some problems you have on your machine if you veer off the PQS path might be technically out of their scope. However, in my experience, they make every honest effort to solve those as well (and usually do). Every machine they shipped us has been stress-tested by an expert for a number of days before they are delivered. Ease of use : The machines come setup to run the PQS chemistry code out of the box. If you are planning on running one PQS parallel job at a time across the whole cluster or multiple serial jobs, the included DQS (not associated with PQS) queuing system works OK. Running multiple parallel codes/jobs on the same cluster through the queue does not work well. Running other codes in parallel through the queue takes some hard work. Setting up other parallel codes also takes some work. This is not really a function of PQS, however, and you'll find this is true no matter what machine you get. Disclaimer : This e-mail does not in any way imply an 'official Kodak' stance, it is merely the personal opinion of a Kodak employee who uses PQS products at work. Dave Dr. Bill Davis wrote: > > 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 > ********************************** > > -- Dr. David J. Giesen Eastman Kodak Company david.giesen@kodak.com 2/83/RL MC 02216 (ph) 1-585-58(8-0480) Rochester, NY 14650 (fax)1-585-588-1839 From chemistry-request@server.ccl.net Tue Apr 9 10:53:29 2002 Received: from goshen.rutgers.edu ([165.230.180.150]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g39ErTp04330 for ; Tue, 9 Apr 2002 10:53:29 -0400 Received: from eden.rutgers.edu (narnia3.rutgers.edu [165.230.180.159]) by goshen.rutgers.edu (Postfix) with ESMTP id 50A7E21703 for ; Tue, 9 Apr 2002 10:49:44 -0400 (EDT) Received: from azrael1.rutgers.edu (azrael1.rutgers.edu [165.230.4.120]) by eden.rutgers.edu (Postfix) with SMTP id 0E4F9A29AD for ; Tue, 9 Apr 2002 10:49:44 -0400 (EDT) From: To: chemistry@ccl.net Subject: add Gasteiger-Marsili charge Date: Tue, 9 Apr 2002 11:08:30 -0400 (EDT) X-Real-Sender: jianquan@eden.rutgers.edu X-Mailer: Postman 1.10 Message-ID: <1723169546jianquan@eden.rutgers.edu> MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id g39ErTp04331 Dear CCl.netter, I have a question. I try to use babel to add Gasteiger-Marsili charge to small organic molecules. But I don't know how to add charges to molecules with 1 or 2 positive or negative charge. If Mopac is used to add charge, you can set the number of charges on the molecule. How can I set the number of charges when I use babel? Or can I set the number of the charges when Gasteiger-Marsili charge is added? I will summarize the replies. Thank you in advance. Jianquan Chen From chemistry-request@server.ccl.net Tue Apr 9 14:32:35 2002 Received: from caduceus.fm.intel.com ([192.55.52.25]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g39IWRp09693 for ; Tue, 9 Apr 2002 14:32:28 -0400 Received: from talaria.fm.intel.com (talaria.fm.intel.com [10.1.192.39]) by caduceus.fm.intel.com (8.11.6/8.11.6/d: outer.mc,v 1.37 2002/04/01 17:50:55 root Exp $) with ESMTP id g39IVkf29781 for ; Tue, 9 Apr 2002 18:31:46 GMT Received: from fmsmsxvs041.fm.intel.com (fmsmsxv041-1.fm.intel.com [132.233.48.109]) by talaria.fm.intel.com (8.11.6/8.11.6/d: inner.mc,v 1.15 2002/04/01 17:51:48 root Exp $) with SMTP id g39IXZB27751 for ; Tue, 9 Apr 2002 18:33:35 GMT Received: from FMSMSX018.fm.intel.com ([132.233.42.197]) by fmsmsxvs041.fm.intel.com (NAVGW 2.5.1.16) with SMTP id M2002040911323428826 for ; Tue, 09 Apr 2002 11:32:34 -0700 Received: by fmsmsx018.fm.intel.com with Internet Mail Service (5.5.2653.19) id <2SD1R6AC>; Tue, 9 Apr 2002 11:32:06 -0700 Message-ID: <86DB568235A8D511ABAC0002A5072CA5032E9317@orsmsx120.jf.intel.com> From: "Wrinn, Michael" To: "'chemistry@ccl.net'" Subject: Intel fortran compiler customer support Date: Tue, 9 Apr 2002 11:32:01 -0700 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2653.19) Content-Type: multipart/alternative; boundary="----_=_NextPart_001_01C1DFF4.D6BE8930" 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_01C1DFF4.D6BE8930 Content-Type: text/plain Dear Dr Radacki and CCLers. There is a very competent customer support staff backing up the Intel(r) compilers; you are welcome to tap into this resource at http://www.intel.com/software/products/ and subsequent links. (For Linux Fortran, for example, the link is http://www.intel.com/software/products/compilers/f50/fsupport1.htm .) regards, Michael Michael Wrinn, Ph.D. Engineering Manager Intel(r) Corporation ------_=_NextPart_001_01C1DFF4.D6BE8930 Content-Type: text/html Content-Transfer-Encoding: quoted-printable Intel fortran compiler customer support

Dear Dr Radacki and = CCLers.

There is = a = very competent customer support staff backing up the Intel(r) compilers; you are welcome = to tap into this resource at http://www.intel.com/software/products/ and subsequent links. (For Linux = Fortran, for example, the link = is http://www.intel.com/software/products/compilers/f50/fsup= port1.htm.)

regards,

Michael

Michael Wrinn, = Ph.D.

Engineering = Manager

Intel(r) Corporation

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