From chemistry-request@server.ccl.net Thu Sep 27 02:25:44 2001 Received: from web14708.mail.yahoo.com ([216.136.224.125]) by server.ccl.net (8.11.6/8.11.0) with SMTP id f8R6Pi500643 for ; Thu, 27 Sep 2001 02:25:44 -0400 Message-ID: <20010927062544.55681.qmail@web14708.mail.yahoo.com> Received: from [202.41.85.161] by web14708.mail.yahoo.com via HTTP; Wed, 26 Sep 2001 23:25:44 PDT Date: Wed, 26 Sep 2001 23:25:44 -0700 (PDT) From: Ashwini Phukan Subject: Gaussview Vs. Spartan To: chemistry@ccl.net MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Dear CCLers, I shall be very much obliged if someone can tell me the differences between GAUSSVIEW and SPARTAN. And also, i will be happy to know the performance of each. Between GAUSSVIEW and SPARTAN, which one is better? Thanks in advance. With regards, Sincerely Yours, Ashwini Ashwini Kr. Phukan Senior Research Scholar School Of Chemistry Univ. Of Hyderabad P.O. Central University Hyderabad-500 046 Andhra Pradesh INDIA __________________________________________________ Do You Yahoo!? Listen to your Yahoo! Mail messages from any phone. http://phone.yahoo.com From chemistry-request@server.ccl.net Thu Sep 27 08:37:21 2001 Received: from gatekeeper2.novartis.com ([194.191.169.74]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id f8RCbA510843 for ; Thu, 27 Sep 2001 08:37:11 -0400 Received: from mta3.is.chbs (mta3.novartis.com [192.37.33.14]) by gatekeeper2.novartis.com (8.11.0/8.11.0) with ESMTP id f8RCaxZ26640 for ; Thu, 27 Sep 2001 14:37:00 +0200 (MET DST) Received: from NVCHBS-S0121.is.chbs (nvchbs-s0121.is.chbs [192.37.33.41]) by mta3.is.chbs (8.11.0/8.11.0) with ESMTP id f8RCZYU04715 for ; Thu, 27 Sep 2001 14:35:34 +0200 (MET DST) Subject: To: chemistry@ccl.net From: maria.brandl@pharma.novartis.com Date: Thu, 27 Sep 2001 14:36:23 +0200 Message-ID: X-MIMETrack: Serialize by Router on CHBSMN12/N1/Novartis(Release 5.0.8 |June 18, 2001) at 09/27/2001 02:36:58 PM MIME-Version: 1.0 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 f8RCbL510846 Dear colleagues, recently I asked for tabulated information on standard covalent bond lengths and angles. I got quite a few answers and would like to heartily thank for all contributions. Below you find a compilation of the information sources I have been suggested to use: TEXTBOOKS: Solomons; Morrison & Boyd; International Tables of Crystallography, Volume C; CRC Handbook of Chemistry (some standard bond lengths); CRC Handbook of Chemistry and Physics; Structure data of polyatomic molecules, Kuchitsu, K. Ed. Springer_Verlag, Berlin, 1992. ARTICLES: "A Standard Geometrical Model for Compounds of the Main Group Elements H Through I", M.R. Peterson and I.G. Csizmadia, J. Mol. Struct. (Theochem), vol. 123, pp. 399-412 (1985). R. A. Engh and R. Huber Accurate Bond and Angle Parameters for {X}-Ray Protein Structure Refinement Acta. Cryst. A. 1991, 47, 392-400. ONLINE: http://www.chem.swin.edu.au/modules/mod2/bondlen.html (some standard values) FORCEFIELDS: MMFF, Tripos Up to now, I could not check all the sources, but I could get a copy of the International Tables of Crystallography, Vol. C, which on pp. 788ff. provides extensive information on "average bond lengths for bonds involving the elements H to I." Again thanks to everybody, Maria From chemistry-request@server.ccl.net Thu Sep 27 07:58:51 2001 Received: from puce.csi.cam.ac.uk (exim@[131.111.8.40]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id f8RBwp510235 for ; Thu, 27 Sep 2001 07:58:51 -0400 Received: from ind1.mrc-lmb.cam.ac.uk ([131.111.85.109]) by puce.csi.cam.ac.uk with esmtp (Exim 3.22 #1) id 15mZoZ-0001oZ-00 for chemistry@ccl.net; Thu, 27 Sep 2001 12:58:51 +0100 Received: from macx73.mrc-lmb.cam.ac.uk (macx73.mrc-lmb.cam.ac.uk [131.111.184.165]) by ind1.mrc-lmb.cam.ac.uk (SGI-8.9.3/8.9.3) with ESMTP id NAA81957 for ; Thu, 27 Sep 2001 13:02:21 +0100 (BST) Date: Thu, 27 Sep 2001 13:00:17 +0100 From: Ivo Krab To: chemistry@ccl.net Subject: TIP5P waters in CHARMM or AMBER Message-ID: <39919284.1001595617@macx73.mrc-lmb.cam.ac.uk> X-Mailer: Mulberry/2.1.0 (Mac OS X) MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii; format=flowed Content-Transfer-Encoding: 7bit Content-Disposition: inline Hi, Does anyone have experience using the TIP5P water model with the CHARMM or AMBER forcefields in simulations with a protein structure? Does it increase calculation time a lot compared to TIP3P or TIP4P? How did you define the parameters (especially mixing rules for the water-protein interactions)? Thanks for your attention, Ivo PS, I'm not subscribed to this list, so please CC me with your answer From chemistry-request@server.ccl.net Thu Sep 27 09:32:04 2001 Received: from chemsg9.tau.ac.il ([132.66.144.30]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id f8RDW3511782 for ; Thu, 27 Sep 2001 09:32:03 -0400 Received: (from bfuchs@localhost) by chemsg9.tau.ac.il (8.11.4/8.11.4) id f8RDWBW178757; Thu, 27 Sep 2001 15:32:11 +0200 (IST) Date: Thu, 27 Sep 2001 15:32:11 +0200 (IST) From: Benzion Fuchs Message-Id: <200109271332.f8RDWBW178757@chemsg9.tau.ac.il> To: chemistry@ccl.net Subject: P4 Cc: bfuchs@chemsg9.tau.ac.il Hi Colleagues, What is the latest about P4 motherboards (compatibility, floating point unit, benchmarks) for current QM and MM software? Best, B. Fuchs From chemistry-request@server.ccl.net Thu Sep 27 02:07:25 2001 Received: from lancelot.imb-jena.de ([192.124.248.76]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id f8R67P532632 for ; Thu, 27 Sep 2001 02:07:25 -0400 Received: (from pineda@localhost) by lancelot.imb-jena.de (SGI-8.9.3/8.8.8) id IAA63098; Thu, 27 Sep 2001 08:07:23 +0200 (CEST) From: pineda@imb-jena.de (Felipe Pineda) Message-Id: <10109270807.ZM175307@lancelot.imb-jena.de> Date: Thu, 27 Sep 2001 08:07:23 +0000 In-Reply-To: Pedro A Reche Gallardo "CCL:protein interfaces" (Sep 26, 10:01am) References: <3BB1DFC7.3B482F3A@research.dfci.harvard.edu> X-Mailer: Z-Mail (3.2.3 08feb96 MediaMail) To: Pedro A Reche Gallardo , chemistry@ccl.net Subject: Re: CCL:protein interfaces Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii hi Pedro! try http://www.umass.edu/microbio/chime/find-ncb/ hope it helps best regards felipe On Sep 26, 10:01am, Pedro A Reche Gallardo wrote: > Subject: CCL:protein interfaces > Hi All, I am looking for a program that will take a pdb file of protein > complex and identify and list the residue atoms of the interface that > interacts together with type of interaction (salt bridge, h-bonds, > vdw). Any idea if that program exists? Comments and/or suggestions for > doing this thing using any free software will also be welcomed. > regards, > > Pedro > *************************************************************************** > PEDRO a. RECHE gallardo, pHD TL: 617 632 > 3824 > Scientist, Mol.Immnunol.Foundation, FX: 617 632 3351 > Dana-Farber Cancer Institute, EM: > reche@research.dfci.harvard.edu > Harvard Medical School, EM: > reche@mifoundation.org > 44 Binney Street, D610C, URL: > http://www.reche.org > Boston, MA 02115 > *************************************************************************** > > > > > > -= 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 > > > > > > >-- End of excerpt from Pedro A Reche Gallardo -- ********************************************************************** * Felipe Pineda,PhD * * Institut fuer Molekulare Biotechnologie * * AG Theoretische Biophysik * * Beutenbergstrasse 11, Jena Vox: +49-3641-65-6491 * * Postfach 100 813, D-07708 Jena, Germany Fax: -6495 * * web: www.imb-jena.de/~pineda * ********************************************************************** ********************************************************************** * DISCLAIMER: Unless indicated otherwise, everything in this note is * * my personal opinion, not an official statement of my employer * ********************************************************************** From chemistry-request@server.ccl.net Wed Sep 26 14:29:53 2001 Received: from maverick.arl.army.mil ([128.63.58.8]) by server.ccl.net (8.11.2/8.11.0) with ESMTP id f8QITr111594 for ; Wed, 26 Sep 2001 14:29:53 -0400 Subject: Computational Chemistry GRID Conference To: CHEMISTRY@ccl.net From: "Mark Zottola - Contractor" Date: Wed, 26 Sep 2001 14:28:33 -0400 Message-ID: X-MIMETrack: Serialize by Router on Maverick/arl(Release 5.0.8 |June 18, 2001) at 09/26/2001 02:28:35 PM MIME-Version: 1.0 Content-type: text/plain; charset=us-ascii Computational Chemistry GRID Conference 3rd Notice SURA, NSF and the PET program at the Army Research Laboratory are pleased to announce that the first Computational Chemistry GRID Conference scheduled for October 16 and 17 WILL take place! Despite recent tragic events, this conference will procede as scheduled. This conference will be hosted at the University of Kentucky. There is NO registration fee for this conference. However, we do ask that all interested parties please register. Registration for this conference will close on October 10, 2001. Information and registration for either on-site or virtual attendance is at the following URL: http://www.sura.org/events/2001/compchem/chemistry.html In addition to a slate of outstanding speakers, there aill be a poster session on Tuesday night. Students, post-doctoral associate and professors are all encouraged to submit posters. The poster session will be simultaneous with the mixer, thus allowing an informal, but fruitful mix of science and socializing. There will be an online publication of these posters, details will follow in the days to come. As part of this conference, we have reserved a set of rooms in Lexington. These rooms are at a substantial discount to the normal rate. However, this rate will only be held through COB Friday, September 28. While you will be able to reserve a room after the 28th, you will not receive the special conference rate. Van service WILL be provided to all attendees for transportation between the hotel and the University. The speakers at this conference are acknowledged to be among the leading researchers in computational chemistry. These speakers include Dr. Keiji Morokuma (Emory), Dr. Weitao Yang (Duke), Dr. William Goddard (Cal Tech) and Dr. Stephen Harvey (UAB). This conference will demonstrate how VRVS can bridge the gulf between Access GRID and H.323 technology. This bridge solves both technological and economic barriers to information sharing via the internet. As an added feature to this conference, an afternoon session on Nanostructures will be held October 17. Given the rapid developments of nanotechnology and its myriad applications, an optional session will be held. This session will include speakers such as Dr. Antonis Andriotis and Dr. Roberto Car. This session will also be available through