From chemistry-request@server.ccl.net Sun Oct 29 21:15:25 2000 Received: from web1702.mail.yahoo.com (web1702.mail.yahoo.com [128.11.23.213]) by server.ccl.net (8.8.7/8.8.7) with SMTP id VAA10322 for ; Sun, 29 Oct 2000 21:15:24 -0500 Message-ID: <20001030021521.16650.qmail@web1702.mail.yahoo.com> Received: from [161.142.4.9] by web1702.mail.yahoo.com; Sun, 29 Oct 2000 18:15:21 PST Date: Sun, 29 Oct 2000 18:15:21 -0800 (PST) From: sohail qamar Subject: hi! To: chemistry@ccl.net MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Dear friends, "An enzyme A converts a drug B into its activated form which then binds with another target enzyme AA" If u know any programme that can help in generating the activated form of drug B .Please inform me. sohail university sains malaysia. __________________________________________________ Do You Yahoo!? Yahoo! Messenger - Talk while you surf! It's FREE. http://im.yahoo.com/ From chemistry-request@server.ccl.net Mon Oct 30 03:03:32 2000 Received: from resu1.ulb.ac.be (resu1.ulb.ac.be [164.15.59.200]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id DAA11628 for ; Mon, 30 Oct 2000 03:03:31 -0500 Received: from ucmb.ulb.ac.be (ucmbsun0.ulb.ac.be [164.15.61.1]) by resu1.ulb.ac.be (8.8.8/3.17.0.ap (resu)) id JAA16650; Mon, 30 Oct 2000 09:01:16 +0100 (MET) for Received: from localhost (leonardo@localhost) by ucmb.ulb.ac.be (8.9.3+Sun/8.9.1) with ESMTP id JAA20142 for ; Mon, 30 Oct 2000 09:03:23 +0100 (MET) Date: Mon, 30 Oct 2000 09:03:23 +0100 (MET) From: Leonardo De Maria X-Sender: leonardo@bouts.ulb.ac.be To: CHEMISTRY@ccl.net Subject: Apollo project & new science and technology Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hello, I have a question for the list. Is there anyone aware of any scientific and/or technological discovery that can be attributed to the Apollo project? For example, in material science, was there any development of new materials associated with the project? In chemistry? What did we learn from the rocks brought from the moon? I'll summarize the answers. Thanks a lot in advance, Leonardo +-------------------------------------------------------+ | Leonardo De Maria, Ph.D. | | Service de Conformation de Macromolecules Biologiques | | et de Bioinformatique | ! Universite Libre de Bruxelles | | Av. F.D. Roosevelt 50 - CP160/16 | | B-1050 Bruxelles | | Tel: 0032 2 6485200 - FAX 0032 2 6488954 | | e-mail: leonardo@ucmb.ulb.ac.be | | | | On leave of absence from Centro Internacional de | | Fisica, Bogota-COLOMBIA | +-------------------------------------------------------+ From chemistry-request@server.ccl.net Mon Oct 30 03:28:55 2000 Received: from yangtze.hku.hk (root@yangtze.hku.hk [147.8.148.244]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id DAA11705 for ; Mon, 30 Oct 2000 03:28:49 -0500 Received: from localhost (andy@localhost) by yangtze.hku.hk (8.9.3/8.9.3) with ESMTP id QAA29922 for ; Mon, 30 Oct 2000 16:33:48 +0800 Date: Mon, 30 Oct 2000 16:33:47 +0800 (HKT) From: Ng Man Fai To: CHEMISTRY@ccl.net Subject: Mg parameter, Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hello, I am looking for the zindo/s parameters for Mg. And which parameters of C, N, O, H and Mg are good for indo/s calculation at TDHF level of theory? Thank you, Andy From chemistry-request@server.ccl.net Mon Oct 30 08:54:25 2000 Received: from mail.univ-reims.fr (mail.univ-reims.fr [193.50.208.6]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id IAA13934 for ; Mon, 30 Oct 2000 08:54:24 -0500 Received: from univ-reims.fr (IDENT:henon@[193.50.208.246]) by mail.univ-reims.fr (8.9.3/8.9.3) with ESMTP id OAA03701 for ; Mon, 30 Oct 2000 14:51:39 +0100 (MET) Sender: henon@mail.univ-reims.fr Message-ID: <39FD8851.23C2D234@univ-reims.fr> Date: Mon, 30 Oct 2000 14:40:17 +0000 From: Eric HENON To: CHEMISTRY@ccl.net Subject: Xeon vs Power3-II RS6000 benchmark Hello, We have a plan to get a workstation with 4 processors to do some ab initio calculations (g98, Molcas). The "Linux/xeon" platform seems to be an interesting alternative but, unfortunately, we have not found recent benchmarks for current xeon. Thus, I would be grateful if anyone could share his/her experience concerning