From chemistry-request@server.ccl.net Mon Mar 19 01:59:33 2001 Received: from ksmail.netcologne.de ([194.8.194.97]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f2J6xXD15681 for ; Mon, 19 Mar 2001 01:59:33 -0500 Received: from cosmologic.de (dial-213-168-92-32.netcologne.de [213.168.92.32]) by ksmail.netcologne.de (8.9.3/8.9.3) with ESMTP id HAA27481; Mon, 19 Mar 2001 07:59:24 +0100 (MET) Message-ID: <3AB5AECD.AA12F6D4@cosmologic.de> Date: Mon, 19 Mar 2001 08:01:33 +0100 From: "Dr. Andreas Klamt" Organization: COSMOlogic GmbH&CoKG X-Mailer: Mozilla 4.7 [de] (Win98; I) X-Accept-Language: en,pdf MIME-Version: 1.0 To: dasf@ifi.unicamp.br CC: CHEMISTRY@ccl.net Subject: Re: CCL:DFT: COSMO vs G98 References: <20010317232516.E540D5515@lua.ifi.unicamp.br> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Demetrio, what does your question have to do with COSMO? In your entire text the word COSMO does not appear? So why the title "COSMO vs G98"? If you are interested in a question regarding COSMO vs. G98 you can ask me. Andreas dasf@ifi.unicamp.br schrieb: > > Dear CCL'ers, > > I'm trying to reproduce some DFT calculations carried out with the DZP basis > using the local density approximation (LDA) implemented in DMOL (MSI/Biosym, > Inc). There is no additional information about the DFT method or functional > used. > > I don't have access to such program and so I want to know if with those > informations I can choose in G98 a functional and a basis set in order to > reproduce those calculations. > > Can anybody help me with this? > > Thanks in advance, > > Demetrio Filho > > -= 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 -- -------------------------------------------------------------------------------- Dr. Andreas Klamt COSMOlogic GmbH&CoKG Burscheider Str. 515 51381 Leverkusen, Germany Tel.: 49-2171-73168-1 Fax: ...-9 e-mail: andreas.klamt@cosmologic.de web: www.cosmologic.de -------------------------------------------------------------------------------- COSMOlogic Your Competent Partner for Computational Chemistry and Fluid Thermodynamics -------------------------------------------------------------------------------- From chemistry-request@server.ccl.net Mon Mar 19 02:54:47 2001 Received: from tigris.klte.hu ([193.6.138.33]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f2J7skD15907 for ; Mon, 19 Mar 2001 02:54:46 -0500 Received: from anti07 (193.6.133.59) by tigris.klte.hu (MX V5.1-A Vn6f) with SMTP; Mon, 19 Mar 2001 08:52:54 +0100 Message-ID: <005201c0b04a$253877a0$3b8506c1@chem.klte.hu> From: "Tamas E. Gunda" To: "chinmoy ranjan" , References: <000a01c0acfb$5403d540$c14c1fac@CHINMOY> Subject: Re: CCL:Difficulty while using babel Date: Mon, 19 Mar 2001 08:56:45 +0100 MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-2" 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 Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id f2J7slD15908 Probably the some manual editing of the file would be necessary, for example the change ATOM label to HETATM of the Mo atoms, and/or correct the atom type of the problematic atoms. It is difficult to say without having seen the file. Could you send me the pdb file to have a look on it ? with regards Dr Tamas E. Gunda Research Group for Antibiotics of the Hungarian Acad. Sci. University of Debrecen, POBox 36 H-4010 Debrecen, Hungary tel.: (+36-52) 512 900/2472 fax: (+36-52) 512 914 e-mail: tamasgunda@tigris.klte.hu home-page: www.klte.hu/~gundat/gunda.htm ----- Original Message ----- From: chinmoy ranjan To: Sent: Thursday, March 15, 2001 3:55 AM Subject: CCL:Difficulty while using babel > Hello All, > While trying to convert a pdb file to mol2 format using babel I get > the following message without the job being done. The proytein molecule > has Mo at its active site .Could anyone suggest how to get around this > problem. > > > > Unable to assign HYB type to atom 1333 type = N > Unable to assign HYB type to atom 1334 type = N > Unable to assign HYB type to atom 2344 type = N > Unable to assign HYB type to atom 3638 type = Mo > Unable to assign HYB type to atom 7294 type = Mo > > Thanks > > CHINMOY RANJAN > INDIAN INSTITUTE OF TECHNOLOGY > KANPUR From chemistry-request@server.ccl.net Mon Mar 19 02:02:30 2001 Received: from ksmail.netcologne.de ([194.8.194.97]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f2J72UD15729 for ; Mon, 19 Mar 2001 02:02:30 -0500 Received: from cosmologic.de (dial-213-168-64-46.netcologne.de [213.168.64.46]) by ksmail.netcologne.de (8.9.3/8.9.3) with ESMTP id IAA27702; Mon, 19 Mar 2001 08:02:17 +0100 (MET) Message-ID: <3AB5AF7B.706D79B9@cosmologic.de> Date: Mon, 19 Mar 2001 08:04:27 +0100 From: "Dr. Andreas Klamt" Organization: COSMOlogic GmbH&CoKG X-Mailer: Mozilla 4.7 [de] (Win98; I) X-Accept-Language: en,pdf MIME-Version: 1.0 To: Robert Jorissen CC: "'chemistry@ccl.net'" Subject: Re: CCL:MOPAC software - free versions for Windows References: <805AD25D3702D311805900062B004E42BD0986@keeper.ludwig.edu.au> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear CCLers, does anyone know whether these no-cost versions of MOPAC7 are bug fixed? It is known that MOPAC7 is not as bug-free as the older versions of MOPAC have been, just since Jimmy Stewart stopped his development work on MOPAC7 shortly after the release. There is no instance any more for people having contributed code to MOPAC7 to get bugs officially fixed. For example I am aware of several severe bugs in COSMO in MOPAC7, which for a long time have been removed in the maintained MOPAC versions. The bugs turned out more or less accidently since some one the apparently very rare MOPAC7 users asked me about strange results. I assume, that the COSMO part in MOPAC7 is not the only one having bugs. The question is, whether it makes sense to recommend the use of an eight year old code (release of MOPAC7 was 1993) of unknown quality, whithout having the contacts to all the contributors who really understand the different parts of the code. Andreas -- -------------------------------------------------------------------------------- Dr. Andreas Klamt COSMOlogic GmbH&CoKG Burscheider Str. 515 51381 Leverkusen, Germany Tel.: 49-2171-73168-1 Fax: ...-9 e-mail: andreas.klamt@cosmologic.de web: www.cosmologic.de -------------------------------------------------------------------------------- COSMOlogic Your Competent Partner for Computational Chemistry and Fluid Thermodynamics -------------------------------------------------------------------------------- Robert Jorissen schrieb: > > There are at least two versions of MOPAC 7 which have user interfaces. > > Winmopac7.21 from Roman Shchepin and Dmitriy Litvinov uses the publicly > available programs MOPAC 7, the Rasmol molecular visualization program and > the molecular coordinate format conversion program Babel and puts them > together in a PC interface. You have to type in the Z-matrix but quick > visualization using Rasmol greatly helps. The relevant Web pages are > http://members.fortunecity.com/winmopac/ and > http://winmopac.narod.ru/english.html. This program is free. > > The program Mopd from Peter Zhou also visualizes the molecules in MOPAC > files. This program, as well as a compiled version of MOPAC 7 (for 60 heavy > atoms and 60 hydrogens), can be downloaded at no cost from > http://www.geocities.com/peterxz/. These programs require Windows 95 or > Windows NT. > > Robert Jorissen > Ludwig Insitute for Cancer Research, Melbourne branch > > -= 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 Mar 19 09:29:55 2001 Received: from mailhost1.rdg.ac.uk ([134.225.16.4]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f2JETsD18229 