From chemistry-request@server.ccl.net Fri Jul 27 09:22:06 2001 Received: from mserv.itpa.lt ([193.219.53.20]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f6RDM3524546 for ; Fri, 27 Jul 2001 09:22:04 -0400 Received: from localhost (tamulis@localhost) by mserv.itpa.lt (8.11.4/8.11.0) with ESMTP id f6RDLxP40794; Fri, 27 Jul 2001 15:22:01 +0200 (EET) (envelope-from tamulis@itpa.lt) Date: Fri, 27 Jul 2001 15:21:59 +0200 (EET) From: Arvydas Tamulis To: cc: Jelena Tamuliene Subject: to ccl (fwd) Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi, I would like to perform investigation of tetraphosphorus molecule that is placed in field created point charge of 2. The coordinates of the above charge are known. I would like to know how is necessary to arrange initial file of such kind investigation for Gaussian 98 or DALTON, or NewChem, or GAMESS programe packages. Thank you in advance. With respect, Jelena Tamuliene From chemistry-request@server.ccl.net Fri Jul 27 07:08:39 2001 Received: from web20207.mail.yahoo.com ([216.136.226.62]) by server.ccl.net (8.11.0/8.11.0) with SMTP id f6RB8d522830 for ; Fri, 27 Jul 2001 07:08:39 -0400 Message-ID: <20010727110838.99307.qmail@web20207.mail.yahoo.com> Received: from [202.238.80.30] by web20207.mail.yahoo.com; Fri, 27 Jul 2001 04:08:38 PDT Date: Fri, 27 Jul 2001 04:08:38 -0700 (PDT) From: bjorn mayer Subject: Solid state reaction thermodynamics prediction? To: chemistry@ccl.net MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii I want to know the free energy change of solid state reactions like e.g. CaCl2 (alpha) --> CaCl2 (beta) --> Ca + Cl2(g) such that I can have the pressure composition phase diagram. I have a search in PRB, they are either caln of melting or configuration in alloys. Is it possible to do the above with ab initio or empirical potential methods? thank you very much mayer __________________________________________________ Do You Yahoo!? Make international calls for as low as $.04/minute with Yahoo! Messenger http://phonecard.yahoo.com/ From chemistry-request@server.ccl.net Fri Jul 27 10:27:27 2001 Received: from hawk.dcu.ie ([136.206.1.5]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f6RERQ526034 for ; Fri, 27 Jul 2001 10:27:26 -0400 Received: from gizmo (136.206.86.88) by hawk.dcu.ie (5.5.031) id 3B5FBC010000705F for chemistry@ccl.net; Fri, 27 Jul 2001 15:27:29 +0100 Message-ID: <3B5FBC010000705F@hawk.dcu.ie> (added by postmaster@dcu.ie) Date: Fri, 27 Jul 2001 15:34:05 +0100 To: chemistry@ccl.net From: Kevin Kincaid Subject: G98 or Jaguar on IBM S/390 with Linux X-Mailer: Opera 5.02 build 855 X-Priority: 3 (Normal) Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Hello! I'm just wondering has anyone successfully got G98 or Jaguar 3.5 running on an IBM S/390 with Linux installed. We have access to such a machine, but seemingly both packages only support IBM RS6000 with AIX. Any help would be appreciated! Thanks in advance, Kevin ___________________ Molecular Modelling Lab Dublin City University Dublin 9 Ireland Tel: +353-1-7008193 From chemistry-request@server.ccl.net Fri Jul 27 11:56:01 2001 Received: from ivory.trentu.ca ([192.75.12.103]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f6RFu1527803 for ; Fri, 27 Jul 2001 11:56:01 -0400 Received: from trentu.ca ([204.225.13.50]) by trentu.ca (PMDF V5.2-32 #37862) with ESMTP id <01K6FAV6VLHQ000LSD@trentu.ca> for chemistry@ccl.net; Fri, 27 Jul 2001 11:55:37 EDT Date: Fri, 27 Jul 2001 12:01:44 -0400 From: elewars Subject: REQUEST FOR CALCULATION To: chemistry@ccl.net Message-id: <3B619068.1A042532@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 2001 July 27, Friday Hello, If anyone has access to the ACES II program (or some other program with a fast CC optimization algorithm), and can find the time, I would appreciate it if they could subject the input structure below to a CCSD(T)/6-31G* optimization and email me the Cartesians of the optimized structure. If the optimization takes too long, the Cartesians for an _unfinished_ job may still be useful to me, to show where the geometry is going. If someone does try this, I would also appreciate knowing what machine was used and how long it took. Thanks, E. Lewars ------------------------------------------------ CCSD(T)/6-31G* requested