the performance of Linux/current Xeon-PIII vs Power 3-II (IBM RS6000). Thank you in advance. E. Henon -- ---------------------------------------------------------- Eric HENON - Maitre de Conférences Groupe de Spectrometrie Moleculaire et Atmospherique (GSMA) Equipe Associee au CNRS ESA 6089 UFR Sciences Exactes et Naturelles B.P. 1039 51687 REIMS Cedex 2 Tel : 03 26 91 33 66 email: eric.henon@univ-reims.fr ---------------------------------------------------------- From chemistry-request@server.ccl.net Mon Oct 30 11:38:52 2000 Received: from uucphost.mcs.net (Kitten2.mcs.com [192.160.127.90]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id LAA14813 for ; Mon, 30 Oct 2000 11:38:52 -0500 Received: from becky (P31-Chi-Dial-17.pool.mcs.net [205.253.228.31]) by uucphost.mcs.net (8.9.3/8.9.3) with SMTP id KAA52852; Mon, 30 Oct 2000 10:38:34 -0600 (CST) (envelope-from rone@mcs.net) Message-ID: <000b01c04358$edc5cc40$1fe4fdcd@becky> From: "Rebecca Rone" To: "Guosheng Wu" , "ccl" References: Subject: Re: CCL:Help on force field for simplified "atoms" Date: Tue, 31 Oct 2000 10:36:45 -0600 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 5.00.2919.6700 X-MimeOLE: Produced By Microsoft MimeOLE V5.00.2919.6700 Dear Guosheng, Your approach will probably not work in most cases. The C6H6 group needs to be able to stack in order to create correct interactions. There are several examples of this in the literature on x-ray structures. The most famous is the herringbone arrangement of benzene and there are several similar interactions for drugs with proteins. I cannot recommend this approach. Please see the Momany & Rone paper on force field development : "Validation of the General Purpose QUANTA 3.2/CHARMm Force Field," J. Comp. Chem. 13 (7), 888-900 (1992). Also check the MSI web site for other related information. This forcefield is currently in use for QUANTA and their CNX product. Friends inform me that it currently provides extensive coverage for drugs interacting with proteins. Becky Dr. Rebecca Rone Rone Biotechnology Consulting 773-646-2585 Chicago, IL. Boston, MA. ----- Original Message ----- From: "Guosheng Wu" To: "ccl" Sent: Monday, October 23, 2000 4:16 PM Subject: CCL:Help on force field for simplified "atoms" > Dear folks, > > Does any of you have the experience on developing force field for > simplified "atoms"? > > I know there are some papers related with simplified "atom" for CH2 > or CH3, but how about biger molecules? > > For example, if I want to get a simple function V(R) for the interction > between C6H6 and C6H6, I may either summarize the LJ(rij) interctions > between all of atoms(i in one molecule and j in the other one), or I can > do ab initio calculations for different intermolecular distances(R). By > both methods I may be able to fit the results into a simple function, say > still in LJ(R) form. However, sometimes this mayn't work, or very > time-consuming for big molecules. > > If anyone could give me some suggestions or related reference, I will be > very grateful. > > Thanks a lot! > > Guosheng Wu > -------------------------------------------- > Guosheng Wu > Dept. of Chem., Northwestern Univ. > 2145 Sheridan Road, Evanston, IL, 60208-3113 > -------------------------------------------- > > > -= 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 Oct 30 13:10:36 2000 Received: from arrhenius.che.chalmers.se (arrhenius.che.chalmers.se [129.16.90.200]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id NAA15414 for ; Mon, 30 Oct 2000 13:10:34 -0500 Received: from localhost (svedung@localhost) by arrhenius.che.chalmers.se (8.9.3/8.9.3) with ESMTP id TAA360754; Mon, 30 Oct 2000 19:12:13 +0100 (MET) Date: Mon, 30 Oct 2000 19:12:12 +0100 From: Harald Svedung To: Rebecca Rone cc: Guosheng Wu , ccl Subject: Re: CCL:Help on force field for simplified "atoms" In-Reply-To: <000b01c04358$edc5cc40$1fe4fdcd@becky> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi, I think this question i very interesting. Indeed there is a need for simple "V(R)-functions" in various contexts. (is there not?... tell me.) The problem with C6H6 and pairwise atom-atom interactions is that the C6H6 molecule shows