for ; Mon, 19 Mar 2001 09:29:54 -0500 Received: from indyp.chemistry ([134.225.168.35] helo=indyp.chemistry.rdg.ac.uk) by mailhost1.rdg.ac.uk with esmtp (University of Reading Email Service) id {14f0fS-0002SJ-00} for CHEMISTRY@server.ccl.net; Mon, 19 Mar 2001 14:29:54 +0000 Received: from reading.ac.uk (localhost [127.0.0.1]) by indyp.chemistry.rdg.ac.uk (SGI-8.9.3/8.9.3) with ESMTP id OAA20147 for ; Mon, 19 Mar 2001 14:29:54 GMT Sender: dave@reading.ac.uk Message-ID: <3AB617E1.E0C51083@reading.ac.uk> Date: Mon, 19 Mar 2001 14:29:53 +0000 From: Dave Price Organization: none-what-so-ever X-Mailer: Mozilla 4.7C-SGI [en] (X11; I; IRIX 6.5 IP22) X-Accept-Language: en MIME-Version: 1.0 To: Comp Chem Mailing List Subject: g94 under RedHat Linux 7.0 with g77/f2c Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear Computational Chemists, Until our copy of g98 arrives (ordered), I am trying to compile g94 on a 1GHz Athlon system with 512 MB RAM under RedHat Linux 7.0. I have checked the archives, but found nothing directly applicable. Anyone any ideas about these problems- Using bsd/bldg94 > bldg94.log We get lots of ...... cc: -sort-common: linker input file unused since linking not done errors/commets, then just before it quits we get ........ cc: -sort-common: linker input file unused since linking not done ml402.f: MAIN ml402: cc: -sort-common: linker input file unused since linking not done bd0402.o(.data+0x0): multiple definition of `natorb_' l402.a(bd0402.o)(.data+0x0): first defined here bd0402.o(.data+0x1c0): multiple definition of `atomic_' l402.a(bd0402.o)(.data+0x1c0): first defined here bd0402.o(.data+0x880): multiple definition of `vsips_' l402.a(bd0402.o)(.data+0x880): first defined here bd0402.o(.data+0x12a0): multiple definition of `istope_' l402.a(bd0402.o)(.data+0x12a0): first defined here bd0402.o(.data+0x1600): multiple definition of `ideas_' l402.a(bd0402.o)(.data+0x1600): first defined here bd0402.o(.data+0x7a60): multiple definition of `ideap_' l402.a(bd0402.o)(.data+0x7a60): first defined here bd0402.o(.data+0xdec0): multiple definition of `mndo_' l402.a(bd0402.o)(.data+0xdec0): first defined here bd0402.o(.data+0x12860): multiple definition of `pm3_' l402.a(bd0402.o)(.data+0x12860): first defined here bd0402.o(.data+0x17200): multiple definition of `alptm_' l402.a(bd0402.o)(.data+0x17200): first defined here bd0402.o(.data+0x173e0): multiple definition of `elemts_' l402.a(bd0402.o)(.data+0x173e0): first defined here bd0402.o(.data+0x174c0): multiple definition of `refs_' l402.a(bd0402.o)(.data+0x174c0): first defined here bd0402.o(.data+0x1fa80): multiple definition of `onele3_' l402.a(bd0402.o)(.data+0x1fa80): first defined here bd0402.o(.data+0x1fba0): multiple definition of `twoel3_' l402.a(bd0402.o)(.data+0x1fba0): first defined here bd0402.o(.data+0x1ff00): multiple definition of `atomi3_' l402.a(bd0402.o)(.data+0x1ff00): first defined here bd0402.o(.data+0x20020): multiple definition of `beta3_' l402.a(bd0402.o)(.data+0x20020): first defined here bd0402.o(.data+0x20500): multiple definition of `alpha3_' l402.a(bd0402.o)(.data+0x20500): first defined here bd0402.o(.data+0x209e0): multiple definition of `expon3_' l402.a(bd0402.o)(.data+0x209e0): first defined here bd0402.o(.data+0x20b00): multiple definition of `alpha_' l402.a(bd0402.o)(.data+0x20b00): first defined here bd0402.o(.data+0x20e60): multiple definition of `core_' l402.a(bd0402.o)(.data+0x20e60): first defined here bd0402.o(.data+0x211c0): multiple definition of `multip_' l402.a(bd0402.o)(.data+0x211c0): first defined here bd0402.o(.data+0x22280): multiple definition of `expont_' l402.a(bd0402.o)(.data+0x22280): first defined here bd0402.o(.data+0x22ca0): multiple definition of `onelec_' l402.a(bd0402.o)(.data+0x22ca0): first defined here bd0402.o(.data+0x236c0): multiple definition of `betas_' l402.a(bd0402.o)(.data+0x236c0): first defined here bd0402.o(.data+0x240e0): multiple definition of `twoele_' l402.a(bd0402.o)(.data+0x240e0): first defined here bd0402.o: In function `bd0402_': bd0402.o(.text+0x0): multiple definition of `bd0402_' l402.a(bd0402.o)(.text+0x0): first defined here collect2: ld returned 1 exit status make: *** [l402.exe] Error 1 Any suggestions most welcome. Or a working makefile :^) Cheers, Dave -- ------------------------------------------------------------------------ Dr. David W. Price MA CChem MRSC Tel: +44 (0)118 9875123 extn 7415 Department of Chemistry, Fax: +44 (0)118 9316331 University of Reading, mailto:d.w.price@reading.ac.uk Whiteknights, READING RG6 6AD U.K. ------------------------------------------------------------------------ From chemistry-request@server.ccl.net Mon Mar 19 10:20:12 2001 Received: from tibre.ujf-grenoble.fr ([193.54.238.31]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f2JFKBD18501 for ; Mon, 19 Mar 2001 10:20:12 -0500 Received: from volga.ujf-grenoble.fr (volga.ujf-grenoble.fr [152.77.6.1]) by tibre.ujf-grenoble.fr (Pro-8.9.3/8.9.3/Configured by AD & JE 25/10/1999) with ESMTP id PAA01675 for ; Mon, 19 Mar 2001 15:34:42 +0100 (MET) Received: from ujf-grenoble.fr (IDENT:antoine@cahn.ujf-grenoble.fr [152.77.209.147]) by volga.ujf-grenoble.fr (8.9.3/8.8.5) with ESMTP id PAA28876 for ; Mon, 19 Mar 2001 15:33:46 +0100 (MET) Sender: Pierre.Antoine@ujf-grenoble.fr Message-ID: <3AB61968.2EFD2B6F@ujf-grenoble.fr> Date: Mon, 19 Mar 2001 15:36:24 +0100 From: Antoine MIME-Version: 1.0 To: chemistry@ccl.net Subject: trouble compiling Autodock3.0.5 for Linux Dear CCLers, I downloaded Autodock3.0.5 last week and can't compile the Autogrid part under linux (mdk 7.02 uptodated) because of an error in main function. Here is the message : main.c: In function `main': main.c:106: `XYZ' undeclared (first use in this function) main.c:106: (Each undeclared identifier is reported only once main.c:106: for each function it appears in.) make: *** [main.o] Error 1 Big bug but did someone download that soft and compile it for linux or have the same problem ? Is there a known fix ? Thank you very much for any answer. Antoine FORTUNE -- ---------------------------------------------- Antoine FORTUNE Ingénieur Modélisation Moléculaire Département de Pharmacologie Moléculaire - DPM UMR 5063 - Universite Joseph Fourier Domainde de la Merci 38706 LA TRONCHE - FRANCE Tel : +33 4 76 63 71 40 Fax : +33 4 76 51 86 67 e-mail : Antoine.Fortune@ujf-grenoble.fr ICQ : 106018150 ---------------------------------------------- From chemistry-request@server.ccl.net Mon Mar 19 10:28:55 2001 Received: from discover-net.net ([208.134.196.20]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f2JFStD18563 for ; Mon, 19 Mar 2001 10:28:55 -0500 Received: from visual (max-sup-92.discover-net.net [208.134.202.92]) by discover-net.net (8.10.1/8.10.1) with SMTP id f2JFN9m22726 for ; Mon, 19 Mar 2001 09:23:09 -0600 From: "Carla Blumberg" To: Subject: SCO UNIX Date: Mon, 19 Mar 2001 09:24:30 -0600 Message-ID: MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_0011_01C0B056.66F45AE0" X-Priority: 3 (Normal) X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook IMO, Build 9.0.2416 (9.0.2910.0) X-MimeOLE: Produced By Microsoft MimeOLE V5.00.2919.6600 Importance: Normal This is a multi-part message in MIME format. ------=_NextPart_000_0011_01C0B056.66F45AE0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit Please forgive this newbie question: Is it possible to form a Beowolf cluster and run Gaussian, etc., using SCO UNIX? Thanks in advance, Carla ------=_NextPart_000_0011_01C0B056.66F45AE0 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable
Please = forgive this=20 newbie question:
Is it = possible to=20 form a Beowolf cluster and run Gaussian, etc., using SCO=20 UNIX?
Thanks = in=20 advance,
Carla
------=_NextPart_000_0011_01C0B056.66F45AE0-- From chemistry-request@server.ccl.net Mon Mar 19 11:34:47 2001 Received: from soul.helsinki.fi ([128.214.3.1]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f2JGYlD19210 for ; Mon, 19 Mar 2001 11:34:47 -0500 Received: from localhost (mpjohans@localhost) by soul.helsinki.fi (8.9.3/8.9.3) with ESMTP id SAA01161; Mon, 19 Mar 2001 18:34:28 +0200 (EET) X-Authentication-Warning: soul.helsinki.fi: mpjohans owned process doing -bs Date: Mon, 19 Mar 2001 18:34:23 +0200 (EET) From: Mikael Johansson X-Sender: To: Antoine cc: Subject: Re: CCL:trouble compiling Autodock3.0.5 for Linux In-Reply-To: <3AB61968.2EFD2B6F@ujf-grenoble.fr> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hello Antoine and All! On Mon, 19 Mar 2001, Antoine wrote: > I downloaded Autodock3.0.5 last week and can't compile the Autogrid part > under linux (mdk 7.02 uptodated) because of an error in main function. > Here is the message : > > main.c: In function `main': > main.c:106: `XYZ' undeclared (first use in this function) The simplest procedure is to edit the autocomm.h file. Find the declaration #define SPACE 3 and add the following line for example under it: #define XYZ 3 Apparently the variable name has changed between versions, but not at every location. Have a nice day, Mikael Johansson University of Helsinki Department of Chemistry From chemistry-request@server.ccl.net Mon Mar 19 12:22:15 2001 Received: from pavo.U.Arizona.EDU ([128.196.137.189]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f2JHMFD19500 for ; Mon, 19 Mar 2001 12:22:15 -0500 Received: from localhost (dasf@localhost) by pavo.U.Arizona.EDU (8.9.3 (PHNE_18546)/8.8.6) with ESMTP id KAA04939; Mon, 19 Mar 2001 10:22:05 -0700 (MST) Date: Mon, 19 Mar 2001 10:22:05 -0700 (MST) From: Demetrio A Filho To: "Dr. Andreas Klamt" cc: dasf@ifi.unicamp.br, CHEMISTRY@ccl.net Subject: DFT: DMOL vs G98 In-Reply-To: <3AB5AECD.AA12F6D4@cosmologic.de> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hello Dr. Andreas, You are right. I was reading a paper where they used COSMO and DMOL and I got confused with the words. The subject should be DMOL vc G98. Thanks in advance, Demetrio FIlho From chemistry-request@server.ccl.net Mon Mar 19 12:07:49 2001 Received: from postoffice.mail.cornell.edu ([132.236.56.7]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f2JH7nD19453 for ; Mon, 19 Mar 2001 12:07:49 -0500 Received: from cornell.edu (sweet1.foodsci.cornell.edu [132.236.147.65]) by postoffice.mail.cornell.edu (8.9.3/8.9.3) with ESMTP id MAA07961 for ; Mon, 19 Mar 2001 12:07:48 -0500 (EST) Sender: dwood@cornell.edu Message-ID: <3AB63A68.704FA651@cornell.edu> Date: Mon, 19 Mar 2001 11:57:12 -0500 From: Richard Wood X-Mailer: Mozilla 4.75C-SGI [en] (X11; I; IRIX 6.5 IP32) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net Subject: Re: CCL:experiment of H-bond strength in solution References: <20010316045354.66012.qmail@web13206.mail.yahoo.com> <3AB52348.A090BE15@usc.edu> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi all I thought that the subject of this posting was the "experimental H-bond strength in solution"? If so, why does everyone cite theoretical papers/methods/results? Richard-- Richard L. Wood, Ph. D. Physical/Computational Chemist Post-doctoral Associate Cornell University, Ithaca, NY 14853 From chemistry-request@server.ccl.net Mon Mar 19 12:05:51 2001 Received: from mail.chem.tamu.edu ([165.91.176.8]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f2JH5pD19434 for ; Mon, 19 Mar 2001 12:05:51 -0500 Received: from mail.chem.tamu.edu ([165.91.177.32]) by mail.chem.tamu.edu (Post.Office MTA v3.5.3 release 223 ID# 0-64333U1000L100S0V35) with ESMTP id edu for ; Mon, 19 Mar 2001 11:06:19 -0600 Sender: yubo@ccl.net Message-ID: <3AB63D0C.58EBC1AD@mail.chem.tamu.edu> Date: Mon, 19 Mar 2001 17:08:28 +0000 From: Yubo Fan Organization: Chemistry Department, Texas A&M University X-Mailer: Mozilla 4.7C-SGI [en] (X11; I; IRIX64 6.5 IP28) X-Accept-Language: zh-CN, en MIME-Version: 1.0 To: CHEMISTRY@ccl.net Subject: Slow celeron Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi, I tried a G98 job on Celeron 667. Unfortunately, the speed is very very slow. The speed of running G98 is on the level of Pentium II/233. I don't know why. Any explanation? Thanks in advance. Yubo -- ============================================================ Yubo Fan Email: yubofan@mail.chem.tamu.edu Department of Chemistry Tel: 1-979-845-7222 Texas A&M University College Station, TX 77843 ============================================================ From chemistry-request@server.ccl.net Mon Mar 19 13:55:42 2001 Received: from hermes.bmc.uu.se ([130.238.39.159]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f2JItgD19970 for ; Mon, 19 Mar 2001 13:55:42 -0500 Received: from XRAY.bmc.uu.se ([130.238.37.10]) by hermes.bmc.uu.se (Post.Office MTA v3.5.3 release 223 ID# 0-62649U1500L1000S0V35) with ESMTP id se for ; Mon, 19 Mar 2001 19:57:04 +0100 Received: from localhost (deva@localhost) by XRAY.bmc.uu.se (8.9.3/8.8.7) with ESMTP id TAA08769 for ; Mon, 19 Mar 2001 19:58:36 +0100 Date: Mon, 19 Mar 2001 19:58:36 +0100 (CET) From: Devapriya Choudhury To: chemistry@ccl.net Subject: Orthographic projections in VMD Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi All, When I generate a picture in VMD using the Orthographic projection mode and subsequently render the image (Raster3D), the view seems to automatically shift to perspective projection mode. Does anyone know a fix ? Thanks in advance, Devapriya -- _____________________________________________________ Devapriya Choudhury Office: Home: Deptt. of Molecular Biology Oskar Arpis Vag 2,2 Box 590, BMC, S75650, Uppsala S75124, Uppsala Sweden Sweden Tel: +46 18 4714523 +46 18 400314 FAX: +46 18 536971 e-mail deva@xray.bmc.uu.se _____________________________________________________ From chemistry-request@server.ccl.net Mon Mar 19 15:10:15 2001 Received: from postoffice.mail.cornell.edu ([132.236.56.7]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f2JKAFD20274 for ; Mon, 19 Mar 2001 15:10:15 -0500 Received: from cornell.edu (sweet1.foodsci.cornell.edu [132.236.147.65]) by postoffice.mail.cornell.edu (8.9.3/8.9.3) with ESMTP id PAA22599; Mon, 19 Mar 2001 15:10:16 -0500 (EST) Sender: dwood@cornell.edu Message-ID: <3AB66528.8C9462DF@cornell.edu> Date: Mon, 19 Mar 2001 14:59:37 -0500 From: Richard Wood X-Mailer: Mozilla 4.75C-SGI [en] (X11; I; IRIX 6.5 IP32) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net Subject: Re: CCL:experiment of H-bond strength in solution References: <20010316045354.66012.qmail@web13206.mail.yahoo.com> <3AB52348.A090BE15@usc.edu> <3AB63A68.704FA651@cornell.edu> <3AB66654.A1AC18FD@usc.edu> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Jordi Villa wrote: > because at the end of the original message the author asked about how > to simulate them. Please, read the messages before implying anything. I wasn't the one doing the implying. The following is from the ORIGINAL post. ========================================= Dear all, Since it's well-known that the H-bond strength will be highly weaken in solution, compared with that in gap phase, I am curious if there is any experimental evidence or hint available. ========================================= Notice the words "theoretical" or "calculated" are not anywhere to be seen. Richard -- Richard L. Wood, Ph. D. Physical/Computational Chemist Post-doctoral