C2F2O, charge=0, multiplicity=1 C1 0.656697 0.220442 -0.044289 O2 -0.457469 0.362686 0.620775 F3 1.476651 -0.761318 -0.036919 C4 0.128983 1.428372 -0.389388 F5 -1.593798 -0.660278 -0.225763 ----------------------------------------------------- From chemistry-request@server.ccl.net Fri Jul 27 12:13:54 2001 Received: from if1.if.ufrgs.br ([143.54.2.1]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f6RGDq528199 for ; Fri, 27 Jul 2001 12:13:53 -0400 Received: from pclap3.if.ufrgs.br by if1.if.ufrgs.br (PMDF V4.3-10 #7035) id <01K6FCXQ0H4G000I8U@if1.if.ufrgs.br>; Fri, 27 Jul 2001 12:54:55 -0003 Date: Fri, 27 Jul 2001 12:54:21 -0300 From: =?UNKNOWN?Q?Cl=E1udio?= Perottoni Subject: Raman intensities in Gamess-US To: chemistry@ccl.net Reply-to: perott@if.ufrgs.br Message-id: <01072713000100.23015@pclap3.if.ufrgs.br> MIME-version: 1.0 X-Mailer: KMail [version 1.0.29] Content-type: text/plain Content-transfer-encoding: 8bit Dear CCLers, Could someone help me to setup an input file suitable to optimize the geometry of a single molecule and to calculate its normal modes wavenumbers, IR and Raman intensities with Gamess-US (PC-GAMESS 6.0) ? Thanks in advance! Cláudio. -- ****************************************************************** Cláudio A. Perottoni Universidade Federal do Rio Grande do Sul Instituto de Física - Lab. de Altas Pressões e Materiais Avançados Av. Bento Gonçalves, 9500 CAIXA POSTAL 15051 91501-970 PORTO ALEGRE - RS BRASIL PHONE:+55-51-3316-6500 FAX :+55-51-3316-7286 http://www.if.ufrgs.br/~perott/index.html ****************************************************************** From chemistry-request@server.ccl.net Fri Jul 27 11:49:52 2001 Received: from outbound.mail.uoguelph.ca ([131.104.96.18]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f6RFnq527707 for ; Fri, 27 Jul 2001 11:49:52 -0400 Received: from msnet.mathstat.uoguelph.ca (msnet.mathstat.uoguelph.ca [131.104.32.59]) by outbound.mail.uoguelph.ca (8.9.3 (PHNE_21697)/8.9.3) with ESMTP id LAA24102 for ; Fri, 27 Jul 2001 11:49:51 -0400 (EDT) Received: from MSNET/SpoolDir by msnet.mathstat.uoguelph.ca (Mercury 1.48); 27 Jul 01 11:47:44 -0500 Received: from SpoolDir by MSNET (Mercury 1.48); 27 Jul 01 11:47:20 -0500 From: "Bill Smith" Organization: Math & Stats, University of Guelph To: chemistry@ccl.net Date: Fri, 27 Jul 2001 11:47:19 -0400 MIME-Version: 1.0 Content-type: text/plain; charset=US-ASCII Content-transfer-encoding: 7BIT Subject: Re: CCL:Solid state reaction thermodynamics prediction? Message-ID: <3B6154B9.7122.8459E6BF@localhost> Priority: normal In-reply-to: <20010727110838.99307.qmail@web20207.mail.yahoo.com> X-mailer: Pegasus Mail for Win32 (v3.12c) You might first try looking in some standard thermochemical databases - e.g. JANAF Tables, Barin's book - for some experimental data. I just looked in JANAF and found data for CaCl2(cr), but lit lists only one crystal type. Data for Ca(alpha) and Ca(beta) are available. If you want to consider the reactions CaCl2(s) -> Ca(alpha) + Cl2(g) CaCl2(s) -> Ca(beta) + Cl2(g) then all the data is available. On 27 Jul 2001, at 4:08, bjorn mayer wrote: > I want to know the free energy change of solid > state reactions like e.g. > > CaCl2 (alpha) --> CaCl2 (beta) --> Ca + Cl2(g) > > such that I can have the pressure composition > phase diagram. > > I have a search in PRB, they are either caln > of melting or configuration in alloys. > > Is it possible to do the above with ab initio or > empirical potential methods? > > thank you very much > mayer > > __________________________________________________ > Do You Yahoo!? > Make international calls for as low as $.04/minute with Yahoo! > Messenger http://phonecard.yahoo.