some quite "non-atomic" or "molecular" qualities (aromatic interaction, anisotropic polarizabilities etc). Theese features are averaged out only at large distances using any atomic potential. Atom-atom LJ(rij) contributions can be taken from the literature as a first-aid in building a potential function. These parameters are not able to represent (in general) the specific qualities of, e.g., C6H6. LJ(12-6) potentials often over-estimate the repulsive hardness of the atom-atom interactions and there is no explicit treatment of the electrostatics. Therefore the mapping of ab-initio potential energy to such a potential must be done with care taken to the energies of interest and also to the angle of approach. Maby a single center angular dependent Buckingham-type (exp-6) potential would do as a first approximation, perhaps with the hydrogens interacting explicitly (...any other suggestions) all yours :-) /Harald On Tue, 31 Oct 2000, Rebecca Rone wrote: > Dear Guosheng, > > Your approach will probably not work in most cases. The C6H6 group needs to > be able to stack in order to create correct interactions. There are several > examples of this in the literature on x-ray structures. The most famous is > the herringbone arrangement of benzene and there are several similar > interactions for drugs with proteins. I cannot recommend this approach. > Please see the Momany & Rone paper on force field development : > > "Validation of the General Purpose QUANTA 3.2/CHARMm Force Field," J. Comp. > Chem. 13 (7), 888-900 (1992). > > Also check the MSI web site for other related information. This forcefield > is currently in use for QUANTA and their CNX product. Friends inform me that > it currently provides extensive coverage for drugs interacting with > proteins. > > Becky > Dr. Rebecca Rone > Rone Biotechnology Consulting > 773-646-2585 > Chicago, IL. > Boston, MA. > > ----- Original Message ----- > From: "Guosheng Wu" > To: "ccl" > Sent: Monday, October 23, 2000 4:16 PM > Subject: CCL:Help on force field for simplified "atoms" > > > > Dear folks, > > > > Does any of you have the experience on developing force field for > > simplified "atoms"? > > > > I know there are some papers related with simplified "atom" for CH2 > > or CH3, but how about biger molecules? > > > > For example, if I want to get a simple function V(R) for the interction > > between C6H6 and C6H6, I may either summarize the LJ(rij) interctions > > between all of atoms(i in one molecule and j in the other one), or I can > > do ab initio calculations for different intermolecular distances(R). By > > both methods I may be able to fit the results into a simple function, say > > still in LJ(R) form. However, sometimes this mayn't work, or very > > time-consuming for big molecules. > > > > If anyone could give me some suggestions or related reference, I will be > > very grateful. > > > > Thanks a lot! > > > > Guosheng Wu > > -------------------------------------------- > > Guosheng Wu > > Dept. of Chem., Northwestern Univ. > > 2145 Sheridan Road, Evanston, IL, 60208-3113 > > -------------------------------------------- > > > > > > CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To > Admins > > 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 > > > > > > > > > > > > > > > > -= 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 Oct 30 10:17:57 2000 Received: from vytautas.vdu.lt (mail@vytautas.vdu.lt [193.219.38.33]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id KAA14472 for ; Mon, 30 Oct 2000 10:16:17 -0500 Received: from vaidila.vdu.lt ([193.219.38.52] ident=root) by vytautas.vdu.lt with esmtp id 13qGfB-0003O9-00; Mon, 30 Oct 2000 17:15:53 +0200 Received: from vaidila.vdu.lt (vejas.vdu.lt [193.219.38.82]) by vaidila.vdu.lt (8.9.3/8.9.3) with ESMTP id RAA02714; Mon, 30 Oct 2000 17:15:53 +0200 (GMT) Message-ID: <39FD741A.1DDE1D56@vaidila.vdu.lt> Date: Mon, 30 Oct 2000 05:14:02 -0800 From: "art'" X-Mailer: Mozilla 4.7 [en] (Win98; I) X-Accept-Language: en MIME-Version: 1.0 To: Eric HENON CC: CHEMISTRY@ccl.net Subject: Re: CCL:Xeon vs Power3-II RS6000 benchmark References: <39FD8851.23C2D234@univ-reims.fr> Content-Type: text/plain; charset=koi8-r