Associate Cornell University, Ithaca, NY 14853 From chemistry-request@server.ccl.net Mon Mar 19 15:42:24 2001 Received: from cougar.it.wsu.edu (root@[134.121.1.10]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f2JKgOD20440 for ; Mon, 19 Mar 2001 15:42:24 -0500 Received: from ucis (ucis.chem.wsu.edu [134.121.41.180]) by cougar.it.wsu.edu (8.9.3/8.9.3) with SMTP id MAA05950; Mon, 19 Mar 2001 12:42:24 -0800 (PST) Message-ID: <002701c0b0b5$19aef740$b4297986@chem.wsu.edu> From: "Phillip D. Matz" To: "Yubo Fan" , References: <3AB63D0C.58EBC1AD@mail.chem.tamu.edu> Subject: Re: CCL:Slow celeron Date: Mon, 19 Mar 2001 12:42:23 -0800 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 5.50.4133.2400 X-MimeOLE: Produced By Microsoft MimeOLE V5.50.4133.2400 Hi, I think I can contribute to this discussion. In my own single processor G98 A.7 Celeron vs. PII comparison testing I found the Celeron outperforms the PII MHz per MHZ by ~10% for the following job types (consistent up to molecules with 70 atoms and 850 basis fncs): Hartree-Fock calculations: both DIIS(L502.EXE) and QC (L508.EXE) with the incore, conventional, and direct algorithms Frequency calculations (L701.EXE, L703.EXE, L1002.EXE, L1101.EXE, L1110.EXE) Excited State calculations (L914.EXE) I compared the processors with G98 A.7 in WIN95, WINNT 4.0 SP5, WIN2000 pro, RedHat 6.0, RedHat 6.1, and RedHat 6.2 and the results were fairly consistent. What I did not compare was correlation methods (ie CCSD, CASSCF, MP2) or DFT. I should also mention that for the same tests the Athlon classic (1/2 and 2/5 L2 cache divisors) outperform the celeron another ~10% MHz per MHz. Having said that, there is no reason, at the CPU level, why your celeron 667 is performing so poorly. How much RAM is accessible by the celeron? If you only have 32MB then you will be suffering. What is your operating system? Also, is this a home-built system or a vendor provided system (such as HP or Gateway)? If you can access the BIOS, is your L2 cache enabled? What about the L1 cache? And is your BIOS current? Since computer hardware debugging is OT for the CCL I would suggest we take this conversation off-line and figure out what is wrong with your particular celeron system. The bottom line for listening CCLers is that your results are atypical. Respectfully, Phillip Matz (just a graduate student at WSU) matz@wsunix.wsu.edu ----- Original Message ----- From: "Yubo Fan" To: Sent: Monday, March 19, 2001 9:08 AM Subject: CCL:Slow celeron > Hi, > > I tried a G98 job on Celeron 667. Unfortunately, the speed is very very > slow. The speed of running G98 is on the level of Pentium II/233. I > don't know why. Any explanation? Thanks in advance. > > Yubo > > -- > ============================================================ > Yubo Fan Email: yubofan@mail.chem.tamu.edu > Department of Chemistry Tel: 1-979-845-7222 > Texas A&M University > College Station, TX 77843 > ============================================================ > > > > > -= 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 Mar 19 17:33:59 2001 Received: from ns2.carb.nist.gov ([129.6.112.2]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f2JMXxD21003 for ; Mon, 19 Mar 2001 17:33:59 -0500 Received: from umbi.umd.edu (hatter.carb.nist.gov [129.6.113.76]) by ns2.carb.nist.gov (8.9.3/8.9.3) with ESMTP id RAA31486 for ; Mon, 19 Mar 2001 17:34:00 -0500 Message-ID: <3AB68987.6250A476@umbi.umd.edu> Date: Mon, 19 Mar 2001 17:34:47 -0500 From: "Michael K. Gilson" X-Mailer: Mozilla 4.72 [en] (WinNT; U) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net Subject: Binding Database Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear Colleagues, I would like to call your attention to a web-accessible database of measured intermolecular binding affinities (BindingDB) that my group is developing at www.bindingdb.org. We think the database will be useful for molecular design and for testing and parameterization of computational models. The user-interface supports queries by molecule name, binding free energy, chemical substructure, sequence homology, and a few other criteria. It also supports on-line data deposition, though it will probably be another month or so before we start accepting data by this route. The data holdings are currently modest and are limited to measurements by isothermal titration calorimetry. However, they are being expanded to include enzyme inhibition data (Ki, IC50, etc.), and we hope to see data start to flow in when the on-line deposition pathway is opened up. If you are interested in the database, I would greatly appreciate your looking it over and filling out the on-line "site evaluation", which asks what you like and dislike about the site, and about how you might like to use the binding database in your own work. This information will help us to improve the site and, we hope, to obtain continued funding for the project. Feel free to contact me directly as well if you would like further information or have other comments or suggestions. Thanks in advance, Mike Gilson From chemistry-request@server.ccl.net Mon Mar 19 12:00:57 2001 Received: from macbeth.if.usp.br ([143.107.133.1]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f2JH0uD19416 for ; Mon, 19 Mar 2001 12:00:56 -0500 Received: from localhost (rivelino@localhost) by macbeth.if.usp.br (8.9.3/8.9.3) with SMTP id NAA04991; Mon, 19 Mar 2001 13:52:54 -0300 (EST) Date: Mon, 19 Mar 2001 13:52:53 -0300 (EST) From: Roberto Rivelino de Melo Moreno To: mike smith cc: chemistry@ccl.net Subject: Re: CCL:experiment of H-bond strength in solution In-Reply-To: <20010314202839.82539.qmail@web13202.mail.yahoo.com> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hello Mike, take a look also at: K Coutinho, N. Saavedra and S. Canuto J. Mol. Struct. THEOCHEM 466 (1999) 69. ========================================================================== Roberto R. M. Moreno || http://macbeth.if.usp.br/~rivelino Instituto de Fisica / DFMT || E-mail: rivelino@if.usp.br Universidade de Sao Paulo || Caixa Postal 66318 05315-970 Sao Paulo, SP || Fax: +55 11 3818 6831 Brasil || Tel: +55 11 3818 6988 ========================================================================== On Wed, 14 Mar 2001, mike smith wrote: > Dear all, > > Since it's well-known that the H-bond strength will be > highly weaken in solution, compared with that in gap > phase, I am curious if there is any experimental > evidence or hint available. > > Also, I found two papers on the potential enrgy curves > of H-bond in gas-phase and solution: > (1)Dang, L X; Kollman, P. A, > J Am Chem Soc, 1990, 112,503 > > AT base pair (H-bond & stacking) > from 12kcal/mol(gas) to 0.8kcal/mol (solution) > > (2)Osapay, K; Young W S; Brooks C L; Case D A > J Phys Chem 1996, 100, 2698 > Updated in Annu Rev Phys Chem, 2000, 51, 129 > > formamide dimer > from 6.7 kcal/mol to 0.8 kcal/mol > > Here, I am wondering if any of you could provide me > more related reference. Also, any discussion on the > method to simulate this accurately would be highly > appreciated. > > Thanks for your attention! > > --Mike > > __________________________________________________ > Do You Yahoo!? > Yahoo! Auctions - Buy the things you want at great prices. > http://auctions.