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 > > > > > Best Regards, W. R. Smith, Professor Dept. of Mathematics and Statistics and School of Engineering Room 546 MacNaughton Building University of Guelph Stone Road and Gordon Streets Guelph, Ontario, CANADA N1G 2W1 Tel: 519-824-4120, ext. 3038; FAX: 519-837-0221; http://www.mathstat.uoguelph.ca/faculty/smith/ From chemistry-request@server.ccl.net Fri Jul 27 13:08:06 2001 Received: from ccl.net ([192.148.249.4]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f6RH86529095 for ; Fri, 27 Jul 2001 13:08:06 -0400 Received: from gap.cco.caltech.edu (gap.cco.caltech.edu [131.215.139.43]) by ccl.net (8.9.3/8.9.3/OSC 2.0) with ESMTP id NAA05499 for ; Fri, 27 Jul 2001 13:08:04 -0400 (EDT) Received: (from news@localhost) by gap.cco.caltech.edu (8.9.3/8.9.3) id JAA27931; Fri, 27 Jul 2001 09:13:14 -0700 (PDT) To: mlist-chemistry@nntp-server.caltech.edu Path: news From: "Richard P. Muller" Newsgroups: mlist.chemistry Subject: LYP correlation functional Date: Fri, 27 Jul 2001 09:11:19 -0700 Organization: California Institute of Technology, Pasadena Lines: 4 Message-ID: <3B6192A7.E8656182@wag.caltech.edu> NNTP-Posting-Host: dhcp-26-205.wag.caltech.edu Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 4.77 [en] (Win98; U) X-Accept-Language: en Does anyone know a reference to fortran subroutines for the LYP functional? Thanks in advance. Rick From chemistry-request@server.ccl.net Fri Jul 27 17:30:45 2001 Received: from dasher.wustl.edu ([128.252.68.48]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f6RLUj502296 for ; Fri, 27 Jul 2001 17:30:45 -0400 Received: from dasher.wustl.edu by dasher.wustl.edu (8.8.8/1.1.20.8/08Dec99-1053AM) id QAA0000495007; Fri, 27 Jul 2001 16:40:50 -0500 (CDT) Sender: ponder@dasher.wustl.edu Message-ID: <3B61DFE2.3B0F5AA9@dasher.wustl.edu> Date: Fri, 27 Jul 2001 16:40:50 -0500 From: Jay Ponder Organization: Biochemistry, Washington University Medical School X-Mailer: Mozilla 4.72 [en] (X11; U; OSF1 V5.0 alpha) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net Subject: TINKER 3.9 is Now Available Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear CCL, A new release of the TINKER Molecular Modeling Package, version 3.9 dated June 2001, is available from the TINKER web site at http://dasher.wustl.edu/tinker/ or via anonymous ftp download > from dasher.wustl.edu in the /pub/tinker area. TINKER is a modular, general package for molecular mechanics and dynamics with some special facilities and parameter sets for biopolymers. It supports several common force fields, including AMBER, CHARMM, MM2, MM3, OPLS-AA, OPLS-UA, and our own TINKER polarizable atomic multipole force field. The package contains advanced algorithms for energy minimization, molecular dynamics, distance geometry and global search including some methods that are not readily available elsewhere. TINKER version 3.9 contains the following new features and updates > from version 3.8: (1) improved nucleic acid building from sequence and automated conversion of nucleic acid PDB files to and from the TINKER format, (2) a new rigid body dynamics facility, (3) ability to handle infinite polymer lattices such as diamond and graphite, (4) treatment of intramolecular polarization via the Thole method, (5) a new utility program to compute molecular polarization, (6) an improved RasMol-based viewer that accepts TINKER coordinate files, allows atom selection, etc., (6) an optional Andersen stochastic collision thermostat for MD, (7) where appropriate TINKER programs such as ANALYZE, SUPERPOSE and SPACEFILL accept multiple coordinate set "archive" files as input, (8) updated parameter sets for various of the supported force fields. TINKER is distributed with full source code, a User's Guide, and several examples and test molecule files. Directions are supplied for building the package on most commonly used CPU/OS combinations. Prebuilt executables limited to a maximum of 10000 atoms are also provided for Linux, Windows, and Macintosh (currently Mac OS 9, OS X executables will be available shortly). Please see the web site above for further information. Comments, questions and suggestions for future improvements can be sent to ponder@dasher.wustl.edu. Jay Ponder -- Jay W. Ponder Phone: (314) 362-4195 Biochemistry, Box 8231 Fax: (314) 362-7183 Washington University Medical School 660 South Euclid Avenue Email: ponder@dasher.wustl.edu St. Louis, Missouri 63110 USA WWW: http://dasher.wustl.edu/ From chemistry-request@server.ccl.net Fri Jul 27 18:06:40 2001 Received: from unlserve.unl.edu ([129.93.1.130]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f6RM6d502717 for ; Fri, 27 Jul 2001 18:06:39 -0400 Received: from localhost (jmazlo@localhost) by unlserve.unl.edu (8.9.1a/8.9.2) with SMTP id RAA59730 for ; Fri, 27 Jul 2001 17:06:38 -0500 Date: Fri, 27 