X-MIME-Autoconverted: from 8bit to quoted-printable by vaidila.vdu.lt id RAA02714 Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id KAA14516 Hi, Xeon .... I dont know. It would be better Athlon, in my mind. It runs Linux also, but has better performance and is cheaper. But consider other answers. A.Ziemys Eric HENON wrote: > Hello, > > We have a plan to get a workstation with 4 processors to do > some ab initio calculations (g98, Molcas). The "Linux/xeon" platform > seems to be an interesting alternative but, unfortunately, we have not > found recent benchmarks for current xeon. > > Thus, I would be grateful if anyone could share his/her > experience concerning the performance of Linux/current Xeon-PIII vs > Power 3-II (IBM RS6000). > > Thank you in advance. > > E. Henon > -- ---------------------------------------------------------- > Eric HENON - Maitre de Conférences > Groupe de Spectrometrie Moleculaire et Atmospherique (GSMA) > Equipe Associee au CNRS ESA 6089 > UFR Sciences Exactes et Naturelles B.P. 1039 > 51687 REIMS Cedex 2 > Tel : 03 26 91 33 66 > email: eric.henon@univ-reims.fr > ---------------------------------------------------------- > > -= 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 Oct 30 13:21:13 2000 Received: from mailhost.msi.com (fire.msi.com [146.202.0.242]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id NAA15533 for ; Mon, 30 Oct 2000 13:21:13 -0500 Received: (from daemon@localhost) by mailhost.msi.com (980427.SGI.8.8.8/970903.SGI.AUTOCF) id KAA03505 for ; Mon, 30 Oct 2000 10:20:38 -0800 (PST) Received: from jnauss-pc.msi.com(146.202.26.50) by mailhost.msi.com via smap (V2.0) id xmac03468; Mon, 30 Oct 00 10:20:20 -0800 Message-Id: <4.3.2.7.0.20001030095335.00b27cb0@146.202.6.217> X-Sender: jnauss@146.202.6.217 X-Mailer: QUALCOMM Windows Eudora Version 4.3.2 Date: Mon, 30 Oct 2000 09:54:32 -0500 To: chemistry@ccl.net From: Jeff Nauss Subject: MSI Workshops on InsightII in San Diego Mime-Version: 1.0 Content-Type: multipart/alternative; boundary="=====================_323659657==_.ALT" --=====================_323659657==_.ALT Content-Type: text/plain; charset="us-ascii"; format=flowed Molecular Simulations Inc. will be holding a pair of 2-day workshops at the San Diego Supercomputer Center, La Jolla, CA, in December. On December 5-6, the workshop "Introduction to Life Science Modeling with InsightII" will be offered. This course provides an overview of molecular modeling techniques for life sciences applications in the InsightII graphical user environment. Prior modeling experience is not assumed making this course a great place to start molecular modeling. On December 7-8, the "Homology-Based Protein Design" training will be offered. This workshop is relevant to any of our customers who are interested in predicting protein structure and who would like to make more effective use of modeling in their work. During the two-day workshop, the process of producing a three-dimensional model from an amino acid sequence will be covered step-by-step. Both manual and automatic methodologies will be discussed. Prerequisites for this course are the "Introduction to Life Science Modeling with InsightII" workshop or extensive experience with InsightII. Fees for each 2-day course are $1000 commercial, $500 government, and $400 academic. However, register for both courses and receive a 25% discount for the second course. Further detailed information about this and other MSI training workshops, as well as on-line course registration, can be found at MSI's website (http://www.msi.com/about/events/training). Please do not hesitate to contact us should you have any questions. Thank you very much. Jeffrey L. Nauss 858-799-5555 Chris Arzt 858-799-5340 -- Jeffrey L. Nauss, PhD Phone: (858) 799-5555 Customer Training Programs Fax: (858) 458-0136 Molecular Simulations Inc. E-mail: jnauss@msi.com 9685 Scranton Road http://www.msi.com/about/events/training San Diego, CA 92121-3752 --=====================_323659657==_.ALT Content-Type: text/html; charset="us-ascii" Molecular Simulations Inc. will be holding a pair of 2-day workshops at the San Diego Supercomputer Center, La Jolla, CA, in December.