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 > > > > > > From chemistry-request@server.ccl.net Mon Mar 19 12:57:56 2001 Received: from admin.cnrs-orleans.fr ([163.9.1.2]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f2JHvuD19737 for ; Mon, 19 Mar 2001 12:57:56 -0500 Received: from chinon.cnrs-orleans.fr (chinon.cnrs-orleans.fr [163.9.6.107]) by admin.cnrs-orleans.fr (8.9.1a/jtpda-5.3.2) with ESMTP id SAA08533 ; Mon, 19 Mar 2001 18:57:54 +0100 (MET) Received: (from hinsen@localhost) by chinon.cnrs-orleans.fr (8.9.3/8.9.3) id SAA04714; Mon, 19 Mar 2001 18:55:06 +0100 Date: Mon, 19 Mar 2001 18:55:06 +0100 Message-Id: <200103191755.SAA04714@chinon.cnrs-orleans.fr> X-Authentication-Warning: chinon.cnrs-orleans.fr: hinsen set sender to hinsen@cnrs-orleans.fr using -f From: Konrad Hinsen To: chemistry@ccl.net In-reply-to: <062801c0af8d$f9300fe0$b9ac323f@josiah> (dalke@acm.org) Subject: Re: CCL:DCD and software reuse (was Qmol: Molecular viewer for Windows) References: <062801c0af8d$f9300fe0$b9ac323f@josiah> > I don't know what can be done to limit this (in my mind) > needless duplication of effort. Open Source code would be an important first step. In fact, I do not understand why this concept isn't standard for academic applications. Much academic code is already free, so why not take the next step and make it freely redistributable, also in modified form? And for those academic packages that are not free, I seriously doubt that they are in any sense profitable. If Open Source were common in computational chemistry, then probably there would also be corresponding Web sites that organize and catalogue development efforts (perhaps even the same that take care of OpenSource development in other application domains). -- ------------------------------------------------------------------------------- Konrad Hinsen | E-Mail: hinsen@cnrs-orleans.fr Centre de Biophysique Moleculaire (CNRS) | Tel.: +33-2.38.25.56.24 Rue Charles Sadron | Fax: +33-2.38.63.15.17 45071 Orleans Cedex 2 | Deutsch/Esperanto/English/ France | Nederlands/Francais ------------------------------------------------------------------------------- From chemistry-request@server.ccl.net Mon Mar 19 15:04:36 2001 Received: from usc.edu (root@[128.125.253.136]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f2JK4aD20239 for ; Mon, 19 Mar 2001 15:04:36 -0500 Received: from rcf-fs.usc.edu (root@rcf-fs.usc.edu [128.125.253.166]) by usc.edu (8.9.3.1/8.9.3/usc) with ESMTP id MAA14390; Mon, 19 Mar 2001 12:04:37 -0800 (PST) Received: from usc.edu (IDENT:jorgevil@futura.usc.edu [128.125.14.59]) by rcf-fs.usc.edu (8.9.3.1/8.9.3/usc) with ESMTP id MAA02726; Mon, 19 Mar 2001 12:04:36 -0800 (PST) Sender: jorgevil@rcf-fs.usc.edu Message-ID: <3AB66654.A1AC18FD@usc.edu> Date: Mon, 19 Mar 2001 12:04:36 -0800 From: Jordi Villa To: Richard Wood CC: chemistry@ccl.net Subject: Re: CCL:experiment of H-bond strength in solution References: <20010316045354.66012.qmail@web13206.mail.yahoo.com> <3AB52348.A090BE15@usc.edu> <3AB63A68.704FA651@cornell.edu> because at the end of the original message the author asked about how to simulate them. Please, read the messages before implying anything. Richard Wood wrote: > Hi all > > I thought that the subject of this posting was the "experimental H-bond > strength in solution"? > If so, why does everyone cite theoretical papers/methods/results? > > Richard-- > Richard L. Wood, Ph. D. > Physical/Computational Chemist > Post-doctoral Associate > Cornell University, Ithaca, NY 14853 > > -= 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 -- Jordi Villa i Freixa jorgevil@usc.edu http://laetro.usc.edu/wgroup/people/jorgevil Department of Chemistry, University of Southern California Los Angeles, CA, USA, 90089-1062 Tlf: 1-(213)-740 7671 Fax: 1-(213)-740 2701 From chemistry-request@server.ccl.net Mon Mar 19 16:15:21 2001 Received: from revere3.musc.edu ([128.23.203.10]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f2JLFLD20574 for ; Mon, 19 Mar 2001 16:15:21 -0500 Received: from musc.edu ([128.23.81.55]) by revere3.musc.edu (8.8.8/8.8.8) with ESMTP id QAA00218 for ; Mon, 19 Mar 2001 16:15:22 -0500 (EST) Message-ID: <3AB67708.893ED914@musc.edu> Date: Mon, 19 Mar 2001 16:15:52 -0500 From: Ilya Vakser X-Mailer: Mozilla 4.7 [en] (Win98; I) X-Accept-Language: en,pdf MIME-Version: 1.0 To: chemistry@ccl.net Subject: Conference on Protein Interactions, June 16-19, 2001, Charleston, SC Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Conference on MODELING OF PROTEIN INTERACTIONS IN GENOMES June 16-19, 2001, Charleston, SC *** CALL FOR PAPERS *** The conference focuses on computational procedures for reconstruction and study of the network of connections between proteins in genomes. The sponsors are: the National Science Foundation, the Department of Energy, and the Medical University of South Carolina. The conference is organized by Ilya Vakser (Medical University of South Carolina) and Sandor Vajda (Boston University). PROGRAM topics: PROTEIN-PROTEIN DOCKING (structure prediction and binding simulation) ENERGETICS AND PROTEIN STRUCTURE-FUNCTION RELATIONSHIPS (energy landscapes, stability of complexes, functional assignment of protein structures, binding site prediction) PROTEIN - SMALL MOLECULE INTERACTIONS (modulation of protein interactions by small molecules, protein mimetics) INTERACTING AND NONINTERACTING PROTEINS (identification of interactions and pathways) Confirmed Speakers include: Charles Brooks, Scripps Institute Adrian Elcock, University of Iowa Mark Gerstein, Yale University Adam Godzik, Burnham Institute Christopher Hogue, Mount Sinai Hospital Toronto Barry Honig, Columbia University Joel Janin, Centre National de la Recherche Scientifique Peter Karp, SRI International Edward Marcotte, University of Texas Andrew McCammon, University of California San Diego Ruth Nussinov, National Cancer Institute Arthur Olson, Scripps Institute Harold Scheraga, Cornell University Benno Schwikowski, Institute for Systems Biology Brian Shoichet, Northwestern University Jeffrey Skolnick, Danforth Center Michael Sternberg, Imperial Cancer Research Fund Lynn Ten Eyck, San Diego Supercomputer Center Shoshana Wodak, University Libre de Bruxelles Peter Wolynes, University of California San Diego ------------- PARTICIPATION The number of participants is limited to 100. In selecting participants, the preference will be given to those who would present a poster on the subject of the conference. If you would like to attend the conference, please submit a request, by e-mail only, to Ilya Vakser (vakseri@musc.edu) or Sandor Vajda (vajda@enga.bu.edu). Include a brief (a few sentences) description of your research, your full affiliation, position (faculty, postdoc, student, etc.), address (email and regular), and the day-time phone number. If you would like to present a poster, please include a half-page abstract. The deadline for the submission of applications is April 16. We will contact you by April 23 to let you know whether your application is accepted. If your application is accepted, we will communicate with you regarding the details of registration, accommodation, and travel. The early registration fee for the participants of the conference will be $200 ($100 for postdocs and students). Limited funds are available to support the participation of postdocs and students. The postdocs and students who wish to be considered for the financial assistance, please, indicate this in your application. The assistance will be provided in the form of reimbursement of your travel expenses, after the conference. The conference will take place at the Lightsey Conference Center in the Charleston historic district. Several hotels are located in the immediate vicinity of the Lightsey Conference Center. The hotel information will be provided in April. The details of the conference can be found at the conference web site, http://reco3.musc.edu/conference , which will be regularly updated. From