From chemistry-request@server.ccl.net Fri Dec 29 04:18:18 2000 Received: from smtp1.dti.ne.jp (smtp1.dti.ne.jp [202.216.228.36]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id EAA03683 for ; Fri, 29 Dec 2000 04:18:17 -0500 Received: from b159504364 (PPP43.fukuoka-ap2.dti.ne.jp [210.159.131.43]) by smtp1.dti.ne.jp (8.9.3/3.7W) with SMTP id SAA19749 for ; Fri, 29 Dec 2000 18:17:57 +0900 (JST) Message-ID: <001701c07177$0e261e80$2b839fd2@b159504364> From: "T.Tsuru" To: References: <000b01c06dc5$d7ca05e0$aa718e8b@ukyd3> Subject: Resent Progress of Extended Huckel MO--summary Date: Fri, 29 Dec 2000 18:09:30 +0900 MIME-Version: 1.0 Content-Type: text/plain; charset="utf-8" Content-Transfer-Encoding: 8bit X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 5.50.4133.2400 X-MimeOLE: Produced By Microsoft MimeOLE V5.50.4133.2400 Hello ! CCLers. Some days ago, I sent a question: > I would like to know about Extended Huckel MO(EHMO) on below > two points. > > 1) I would like to install the Free good EHMO program into my Win98 PC. > Does somebody know such program ? And if you are using the program, > please add the comment of it. > > 2) Is there resent review of EHMO? Also, I will accept the such Web Sites > and books when you recommend. I received a very useful and helpful reply. Here, I introduce it. Thank you Irena ! Now, CCLers, if you have any additional information, please let me know. ======= from Irena Efremenko ======= Dear Telkuni Tsuru, The best EHMO program running with Windows I know is cacao98. It has excellent graphics for visualization of MOs, Walsh diagram and fragment interaction. It is set for 3500 orbitals, 20 steps and 50 variables for Walsh diagram. Cacao98 is a betaversion 5.0 and is available upon request from Dr. Davide M. Proserpio (Milano, Italy); e-mail: davide@csmtbo.mi.cnr.it The old distribution of the program contained manual with detailed description of the current status of EH theory. This distribution is available from CCL web site (under Windows or DOS directory). The discussion on "Extended Hueckel Today--opinions" on CCL was initiated by E. Lewars about two years ago. Try to search CCL, or I can forward some of the messages that I saved. Recently there were the following announcments on CCL: --1.-- Subject: CCL:Software announcement: Extended Huckel calculator for Windows95 Date: Mon, 5 May 1997 17:44:52 -0400 (EDT) From: To: chemistry@www.ccl.net I want to announce Huckel 3.0, a shareware program I developed. With the program you can perform the Huckel analysis on any molecule you wish. The number of atoms is unlimited, the number of kinds of atoms is unlimited and you have full control of the parameters involved. I tried to make this program for students as well as for researchers. Extensive help is available online for all the options available. A short tutorial can be taken as a quick guide through the program. A theory section is available for students that get interested in the theory behind the calculations. As input to the program you draw a structure formula. The results of a calculations can be viewed as a level diagram and as a MO diagram. At any stage the bare numbers can be viewed: the Huckel matrix, the diagonal Hamiltonian, the eigenvectors and the eigenfunctions. To preview of the software, turn to the Huckel project pages on my web site. Go to the downloads section to download the program (about 4.3 MB). http://members.aol.com/gjlinker/ Key program characteristics: -windows 95 version only. -draw a structure formula to define the molecule you want to calculate. -output is presented in MO diagrams, a level diagram and in bare numbers. -full control of all alpha and beta parameters. -define your own atoms in the atoms database. -save molecules to files for later use. -extensive help file. -calculation of pi charges and bond orders. -size: about 4.3 MB download -no specific memory/hardware required There is more information available on my web site. Please send your comments and feedback to linker@ilovechocolate.com drs Gerrit-Jan Linker Analyst programmer @ SCT international Ltd. Manchester UK email: linker@ilovechocolate.com web: http://members.aol.com/gjlinker/index.htm --2.