Jul 2001 17:06:38 -0500 (CDT) From: Johanna Mazlo To: chemistry@ccl.net Subject: Re: CCL:autodock -active site-summary In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear CCL group, Thank you all for help regarding searching only the active site when docking the ligand to the receptor in Autodock. As I promised, below are the responses. Johanna Mazlo ___________________________________________________________ You can do that by precisely tailoring the grid size as to include only the region of interest. Start from a receptor- ligand complex (ie the ligand bound to the active site). mkgdf3 build a grid centered on the ligand (gridcenter keyword on your gpf file) that will be explored by the ligand during the search. if the grid fits the active site, your ligand will only move within that site. you have to play with npts keyword in the gpf file (number of gridpoint per direction, only even number!) in order to size the grid exactly. a useful program to visualise the extents of the grid is avs regards, fabrizio ____________________________________________________ I read your mail regarding autodock. I'm using autodock as well for my work. I'm using a crystal structure of my protein-ligand and I specify the active site according to the where the ligand is docked. So whatever atoms which is within maybe say 3 angstrom of my ligand, i take those atoms and get the average as the center of my grid. I don't know about your receptor or ligand but I hope this maybe will help. Regards, Rowyna _____________________________________________________ Hi Johanna, can you just change the grid parameter file so that the 3D cube only encompasses the active site? Then you will only be able to search within this area. Simon Cross _____________________________________________________ Define the x,y,z coordinates of the center of your active site, then in your glg file change the x,y,z coordinates of the grid center with your data. In addition to this you can specify the dimensions of your grid box based on the active site of the protein. Istvan From chemistry-request@server.ccl.net Fri Jul 27 22:35:59 2001 Received: from phobos.email.Arizona.EDU (IDENT:root@[128.196.133.165]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f6S2Zx505330 for ; Fri, 27 Jul 2001 22:35:59 -0400 Received: from demetrio.u.arizona.edu (128.196.86.129) by phobos.email.Arizona.EDU (5.1.056) id 3B5F19E5000378BA for chemistry@ccl.net; Fri, 27 Jul 2001 19:35:57 -0700 Message-Id: <5.1.0.14.0.20010727151346.025346b0@deimos.email.arizona.edu> X-Sender: dasf@deimos.email.arizona.edu X-Mailer: QUALCOMM Windows Eudora Version 5.1 Date: Fri, 27 Jul 2001 19:34:47 -0700 To: chemistry@ccl.net From: Demetrio Antonio da Silva Filho Subject: Gaussian vs Lorenzian. Mime-Version: 1.0 Content-Type: multipart/alternative; boundary="=====================_8183471==_.ALT" --=====================_8183471==_.ALT Content-Type: text/plain; charset="us-ascii"; format=flowed Dear CCL'ers, I am interested in doing some simulations of UPS/Absorption spectra in organic systems and I have one question about the convolution procedure. For the case of the absorption spectrum, for example, the theoretical calculations gives us a table of oscilator strengths and frequencies and most of the articles uses gaussians to convolute with the delta function spectral lines. My question is: There exist any justificative to use Gaussians? Which one? We can use Lorenzians instead of Gaussians? Why people preffer Gaussians? Thanks a lot for your help. I will sumarize. Demetrio Filho --=====================_8183471==_.ALT Content-Type: text/html; charset="us-ascii" Dear CCL'ers,

I am interested in doing some simulations of UPS/Absorption spectra in organic
systems and I have one question about the convolution procedure.

For the case of the absorption spectrum, for example, the theoretical calculations
gives us a table of oscilator strengths and frequencies and most of the articles
uses gaussians to convolute with the delta function spectral lines.

My question is: There exist any justificative to use Gaussians? Which one?

We can use Lorenzians instead of Gaussians?

Why people preffer Gaussians?

Thanks a lot for your help. I will sumarize.

Demetrio Filho
 --=====================_8183471==_.ALT--