chemistry-request@server.ccl.net Mon Mar 19 17:07:02 2001 Received: from hermes.bmc.uu.se ([130.238.39.159]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f2JM72D20748 for ; Mon, 19 Mar 2001 17:07:02 -0500 Received: from XRAY.bmc.uu.se ([130.238.37.10]) by hermes.bmc.uu.se (Post.Office MTA v3.5.3 release 223 ID# 0-62649U1500L1000S0V35) with ESMTP id se for ; Mon, 19 Mar 2001 23:08:25 +0100 Received: from localhost (deva@localhost) by XRAY.bmc.uu.se (8.9.3/8.8.7) with ESMTP id XAA11930 for ; Mon, 19 Mar 2001 23:09:57 +0100 Date: Mon, 19 Mar 2001 23:09:57 +0100 (CET) From: Devapriya Choudhury To: chemistry@ccl.net Subject: CCL:Orthographic projections in VMD: SUMMARY In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi All, Thanks to Barry Israelevich for the quick reply. Although in Raster3D there are no explicit camera position or zoom variables. But I think I managed to do that by tweaking the global X-form matrix. Come to think of it, it would be nice if once the orthographic/perspective projections are set, the same be taken into account while generating the ray-tracer input file. Thanks once again. Devapriya Original question: > > Hi All, > When I generate a picture in VMD using the Orthographic projection mode > and subsequently render the image (Raster3D), the view seems to > automatically shift to perspective projection mode. > Does anyone know a fix ? ----Replies--------------------------------------------- (1) From: Barry Isralewitz A near-perfect way to simulate orthographic coordinates with any raytracing program (such as Raster3D) is: move the camera far back, increase the zoom appropriately. Most raytracing programs have these two paramaters early in their input files (written by VMD), so just alter the settings, then re-run the ouput file (i.e. plot.r3d) through the renderer. (2) From: Adrian E. Roitberg would love to know the answer to that one ! THe same thing happens with povray... -- _____________________________________________________ Devapriya Choudhury Office: Home: Deptt. of Molecular Biology Oskar Arpis Vag 2,2 Box 590, BMC, S75650, Uppsala S75124, Uppsala Sweden Sweden Tel: +46 18 4714523 +46 18 400314 FAX: +46 18 536971 e-mail deva@xray.bmc.uu.se _____________________________________________________ From chemistry-request@server.ccl.net Mon Mar 19 17:17:02 2001 Received: from ccl.net ([192.148.249.4]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f2JMH2D20840 for ; Mon, 19 Mar 2001 17:17:02 -0500 Received: from krakow.ccl.net (krakow.ccl.net [192.148.249.195]) by ccl.net (8.9.3/8.9.3/OSC 2.0) with ESMTP id RAA05687 for ; Mon, 19 Mar 2001 17:17:02 -0500 (EST) Date: Mon, 19 Mar 2001 17:17:02 -0500 (EST) From: Jan Labanowski To: chemistry@ccl.net Subject: Computational Chemistry Users Meeting at Pacific Northwest Nation al Laboratory (fwd) Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII The William R. Wiley Environmental Molecular Science Laboratory (EMSL) The Theory, Modeling and Simulation Directorate would like to invite you to attend a special two day Computational Chemistry Users Meeting June 18-19. This year's event will focus upon the users of the Molecular Science Software Suite (MS3) consisting of the high performance computational chemistry software, NWChem, its associated user interface, Ecce, and the underpinning set of high performance tools, ParSoft, as well as chemistry users of the Molecular Science Computing Facility. This two-day meeting will feature: * A half-day session of presentations by MS3 developers highlighting the current functionality and capabilities of the software as well as potential new capabilities, * Two half-day sessions of short talks by users of the MS3 and the MSCF computing facility describing their research and needs for new capabilities, * A half-day tutorial for people who wish to develop computational chemistry software within NWChem, * An Ecce installation tutorial, and * A Poster session The users meeting will be held at the EMSL and we will provide access to the MSCF software and hardware facilities as needed. This notice will be followed very shortly by a second announcement with links to the appropriate registration web site. Please mark your calendars and join us with presentations of your computational chemistry successes as well as identifying important future requirements. Registration for foreign nationals need to be submitted as soon as possible and no later than April 6th. Erich R. Vorpagel, Ph.D. Senior Staff Scientist MSCF Visualization and User Services Group Environmental Molecular Sciences Laboratory Pacific Northwest National Laboratory 3335 Q Ave., MS K8-91 Phone: 509-376-0751 Richland, WA 99352 FAX: 509-376-0420 Email: erich.vorpagel@pnl.gov Web: http://www.emsl.pnl.gov/pub/mscf From chemistry-request@server.ccl.net Mon Mar 19 17:28:09 2001 Received: from web12708.mail.yahoo.com ([216.136.173.245]) by server.ccl.net (8.11.0/8.11.0) with SMTP id f2JMS9D20969 for ; Mon, 19 Mar 2001 17:28:09 -0500 Message-ID: <20010319222807.54184.qmail@web12708.mail.yahoo.com> Received: from [129.105.55.29] by web12708.mail.yahoo.com; Mon, 19 Mar 2001 14:28:07 PST Date: Mon, 19 Mar 2001 14:28:07 -0800 (PST) From: water Miller Subject: Re: CCL:experiment of H-bond strength in solution To: Richard Wood , chemistry@ccl.net In-Reply-To: <3AB63A68.704FA651@cornell.edu> MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii I can imagine someone may have been sick of such discussions away from the topic, however, it's still related, and the only problem could be that the title wasn't changed... The real problem could be almost no experimental evidence available, at lease for those listers who know how to use email and are kind rnough to share their knowledge with others :-)... Water Miller >From: Richard Wood >To: chemistry@ccl.net >Subject: CCL:experiment of H-bond strength in solution >Jordi Villa wrote: >> because at the end of the original message the >>author asked about how >> to simulate them. Please, read the messages before >implying anything. >I wasn't the one doing the implying. >The following is from the ORIGINAL post. >========================================= >Dear all, >Since it's well-known that the H-bond strength will be >highly weaken in solution, compared with that in gap >phase, I am curious if there is any experimental >evidence or hint available. >========================================= >Notice the words "theoretical" or "calculated" are not >anywhere >to be seen. > >Richard -- >Richard L. Wood, Ph. D. >Physical/Computational Chemist >Post-doctoral Associate >Cornell University, Ithaca, NY 14853 --- Richard Wood wrote: > Hi all > > I thought that the subject of this posting was the > "experimental H-bond > strength in solution"? > If so, why does everyone cite theoretical > papers/methods/results? > > Richard-- > Richard L. Wood, Ph. D. > Physical/Computational Chemist > Post-doctoral Associate > Cornell University, Ithaca, NY 14853 > > > > -= 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 > > > > > __________________________________________________ Do You Yahoo!? Get email at your own domain with Yahoo! Mail. http://personal.mail.yahoo.com/ From chemistry-request@server.ccl.net Mon Mar 19 17:29:14 2001 Received: from mail.virginia.edu ([128.143.2.9]) by server.ccl.net (8.11.0/8.11.0) with SMTP id f2JMTED20981 for ; Mon, 19 Mar 2001 17:29:14 -0500 Received: from unix.mail.virginia.edu by mail.virginia.edu id aa23801; 19 Mar 2001 17:29 EST Received: from patch2 (bootp-44-24.bootp.Virginia.EDU [128.143.44.24]) by unix.mail.Virginia.EDU (8.9.3/8.9.3) with SMTP id RAA04058 for ; Mon, 19 