-- Subject: CCL:ICON-EDiT and BICON-CEDiT Date: Wed, 1 Oct 1997 13:55:26 +0200 From: Dominik Bruehwiler To: chemistry Dear CCLers We can offer the full versions (the WindowsNT binaries along with the FORTRAN sources) of the following TWO program packages: o ICON-EDiT o BICON-CEDiT ICON-EDiT performs extended Hueckel molecular orbital and oscillator strengths (i.e. UV/VIS spectra) calculations on molecules. s,p,d orbitals, a two-body repulsive energy term, different Wolfsberg-Helmholz formulas, charge iteration procedures, geometry variation and an FMO option are included. BICON-CEDiT performs extended Hueckel molecular and crystal orbital as well as oscillator strengths calculations on solids. Numerous tools such as to generate k-point sets or to transform Cartesian into fractional coordinates and vice versa are also supplied. The energy band and density of states plot programs make use of Tim Pearsons pgplot graphic library freely available at http://astro.caltech.edu/~tjp/pgplot (supported on numerous platforms). UNIX Makefiles and a dos2unix shell script are included for those wishing to compile and run the programs under such operating systems. Both program packages along with extensive manuals can be downloaded at http://iacrs1.unibe.ch/ Enjoy the programs! Gion Calzaferri, Martin Braendle, Ruedi Rytz and Dominik Bruehwiler Department of Chemistry and Biochemistry, University of Bern, Switzerland. Thanks a lot ! --------------------------------------------------- Telkuni Tsuru telkuni@venus.dti.ne.jp Representative of Research Information Service of Molecular/with Knowledge Management　 Bunshi Gijyutu --------------------------------------------------- From chemistry-request@server.ccl.net Fri Dec 29 14:15:35 2000 Received: from fbcb.unl.edu.ar (root@fbcb.unl.edu.ar [170.210.10.2]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id OAA06662 for ; Fri, 29 Dec 2000 14:15:28 -0500 From: sgaray@fbcb.unl.edu.ar Received: from p5j6j9 (fzalazar@fbcb.unl.edu.ar [170.210.10.2]) by fbcb.unl.edu.ar (8.8.7/8.8.7) with SMTP id QAA13739 for ; Fri, 29 Dec 2000 16:38:55 -0300 Message-Id: <200012291938.QAA13739@fbcb.unl.edu.ar> To: chemistry@ccl.net Date: Fri, 29 Dec 2000 16:12:00 -0600 MIME-Version: 1.0 Content-type: text/plain; charset=US-ASCII Content-transfer-encoding: 7BIT Subject: Need to Change from WINNMR bruker file to XWINNMR bruker file X-Confirm-Reading-To: sgaray@fbcb.unl.edu.ar X-pmrqc: 1 Priority: urgent X-mailer: Pegasus Mail for Win32 (v3.01b) I would like to use Sparky software in order to make the NMR assignment of my peptide, but first I need to transform my WINNMR files into XWINNMR files. How can I do it? thank you to all in advance From chemistry-request@server.ccl.net Fri Dec 29 10:56:18 2000 Received: from server.nybc.org (server.nybc.org [192.94.249.2]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id KAA05942 for ; Fri, 29 Dec 2000 10:56:18 -0500 Received: from iris.nybc.org ([192.94.249.42]) by server.nybc.org (Netscape Mail Server v2.0) with ESMTP id AAA27988; Fri, 29 Dec 2000 10:55:06 -0400 Received: from nybc.org (localhost [127.0.0.1]) by iris.nybc.org (SGI-8.9.3/8.9.3) with ESMTP id KAA35237; Fri, 29 Dec 2000 10:57:01 -0500 (EST) Sender: debnath@iris.nybc.org Message-ID: <3A4CB44C.894DE05F@nybc.org> Date: Fri, 29 Dec 2000 10:57:01 -0500 From: Asim Kumar Debnath Organization: New York Blood Center X-Mailer: Mozilla 4.75C-SGI [en] (X11; I; IRIX 6.5 IP22) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net CC: adebnath@nybc.org Subject: file convertion Content-Type: multipart/alternative; boundary="------------1FAC9861080F5A3021A49A0C" --------------1FAC9861080F5A3021A49A0C Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi! I would greatly appreciate if someone can give me suggestions on how to convert a pdb file [containing multiple small molecules that was obtained from DOCK (UCSF) run] to a mult-mol2 or multi-sdf file. I would also like to keep the mol-ID of each compound in those files. Thank you in advance for your help and Happy New Year to all of you! Asim -- ======================================================================= *** *** **** Asim K. Debnath, Ph.D. **** Lindsley F. Kimball Research Institute **** *** The New York Blood Center **** **** 310 E 67 Th Street **** ** **** New York, NY 10021 **** **** **** Tel. (212) 570-3373 **** ** **** Fax. (212) 570-3299 **************** E-mail: adebnath@nybc.org ************** ======================================================================== --------------1FAC9861080F5A3021A49A0C Content-Type: text/html; charset=us-ascii Content-Transfer-Encoding: 7bit Hi!
    I would greatly appreciate if someone can give me suggestions on how to convert a pdb file [containing multiple small molecules that was obtained from DOCK (UCSF) run] to a mult-mol2 or multi-sdf file. I would also like to keep the mol-ID of each compound in those files.
    Thank you in advance for your help and Happy New Year to all of you!

