From chemistry-request@server.ccl.net Tue Dec 28 14:36:10 1999 Received: from aorta.physiome.com (mail.physiome.com [204.142.61.124]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id OAA29682 for ; Tue, 28 Dec 1999 14:36:09 -0500 Received: from COMPCHEM ([192.168.1.67]) by aorta.physiome.com with SMTP (Microsoft Exchange Internet Mail Service Version 5.5.2448.0) id ZJKLYJQX; Tue, 28 Dec 1999 13:31:06 -0500 Message-ID: <000e01bf5162$8e23a9d0$4301a8c0@physiome.com> From: "Roberta Susnow" To: Subject: metabolism prediction Date: Tue, 28 Dec 1999 13:37:12 -0500 MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_000B_01BF5138.A542F370" 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 This is a multi-part message in MIME format. ------=_NextPart_000_000B_01BF5138.A542F370 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Hi, I would like to find out what software is available for the = prediction of metabolites from a parent compound. I am also interested in the = associated toxicology prediction. Please send the response directly to me and I = will post them on the list. Thank you. Roberta Susnow, PhD Physiome Sciences rsusnow@physiome.com ------=_NextPart_000_000B_01BF5138.A542F370 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable

Hi,

I would like to find out what software is = available=20 for the prediction of

metabolites from a parent compound. I am also interested in the=20 associated

toxicology prediction. Please send the response directly to me and = I will=20 post them

on the list. Thank you.