On December 5-6, the workshop "Introduction to Life Science Modeling with InsightII" will be offered.  This course provides an overview of molecular modeling techniques for life sciences applications in the InsightII graphical user environment.  Prior modeling experience is not assumed making this course a great place to start molecular modeling.

On December 7-8, the "Homology-Based Protein Design" training will be offered. This workshop is relevant to any of our customers who are interested in predicting protein structure and who would like to make more effective use of modeling in their work. During the two-day workshop, the process of producing a three-dimensional model from an amino acid sequence will be covered step-by-step.  Both manual and automatic methodologies will be discussed.  Prerequisites for this course are the "Introduction to Life Science Modeling with InsightII" workshop or extensive experience with InsightII.

Fees for each 2-day course are $1000 commercial, $500 government, and $400 academic.  However, register for both courses and receive a 25% discount for the second course.

Further detailed information about this and other MSI training workshops, as well as on-line course registration, can be found at MSI's website (http://www.msi.com/about/events/training).  Please do not hesitate to contact us should you have any questions.

Thank you very much.

                                Jeffrey L. Nauss
                                858-799-5555
        Chris Arzt
                                858-799-5340






--
Jeffrey L. Nauss, PhD           Phone: (858) 799-5555
Customer Training Programs      Fax: (858) 458-0136
Molecular Simulations Inc.      E-mail: jnauss@msi.com
9685 Scranton Road              http://www.msi.com/about/events/training
San Diego, CA 92121-3752
--=====================_323659657==_.ALT-- From chemistry-request@server.ccl.net Mon Oct 30 15:36:01 2000 Received: from mailcity.com (fes-qout.whowhere.com [209.185.123.96]) by server.ccl.net (8.8.7/8.8.7) with SMTP id PAA17145 for ; Mon, 30 Oct 2000 15:36:01 -0500 Received: from Unknown/Local ([?.?.?.?]) by mailcity.com; Mon Oct 30 12:34:54 2000 To: chemistry@ccl.net Date: Mon, 30 Oct 2000 15:34:54 -0500 From: "Sam Andersen" Message-ID: Mime-Version: 1.0 X-Sent-Mail: on Reply-To: sam_ccl@lycos.com X-Mailer: MailCity Service Subject: protein-protein docking X-Sender-Ip: 152.2.48.28 Organization: Lycos Communications (http://comm.lycos.com:80) Content-Type: text/plain; charset=us-ascii Content-Language: en Content-Transfer-Encoding: 7bit Hi all, I am interested in docking two large globular proteins (about 300 residues each). I know experimental studies that point out few sites in either protein domains that "might" be involved in protein-protein interactions. Is there any reliable method that returns reasonable docked models? I guess DOCK4.0/autodock might be good for small ligand-receptor interactions. Experience of people with systems of my interest may kindly share their ideas. Thanks Sam Get FREE Email/Voicemail with 15MB at Lycos Communications at http://comm.lycos.com From chemistry-request@server.ccl.net Mon Oct 30 16:04:25 2000 Received: from chemik.chem.univ.gda.pl (chemik.chem.univ.gda.pl [153.19.29.1]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id QAA17601 for ; Mon, 30 Oct 2000 16:04:23 -0500 Received: from localhost (stan@localhost) by chemik.chem.univ.gda.pl (8.9.3+Sun/8.9.1) with