Mar 2001 17:28:58 -0500 Message-Id: <3.0.6.32.20010319172759.0097a6c0@unix.mail.virginia.edu> X-Sender: ps2t@unix.mail.virginia.edu X-Mailer: QUALCOMM Windows Eudora Light Version 3.0.6 (32) Date: Mon, 19 Mar 2001 17:27:59 -0500 To: chemistry@ccl.net From: Pornthep Sompornpisut Subject: textbook or reference of distance geometry Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Dear Sir, Are there any good references to learn and to help in writing a program using distance geometry approach in structure calculation? Any comments are appreciated. Thank you. Thep ======================================================================= Pornthep Sompornpisut, Ph.D Postdoctoral Fellow Department of Physiology University of Virginia Tel: 804-924-5473 Fax: 804-982-1616 Email:ps2t@virginia.edu ======================================================================= From chemistry-request@server.ccl.net Mon Mar 19 18:00:19 2001 Received: from ccl.net ([192.148.249.4]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f2JN0JD21499 for ; Mon, 19 Mar 2001 18:00:19 -0500 Received: from mercury.chem.csiro.au (mercury.chem.CSIRO.AU [138.194.50.8]) by ccl.net (8.9.3/8.9.3/OSC 2.0) with ESMTP id SAA06809 for ; Mon, 19 Mar 2001 18:00:17 -0500 (EST) Received: from [138.194.46.107] (cpr-46107.chem.csiro.au [138.194.46.107]) by mercury.chem.csiro.au (8.9.3/8.9.3) with ESMTP id KAA21107; Tue, 20 Mar 2001 10:00:10 +1100 (EST) X-Sender: win097@clex1.vic.csiro.au Message-Id: Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Tue, 20 Mar 2001 10:00:08 +1100 To: CHMINF-L@LISTSERV.INDIANA.EDU, chemistry@ccl.net From: "Dr. Dave Winkler" Subject: World Chemistry Congress, July 1-6, 2001, Australia, Update Dear Colleagues, Time is running short for registration and abstract submsission for the IUPAC World Chemistry Congress. This promises to be the largest chemistry congress ever held in Australia. There is a first class program and excellent networking opportunities. W O R L D C H E M I S T R Y C O N G R E S S 1 - 6 JULY 2001, BRISBANE AUSTRALIA Dear Colleague The World Chemistry Congress takes place in Brisbane from July 1-6 2001.The Congress comprises: ... the IUPAC 38th Scientific Congress ... the 9th Asian Chemical Congress ... the Asian Federation of Medicinal Chemistry conference - AIMECS 01. All three meetings are held together in the same venue (Brisbane Convention and Exhibition centre) at the same time. We have put together an exciting program of plenary lectures and invited talks, details of which can be found on our website (http://www.ccm.com.au/wcc.). Invited speakers include several Nobel laureates. The Congress has a wide range of social events and a trade exhibition. The call for abstracts closes on March 31st, so if you are planning to attend and to give a paper, now is a good time to finalise and submit your abstract. Details of how to prepare and to submit abstracts are available on the web site. Abstracts will not be considered or published unless one of the authors is a registered delegate. The standard registration fee of $780 Australian (approx $390 USD) for members of national chemical societies applies until March 31st 2001. Student registration costs (for student members of national chemical societies) are $350 Australian ($175 USD) until March 31st. A limited number of concessional registrations ( $350 Australian) are available to delegates from emerging countries. Please see our web site (please look under the 9ACC Program button for further details of eligibility for a concessional rate). Registration rates for delegates who are not members of a national chemical society are $1040 (non-student), $470 (student, concessional) Australian respectively. All registrations include: ... access to the Congress technical sessions ... abstract booklet, ... tea/coffee and lunch each day of the scientific program, ... plus a free travel pass for travel on public transport in the Brisbane area. The registration rates for the World Chemistry Congress increase after March 31st, so if you have not yet completed registration formalities, now is a very convenient time to do so. Timely submission of your registration forms will also help us provide you with the style and quality of accommodation you request. There is exceptionally heavy demand for accommodation in Brisbane over the conference dates and we urge you to book as soon as possible. Finally we wish to advise that we have received some funding from IUPAC to provide a limited number (approx 25 each of value up to $1500 Australian) of travel grants for delegates from lower income countries who present posters. Details of this are being placed on the website right now. These delegates are also eligible for the concessional rate rather than the full rate of registration. Please note that travel grants can only be awarded to delegates who are presenting a poster at the Congress. Applicants for a travel grant should (i) return a registration form (by March 31st please) (ii) submit an abstract for a poster presentation (iii) send a very brief (max. 50 word) email to wcc2001@chemistry.uq.edu.au requesting a travel grant and providing country of residence details. The Organising Committee will select travel grantees on the basis of the submitted abstracts. Delegates selected for travel grants will be notified by email during April. We look forward to greeting you in Brisbane in July 2001. Yours sincerely Mary Garson (Executive Secretariat) Cheers, Dave Dr. David A. Winkler Email: dave.winkler@molsci.csiro.au Senior Principal Research Scientist Voice: 61-3-9545-2477 CSIRO Molecular Science Fax: 61-3-9545-2446 Private Bag 10,Clayton South MDC 3169 http://www.csiro.au Australia http://www.molsci.csiro.au For the World Chemical Congress in Brisbane, July 2001 check the details at http://www.ccm.com.au/wcc From chemistry-request@server.ccl.net Mon Mar 19 22:57:40 2001 Received: from relay.it.northwestern.edu ([129.105.16.56]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f2K3veD22639 for ; Mon, 19 Mar 2001 22:57:40 -0500 Received: (from mailnull@localhost) by relay.it.northwestern.edu (8.9.3/8.9.3) id VAA13459; Mon, 19 Mar 2001 21:57:41 -0600 (CST) Received: from [129.105.186.46] (quandong-39-186059.nuts.nwu.edu [129.105.186.59]) by relay.acns.nwu.edu via smap (V2.0) id xma013135; Mon, 19 Mar 01 21:57:10 -0600 Mime-Version: 1.0 X-Sender: hutchisn@mercury.chem.northwestern.edu Message-Id: In-Reply-To: <200103191755.SAA04714@chinon.cnrs-orleans.fr> References: <062801c0af8d$f9300fe0$b9ac323f@josiah> <200103191755.SAA04714@chinon.cnrs-orleans.fr> Date: Mon, 19 Mar 2001 19:45:33 -0600 To: Konrad Hinsen From: Geoff Hutchison Subject: Re: CCL:DCD and software reuse (was Qmol: Molecular viewer for Windows) Cc: chemistry@ccl.net Content-Type: text/plain; charset="us-ascii" ; format="flowed" At 6:55 PM +0100 3/19/01, Konrad Hinsen wrote: > > I don't know what can be done to limit this (in my mind) > > needless duplication of effort. > >If Open Source were common in computational chemistry, then probably >there would also be corresponding Web sites that organize and >catalogue development efforts (perhaps even the same that take care of >OpenSource development in other application domains). Indeed, isn't this partly the aim of the OpenScience project at openscience.org? (I will note that I am not affiliated with the group, but have encountered it using the JMol and JChemPaint programs.) And, of course, there are several chemistry-related projects hosted at places like SourceForge. I'll also echo your call for more use of open source and free licenses in academic