Roberta Susnow, PhD

Physiome Sciences

rsusnow@physiome.com

------=_NextPart_000_000B_01BF5138.A542F370-- From chemistry-request@server.ccl.net Wed Dec 29 05:38:35 1999 Received: from sunu450.rz.ruhr-uni-bochum.de (sunu450.rz.ruhr-uni-bochum.de [134.147.64.5]) by server.ccl.net (8.8.7/8.8.7) with SMTP id FAA00968 for ; Wed, 29 Dec 1999 05:38:35 -0500 From: Christoph.van.Wuellen@ruhr-uni-bochum.de Received: (qmail 12774 invoked from network); 29 Dec 1999 09:31:44 -0000 Received: from sgi249.rz.ruhr-uni-bochum.de (134.147.64.2) by mailhost.rz.ruhr-uni-bochum.de with SMTP; 29 Dec 1999 09:31:44 -0000 Received: (qmail 27261 invoked by uid 10283); 29 Dec 1999 09:31:43 -0000 Message-ID: <19991229093143.27260.qmail@sgi249.rz.ruhr-uni-bochum.de> Subject: What exactly is LINDA To: chemistry@ccl.net Date: Wed, 29 Dec 1999 10:31:43 +0100 (MET) X-Mailer: ELM [version 2.4 PL24] MIME-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit What (exactly) is LINDA? Is it (merely) a message-passing library a la PVM or MPI with a user-interface simulating a virtual shared memory? What are you really paying for if you buy LINDA? LINDA is known to me only in the context of parallel GAUSSIAN, so what is the advantage of LINDA over PVM or MPI or other portable and more-or-less standardized message passing systems? -- Does the combination GAUSSIN/LINDA beat alternative implementations (e.g. with PVM) in terms of speed or ease-of-use? ---------------------------+------------------------------------------------ Christoph van Wullen | Fon (University): +49 234 32 26485 Theoretical Chemistry | Fax (University): +49 234 32 14109 Ruhr-Universitaet | Fon/Fax (private): +49 234 33 22 75 D-44780 Bochum, Germany | eMail: Christoph.van.Wuellen@Ruhr-Uni-Bochum.de ---------------------------+------------------------------------------------ From chemistry-request@server.ccl.net Wed Dec 29 08:21:01 1999 Received: from sunu450.rz.ruhr-uni-bochum.de (sunu450.rz.ruhr-uni-bochum.de [134.147.64.5]) by server.ccl.net (8.8.7/8.8.7) with SMTP id IAA02485 for ; Wed, 29 Dec 1999 08:21:00 -0500 From: Christoph.van.Wuellen@ruhr-uni-bochum.de Received: (qmail 10388 invoked from network); 29 Dec 1999 12:14:08 -0000 Received: from sgi249.rz.ruhr-uni-bochum.de (134.147.64.2) by mailhost.rz.ruhr-uni-bochum.de with SMTP; 29 Dec 1999 12:14:08 -0000 Received: (qmail 4105 invoked by uid 10283); 29 Dec 1999 12:14:07 -0000 Message-ID: <19991229121407.4104.qmail@sgi249.rz.ruhr-uni-bochum.de> Subject: Re: CCL:**** Fatal Problem: The largest alpha MO coeffient is 0.12116834D+04 To: dr.keung-lau@graduate.hku.hk (Keung Lau) Date: Wed, 29 Dec 1999 13:14:07 +0100 (MET) Cc: chemistry@ccl.net In-Reply-To: <38683930.CD588E0F@graduate.hku.hk> from "Keung Lau" at Dec 28, 99 12:14:40 pm X-Mailer: ELM [version 2.4 PL24] MIME-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Such large MO coefficients can only arise if the overlap matrix has a very small eigenvalue. Perhaps something went wrong with the basis input? ---------------------------+------------------------------------------------ Christoph van Wullen | Fon (University): +49 234 32 26485 Theoretical Chemistry | Fax (University): +49 234 32 14109 Ruhr-Universitaet | Fon/Fax (private): +49 234 33 22 75 D-44780 Bochum, Germany | eMail: Christoph.van.Wuellen@Ruhr-Uni-Bochum.de ---------------------------+------------------------------------------------ From chemistry-request@server.ccl.net Wed Dec 29 10:57:44 1999 Received: from email.nist.gov (email.nist.gov [129.6.2.7]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id KAA03063 for ; Wed, 29 Dec 1999 10:57:44 -0500 Received: from bratsche (bratsche.nist.gov [129.6.194.154]) by email.nist.gov (8.9.3/8.9.3) with SMTP id JAA19005 for ; Wed, 29 Dec 1999 09:51:26 -0500 (EST) Message-Id: <4.1.19991229085122.00ba3100@mailserver3.nist.gov> X-Sender: irikura@mailserver3.nist.gov X-Mailer: QUALCOMM Windows Eudora Pro Version 4.1 Date: Wed, 29 Dec 1999 08:57:39 -0500 To: chemistry@ccl.net From: Karl Irikura Subject: Re: CCL:**** Fatal Problem: The largest alpha MO coeffient is 0.12116834D+04 In-Reply-To: <38683930.CD588E0F@graduate.hku.hk> Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Do you have diffuse functions in your basis set? With the small C-C distances in your molecule, diffuse functions may give linear-dependence problems in the basis set. Try deleting the most diffuse function from each C atom, or try a code that will delete functions automatically (e.g., Gaussian98, ACES II). I hope this helps--good luck! Karl