Asim 

-- 



=======================================================================

             ***
             ***                
            ****                Asim K. Debnath, Ph.D.
           ****                 Lindsley F. Kimball Research Institute 
          ****  ***             The New York Blood Center
         ****    ****           310 E 67 Th Street
        ****  **  ****          New York, NY 10021
       ****  ****  ****         Tel. (212) 570-3373
      ****    **    ****        Fax. (212) 570-3299
       ****************         E-mail: adebnath@nybc.org
        **************                                  
                                        
========================================================================
  --------------1FAC9861080F5A3021A49A0C-- From chemistry-request@server.ccl.net Fri Dec 29 13:19:54 2000 Received: from kanga.INS.CWRU.Edu (root@kanga.INS.CWRU.Edu [129.22.8.32]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id NAA06488 for ; Fri, 29 Dec 2000 13:19:53 -0500 Received: from eje (chem51439.CHEM.CWRU.Edu [129.22.200.239]) by kanga.INS.CWRU.Edu with SMTP (8.8.8+cwru/CWRU-3.6) id NAA28775; Fri, 29 Dec 2000 13:19:40 -0500 (EST) (from hxt19@po.cwru.edu for ) Message-ID: <002a01c071c4$b2cecd40$efc81681@cwru.edu> Reply-To: "Hui-Hsu (Gavin) Tsai" From: "Hui-Hsu (Gavin) Tsai" To: Subject: DFT performance Date: Fri, 29 Dec 2000 13:25:17 -0500 MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_0027_01C0719A.C890A9C0" X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 5.00.2615.200 X-MimeOLE: Produced By Microsoft MimeOLE V5.00.2615.200 This is a multi-part message in MIME format. ------=_NextPart_000_0027_01C0719A.C890A9C0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Dear CCLers: Could anyone of you direct me to references/websites which compare the = performance of different DFT calculations? Thanks! Gavin=20 ------=_NextPart_000_0027_01C0719A.C890A9C0 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable
Dear CCLers:


Could anyone of = you direct=20 me to references/websites which compare the performance of = different DFT=20 calculations?
Thanks!
 
Gavin
------=_NextPart_000_0027_01C0719A.C890A9C0-- From chemistry-request@server.ccl.net Fri Dec 29 19:02:14 2000 Received: from dns2.seanet.com (dns2.seanet.com [199.181.164.2]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id TAA07766 for ; Fri, 29 Dec 2000 19:02:14 -0500 Received: from biggeek (dialup-209.245.173.17.Seattle1.Level3.net [209.245.173.17]) by dns2.seanet.com (8.9.3/8.9.0) with SMTP id QAA21104; Fri, 29 Dec 2000 16:02:10 -0800 (PST) Message-ID: <002401c071f3$5ac649f0$01808080@biggeek> From: "Mark A. Thompson" To: "T.Tsuru" , References: <000b01c06dc5$d7ca05e0$aa718e8b@ukyd3> <001701c07177$0e261e80$2b839fd2@b159504364> Subject: Re: CCL:Resent Progress of Extended Huckel MO--summary Date: Fri, 29 Dec 2000 15:59:15 -0800 MIME-Version: 1.0 Content-Type: text/plain; charset="utf-8" Content-Transfer-Encoding: 7bit X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 5.00.2314.1300 X-MimeOLE: Produced By Microsoft MimeOLE V5.00.2314.1300 Dear Dr. Tsuru, ArgusLab 2.0 has a decent implementation of EHT with parameters for the entire periodic table. You can download it at http://www.seanet.com/~mthompson/ArgusLab ArgusLab is a molecular modeling program for Microsoft Windows operating systems. Overview of 2.0 features: ----------------------------- 1. Interactive 3D Molecule Builder with: Interactive 3D manipulator Fragment Library Beautify Geometry Automatically Add/Hide/Delete Hydrogens Cut & Paste Supports Multiple-Level Undo/Redo. Multiple Rendering Styles for Atoms and Bonds Geometry Monitors 2. Calculation Types Single-Point Energies Optimize Geometries Electronic Excitation Spectra Self Consistent Reaction Field (SCRF) Solvent Model for Electronic Spectra 3. Molecular Mechanics Universal Force Field (UFF) for the entire periodic table 4. Quantum Mechanics Extended Huckel for entire periodic table MNDO, AM1, and PM3 semi-empirical Hamiltonians INDO1/s semi-empirical Hamiltonian Restricted and Unrestricted Hartree-Fock SCF 5. File Types: supports XYZ, PDB, and ArgusLab XML file formats. 6. HTML Help 7. No size limitations for molecules or calculations other than available system resources 8. Multi-threaded architecture allows multiple molecules opened simultaneously and running calculations 9. Runs on Windows 95/98, Windows NT 4.0, Windows 2000 Mark Thompson ----- Original Message ----- From: T.Tsuru To: Sent: Friday, December 29, 2000 1:09 AM Subject: CCL:Resent Progress of Extended Huckel MO--summary > Hello ! CCLers. > > Some days ago, I sent a question: > > I would like to know about Extended Huckel MO(EHMO) on below > > two points. > > > > 1) I would like to install the Free good EHMO program into my Win98 PC. > > Does somebody know such program ? And if you are using the program, > > please add the comment of it. > > > > 2) Is there resent review of EHMO? Also, I will accept the such Web Sites > > and books when you recommend. > > I received a very useful and helpful reply. Here, I introduce it. > Thank you Irena ! > > Now, CCLers, if you have any additional information, please let me know. > >