computational chemistry. I can think of more than a few cases where code has fallen by the wayside as groups move to other projects, etc. Proper citation is still required in publications, so am I wrong in saying that an academic group loses little by releasing the source to the community? Do others have a different viewpoint? I would be glad to summarize responses to the list one way or the other. Best regards, -- -- -Geoff Hutchison Ratner/Marks Groups (847) 491-3295 Northwestern Chemistry http://www.chem.nwu.edu/ From chemistry-request@server.ccl.net Mon Mar 19 18:47:36 2001 Received: from usc.edu (root@[128.125.253.136]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f2JNlZD21725 for ; Mon, 19 Mar 2001 18:47:35 -0500 Received: from rcf-fs.usc.edu (root@rcf-fs.usc.edu [128.125.253.166]) by usc.edu (8.9.3.1/8.9.3/usc) with ESMTP id PAA24001; Mon, 19 Mar 2001 15:47:37 -0800 (PST) Received: from usc.edu (IDENT:jorgevil@futura.usc.edu [128.125.14.59]) by rcf-fs.usc.edu (8.9.3.1/8.9.3/usc) with ESMTP id PAA04815; Mon, 19 Mar 2001 15:47:35 -0800 (PST) Sender: jorgevil@rcf-fs.usc.edu Message-ID: <3AB69A98.568AAFD2@usc.edu> Date: Mon, 19 Mar 2001 15:47:36 -0800 From: Jordi Villa X-Mailer: Mozilla 4.61 [en] (X11; I; Linux 2.2.12-20 i686) X-Accept-Language: en MIME-Version: 1.0 To: Richard Wood CC: chemistry@ccl.net Subject: Re: CCL:experiment of H-bond strength in solution References: <20010316045354.66012.qmail@web13206.mail.yahoo.com> <3AB52348.A090BE15@usc.edu> <3AB63A68.704FA651@cornell.edu> <3AB66654.A1AC18FD@usc.edu> <3AB66528.8C9462DF@cornell.edu> Dear Richard, I would not like to start a non-sense discussion here, but if you look at the end of the message you quote you will see the following paragraph: > Here, I am wondering if any of you could provide me > more related reference. Also, any discussion on the > method to simulate this accurately would be highly > appreciated. I guess you did not see that part. Sorry about my message. I did not pretend to upset you and I don't think starting an argument about understanding of e-mails will be good for any of us. Apart from that, I would say that it is interesting from time to time to bring some scientific discussion to the CCL, apart from keywords problems in Gaussian and computer power of machines. That is why I liked the question from Mike Smit. Sorry if I was too long in my arguments, but sometimes I wonder if the CCL should change the name for CGL ("computer guru list"). And, please, nobody feel bad about what I say, it is just the feeling I get sometimes I open the CCL e-mails. I still consider the list a valuable source of information, but sometimes people should be more careful. Best regards to all of you and sorry for the complain, Richard Wood wrote: > Jordi Villa wrote: > > > because at the end of the original message the author asked about how > > to simulate them. Please, read the messages before implying anything. > > I wasn't the one doing the implying. > > The following is from the ORIGINAL post. > > ========================================= > Dear all, > > Since it's well-known that the H-bond strength will be > highly weaken in solution, compared with that in gap > phase, I am curious if there is any experimental > evidence or hint available. > ========================================= > > Notice the words "theoretical" or "calculated" are not anywhere > to be seen. > > Richard > > -- > Richard L. Wood, Ph. D. > Physical/Computational Chemist > Post-doctoral Associate > Cornell University, Ithaca, NY 14853 > > -= 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 -- Jordi Villa i Freixa jorgevil@usc.edu http://laetro.usc.edu/wgroup/people/jorgevil Department of Chemistry, University of Southern California Los Angeles, CA, USA, 90089-1062 Tlf: 1-(213)-740 7671 Fax: 1-(213)-740 2701 From chemistry-request@server.ccl.net Mon Mar 19 22:38:39 2001 Received: from mail.sunesis-pharma.com ([64.242.145.194]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f2K3cZD22541 for ; Mon, 19 Mar 2001 22:38:39 -0500 Received: from sunesis-pharma.com ([192.168.1.227]) by mail.sunesis-pharma.com (Netscape Messaging Server 4.15) with ESMTP id GAH8Q100.88G for ; Mon, 19 Mar 2001 19:37:13 -0800 Message-ID: <3AB6D022.319959E9@sunesis-pharma.com> Date: Mon, 19 Mar 2001 19:36:02 -0800 From: "Warren DeLano" X-Mailer: Mozilla 4.7 [en] (WinNT; I) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net Subject: Re: CCL:DCD and software reuse (was Qmol: Molecular viewer for Windows) References: <062801c0af8d$f9300fe0$b9ac323f@josiah> <200103191755.SAA04714@chinon.cnrs-orleans.fr> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Konrad Hinsen wrote: > > I don't know what can be done to limit this (in my mind) > > needless duplication of effort. > > Open Source code would be an important first step. In fact, I do not > understand why this concept isn't standard for academic applications. > Much academic code is already free, so why not take the next step and > make it freely redistributable, also in modified form? And for those > academic packages that are not free, I seriously doubt that they are > in any sense profitable. > Some academic code is very profitable. MSI and others make a living (or should I say a killing?) off of academic packages that have been commercialized. I think the critical question is whether we as computational Scientists are happy with this arrangement or whether we and our Science would benefit from more free source code written by other scientists. My guess is that the impact of significant amounts of *reusable* source-code building blocks would be profound and world changing. At the very least, competition from open-source would force commercial software developers to greatly improve the quality of their packages. I applaud the work Konrad has done in this direction with the MMTK package. My efforts to create a free professional-strength, interoperable, and open-source molecular graphics/editing system (PyMOL) reflect this shared vision. If only more scientists/developers would do likewise with their projects! After all, if you are not going to commercialize your code, then why not make it available to other scientists unconditionally? Instead of allowing your great work to languish on some back-up tape, please release it to the world and allow it to be *modified* and *redistributed*. By doing so, you will change the field irrevocably and enable the next generation of computational research tools to be built on *your* foundation. As it stands, each of us is so busy pouring foundations that we never get around to building cathedrals. Let's change that. Thanks to the internet's exceedingly low distribution costs, and the advent of modular, extensible scripting languages such as Perl and Python, you now have no excuse other than vanity for allowing your good code to remain restricted and unutilized. I propose initiating an effort to accumulate unrestricted computational chemistry source-code into a single curated distribution, probably on a SourceForge instance. This "Free Molecule Project" would require a significant number of volunteers -- so I am going to float this trail balloon: If you have interest in such a project and would consider contributing, please email me directly. Assuming there are enough interested parties, I'll set up a mailing list, and we will start a discussion about how such a project might come together. - Warren -- mailto:warren@sunesis-pharma.com Warren L. DeLano, Ph.D. Informatics Scientist Sunesis Pharmaceuticals, Inc. 3696 Haven Ave., Suite C Redwood City, CA 94063 (650)-562-3106 fax: (650)-556-8824