I. At 12:14 PM 12/28/1999 +0800, you wrote: >Dear netters, > > When I used g94 to perform a mp2 optimization on the molecule: >1,3-buta-diyne. I got the error message shown in the title. > Similarly, when I performed a CIS calculation on the same molecule, a >similar error result. > Any help and advice will be highly appreciated. > Thanks in advance. > > >Best Regards, > > >-= 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. Karl K. Irikura National Institute of Standards and Technology 100 Bureau Drive, Stop 8380 Gaithersburg, MD 20899-8380 voice: 301-975-2510 fax: 301-869-4020 e-mail: karl.irikura@nist.gov http://www.nist.gov/compchem/ ---------------------------------------------- From chemistry-request@server.ccl.net Wed Dec 29 18:38:15 1999 Received: from ganymede.or.intel.com (ganymede.or.intel.com [134.134.248.3]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id SAA05797 for ; Wed, 29 Dec 1999 18:38:15 -0500 Received: from SMTP (orsmsxvs02-1.jf.intel.com [192.168.65.201]) by ganymede.or.intel.com (8.9.1a+p1/8.9.1/d: relay.m4,v 1.11 1999/11/10 17:27:15 spurcell Exp $) with SMTP id OAA09084; Wed, 29 Dec 1999 14:30:59 -0800 (PST) Received: from orsmsx29.jf.intel.com ([192.168.70.29]) by 192.168.70.201 (Norton AntiVirus for Internet Email Gateways 1.0) ; Wed, 29 Dec 1999 22:30:59 0000 (GMT) Received: by orsmsx29.jf.intel.com with Internet Mail Service (5.5.2448.0) id ; Wed, 29 Dec 1999 14:30:57 -0800 Message-ID: From: "Mattson, Timothy G" To: "'Christoph.van.Wuellen@ruhr-uni-bochum.de'" , chemistry@ccl.net Subject: RE: What exactly is LINDA Date: Wed, 29 Dec 1999 14:30:56 -0800 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2448.0) Content-Type: text/plain; charset="ISO-8859-1" Linda is NOT just another message passing programming environment. Linda is a coordination language for parallel programming. It is based on the generative communication model proposed by David Gelernter and first implemented by Nick Carriero -- both of Yale University. It is (in my only slightly biased opinion) one of the most elegant and effetive parallel programming models available. With Linda, processes interacts through 6 operations that write and read a virtual shared memory called a tuple space. These 6 operations are added to a standard sequential programming language (C and Fortran --- I don't know if they've got C++ done yet) to give you one of the simplest parallel programming environments you can find. How about efficiency? Well, using very clever compile time analysis (fully described in Nick Carriero's Ph.D. dissertation and partially described in one of my Linda papers -- "The efficiency of Linda for general purpose Scientific Computing", Scientific Programming, vol 3, p. 61 (1994)) the overhead due to management of the tuple space is largely eliminated. The result is that for many applications, Linda performs as well as MPI or PVM. So to the programmer, Linda can be a God-send. To the user of a parallel program written by someone else, however, it doesn't make any significant difference if a program was parallelized with Linda, PVM or MPI. Its pretty much all the same. If you have further questions (or better yet, disagreements --- I love contorversy), feel free to email me. --Tim Mattson P.S. In the spirit of full disclosure, I used to work with Scientific Computing Associates. I left just as the Gaussian project was getting off the ground. P.P.S. Of course, these opinions are my own and in now way reflect the view of my current employer. -----Original Message----- From: Christoph.van.Wuellen@ruhr-uni-bochum.de [mailto:Christoph.van.Wuellen@ruhr-uni-bochum.de] Sent: Wednesday, December 29, 1999 1:32 AM To: chemistry@ccl.net Subject: CCL:What exactly is LINDA What (exactly) is LINDA? Is it (merely) a message-passing library a la PVM or MPI with a user-interface simulating a virtual shared memory? What are you really paying for if you buy LINDA? LINDA is known to me only in the context of parallel GAUSSIAN, so what is the advantage of LINDA over PVM or MPI or other portable and more-or-less standardized message passing systems? -- Does the combination GAUSSIN/LINDA beat alternative implementations (e.g. with PVM) in terms of speed or ease-of-use? ---------------------------+------------------------------------------------ Christoph van Wullen | Fon (University): +49 234 32 26485 Theoretical Chemistry | Fax (University): +49 234 32 14109 Ruhr-Universitaet | Fon/Fax (private): +49 234 33 22 75 D-44780 Bochum, Germany | eMail: Christoph.van.Wuellen@Ruhr-Uni-Bochum.de ---------------------------+------------------------------------------------ -= 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 Wed Dec 29 17:34:00 1999 Received: from aorta.physiome.com (mail.physiome.com [204.142.61.124]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id RAA04968 for ; Wed, 29 Dec 1999 17:33:59 -0500 Received: from COMPCHEM ([192.168.1.67]) by aorta.physiome.com with SMTP (Microsoft Exchange Internet Mail Service Version 5.5.2448.0) id ZJKLYJ9C; Wed, 29 Dec 1999 16:28:38 -0500 Message-ID: <001001bf5244$89b4bb40$4301a8c0@physiome.com> From: "Roberta Susnow" To: Subject: Fw: CCL:metabolism prediction Date: Wed, 29 Dec 1999 16:34:51 -0500 ----- Original Message ----- From: Carlos Faerman To: Roberta Susnow Sent: Wednesday, December 29, 1999 9:43 AM Subject: Re: CCL:metabolism prediction Hello Roberta, two databases from MDL provide some information about metabolites: 1) METABOLITE database This database contains bibliographic references to all the known metabolites known from a specific molecule. It allows you to input the 2D structure of your 'parent' molecule and search for known metabolites of your parent structure (if any). 2) TOXICOLOGY database This contains tox data once again will allow to input your 2D structure and search for known data (which is stored in this database). MDL has already linked these two databases. You can effortlessly switch from database 1) to 2) and vice versa. You should contact your MDL sales rep in your area. Both databases assume that you already have ISIS/Base & ISIS/Draw. http://www.mdli.com I hope this helps Carlos -----Original Message----- From: Roberta Susnow To: chemistry@ccl.net Date: Wednesday, December 29, 1999 8:10 AM Subject: CCL:metabolism prediction Hi, I would like to find out what software is available for the prediction of metabolites from a parent compound. I am also interested in the associated toxicology prediction. Please send the response directly to me and I will post them on the list. Thank you. Roberta Susnow, PhD Physiome Sciences rsusnow@physiome.com From chemistry-request@server.ccl.net Wed Dec 29 21:39:08 1999 Received: from shell.monmouth.com (shell.monmouth.com [209.191.58.1]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id VAA06886 for ; Wed, 29 Dec 1999 21:39:07 -0500 Received: from monmouth.com (sl-max-ppp63.monmouth.com [209.191.21.65]) by shell.monmouth.com (8.9.3/8.9.3) with ESMTP id UAA11910 for ; Wed, 29 Dec 1999 20:31:51 -0500 (EST) Message-ID: <386AB619.C2418252@monmouth.com> Date: Wed, 29 Dec 1999 20:32:09 -0500 From: ASG Organization: self-organized assembly X-Mailer: Mozilla 4.04 [en] (WinNT; U) MIME-Version: 1.0 To: chemistry@ccl.net Subject: high-quality GAMESS-US basis set for iodine? Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Having reviewed past CCL messages on the subject, I'm aware of the fact that the question has been asked before--but no good answer to be found... Is it possible that there are none available? The oft-cited PNL site offers a bunch of basis sets for iodine: STO-3G 3-21G MIDI! WTBS Sadlej pVTZ LANL2DZ ECP SBKJC VDZ ECP CRENBL ECP Stuttgart RLC ECP DZVP (DFT Orbital) DeMon Coulomb Fitting DGauss A1 DFT Coulomb Fitting DGauss A1 DFT Exchange Fitting Ahlrichs Coulomb Fitting Huzinaga Polarization but, at least to my untrained eye, none of them seem to be of high quality, esp. if an all-electron basis set ready-made for use in GAMESS-US is sought. The Sadlej pTZV set is not well optimized, at least based on my reading of the attached comments. I don't want to (or can't) use ECP and DFT bases, don't know anything about the last two. Why the problem? Somebody was asking why [ICl2]- is linear, and I tried to use the GAMESS-US/MolDen duo to take a look at the orbitals, bonds etc., and noticed that the bond length at the 3-21G(d) level is wrong by 0.07 A. And then started looking for a better basis set, and...couldn't find it. I realize the general picture at the HF/3-21G(d) level should be correct, but I'd love to have something closer to 6-311+G(d) basis--or better. What do the professionals use to get good geometries and energies of iodine compounds, even as simple as HI? How much better can MIDI! be than 3-21G* in this situation? Is my aversion to ECP justified? I appreciate any comments. I should note that doing such calculations are just a hobby to me to better understand the compounds I'm working with in an otherwise very practical millieu... Happy Y2K to everybody! Tony Gozdz agozdz@monmouth.com