videoconferencing. This conference is supported by SURA, under a grant from the National Computational Science Alliance (NCSA), serving as a Partner for Advanced Computational Services (PACS). From chemistry-request@server.ccl.net Wed Sep 26 21:24:44 2001 Received: from mdl.ipc.pku.edu.cn (IDENT:postfix@[162.105.177.40]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id f8R1Od524180 for ; Wed, 26 Sep 2001 21:24:40 -0400 Received: by mdl.ipc.pku.edu.cn (Postfix, from userid 2556) id B56D12B590; Thu, 27 Sep 2001 09:26:15 +0800 (CST) Received: from localhost (localhost [127.0.0.1]) by mdl.ipc.pku.edu.cn (Postfix) with ESMTP id A12172B560; Thu, 27 Sep 2001 09:26:15 +0800 (CST) Date: Thu, 27 Sep 2001 09:26:15 +0800 (CST) From: Gao Ying To: Pedro A Reche Gallardo Cc: chemistry@ccl.net Subject: Re: CCL:protein interfaces In-Reply-To: <3BB1DFC7.3B482F3A@research.dfci.harvard.edu> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear Dr. Pedro A Reche Gallardo, Our lab have developed a method to analyse protein-protein interface. You can download it from our ftp server mdl.ipc.pku.edu.cn/pub/software/PP_SITE . Though this program won't fit all your need, you can try it to get something useful. It is a free software just need you fill in a register form. Hope this will be helpful! Gao Ying Molecular Design Lab Institute of Physical Chemistry Peking University Beijing, P.R. China From chemistry-request@server.ccl.net Thu Sep 27 10:54:45 2001 Received: from ccmsi.jsums.edu ([143.132.103.54]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id f8REsj513900 for ; Thu, 27 Sep 2001 10:54:45 -0400 Received: from ccmsi.jsums.edu [10.30.3.44] by ccmsi.jsums.edu with ESMTP (SMTPD32-7.03) id ADB6320154; Thu, 27 Sep 2001 09:54:46 -0500 Message-ID: <3BB33DB6.CD3A304C@ccmsi.jsums.edu> Date: Thu, 27 Sep 2001 09:54:46 -0500 From: "Dr. Giju Thomas Kalathingal" Organization: Jackson State University X-Mailer: Mozilla 4.77 [en] (Windows NT 5.0; U) X-Accept-Language: en MIME-Version: 1.0 To: Ivo Krab , CCL Subject: Re: CCL:TIP5P waters in CHARMM or AMBER References: <39919284.1001595617@macx73.mrc-lmb.cam.ac.uk> Content-Type: multipart/mixed; boundary="------------E420ABF942E49B8CDDE6FA3C" This is a multi-part message in MIME format. --------------E420ABF942E49B8CDDE6FA3C Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi: Have you tried TIP4P-FQ model? It has been found very good even with QM/MM method. Giju Ivo Krab wrote: > Hi, > > Does anyone have experience using the TIP5P water model with the CHARMM or > AMBER forcefields in simulations with a protein structure? Does it increase > calculation time a lot compared to TIP3P or TIP4P? How did you define the > parameters (especially mixing rules for the water-protein interactions)? > > Thanks for your attention, > > Ivo > > PS, I'm not subscribed to this list, so please CC me with your answer > > -= 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 --------------E420ABF942E49B8CDDE6FA3C Content-Type: text/x-vcard; charset=us-ascii; name="giju.vcf" Content-Transfer-Encoding: 7bit Content-Description: Card for Dr. Giju Thomas Kalathingal Content-Disposition: attachment; filename="giju.vcf" begin:vcard n:; tel;fax:++1-601-979-7823 tel;home:++1-601-979-2749 tel;work:++1-601-979-7824 x-mozilla-html:FALSE url:http://dogstar.duch.udel.edu/gijukt/welcome.html org:;Department of Chemistry version:2.1 email;internet:giju@ccmsi.jsums.edu adr;quoted-printable:;;Jackson State University=0D=0AP.O.Box 17910=0D=0A;Jackson, MS - 39217;;;USA fn:Dr. Giju T. Kalathingal end:vcard --------------E420ABF942E49B8CDDE6FA3C--