SMTP id WAA11947; Mon, 30 Oct 2000 22:00:44 +0100 (MET) Date: Mon, 30 Oct 2000 22:00:44 +0100 (MET) From: "Stanislaw Oldziej (Wizytator Nowej Francji)" To: Eric HENON cc: CHEMISTRY@ccl.net Subject: Re: CCL:Xeon vs Power3-II RS6000 benchmark In-Reply-To: <39FD8851.23C2D234@univ-reims.fr> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from QUOTED-PRINTABLE to 8bit by server.ccl.net id QAA17602 Hi all, As usual all is about $$$$$. First of all the g98 is not very well scalable on the multiprocesor machines in my opinion is better (and cheaper) to buy four machines (1CPU) than one 4xCPUs. I'm not using g98 however and I do not have acess to Power-3-II IBM machine but, I have some benchmark for GAMESS on PC-like processors (single point MP2 energy calculations), the results are below (time in seconds): DURON 600MHz - 1227.9 K-7 ATHLON 600MHz - 1093.0 PIII CELERON 433MHz - 2029.2 (app 600Mhz 1462.1) PIII 650MHz - 1195.0 (app 600MHz 1294.2) PIII XEON 700Mhz/1MB Cache - 1081.1 (app 600MHz 1261.1) I do not have access to the T-Bird AMD but I'm sure that T-Bird AMD will be the best. The second point is that Xeon is very expensive. If you want to have 4-way motherboard the XEON 700Mhz/1MB Cache will cost you 1349 USD, XEON 550MHz/512K 975 USD. If you will buy 1-way motherboards you can get XEON 933/256k for 670 USD. The 4-way motherboard for Xeon is SC450NX and it cost c.a. 1800USD, or S2QR6 c.a 2500 USD. It is mean that 4-way motherboards + 4 XEONs 700MHz is ~7000 USD and you should add memory disks and all another stuff. For comparison the 1000Mhz T-Bird + motherboard ASUSTek, 1GB RAM, 18 GB HD SCSII cost ~1600 USD. Have fun, Stan P.S. All prices are from: www.pricewatch.com. =============================================================================== Dr Stanislaw Oldziej Faculty of Chemistry, University of Gdansk, "Plucie to nie to samo co wolnosc wypowiedzi" Molecular Modelling Group Sobieskiego 18, 80-952 Gdansk POLAND tel:(048-58)-345-0361 fax:(048-58)-341-0357 =============================================================================== On Mon, 30 Oct 2000, Eric HENON wrote: > Hello, > > We have a plan to get a workstation with 4 processors to do > some ab initio calculations (g98, Molcas). The "Linux/xeon" platform > seems to be an interesting alternative but, unfortunately, we have not > found recent benchmarks for current xeon. > > Thus, I would be grateful if anyone could share his/her > experience concerning the performance of Linux/current Xeon-PIII vs > Power 3-II (IBM RS6000). > > Thank you in advance. > > E. Henon > -- ---------------------------------------------------------- > Eric HENON - Maitre de Conférences > Groupe de Spectrometrie Moleculaire et Atmospherique (GSMA) > Equipe Associee au CNRS ESA 6089 > UFR Sciences Exactes et Naturelles B.P. 1039 > 51687 REIMS Cedex 2 > Tel : 03 26 91 33 66 > email: eric.henon@univ-reims.fr > ---------------------------------------------------------- > > > > > -= 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 Oct 30 18:17:49 2000 Received: from Mercury.acs.unt.edu (mercury.acs.unt.edu [129.120.220.1]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id SAA18324 for ; Mon, 30 Oct 2000 18:17:48 -0500 Received: from jove.acs.unt.edu (10759@jove.acs.unt.edu [129.120.220.41]) by Mercury.acs.unt.edu (8.8.8/8.8.8) with ESMTP id RAA06837 for ; Mon, 30 Oct 2000 17:17:26 -0600 (CST) Received: from localhost (tdp0006@localhost) by jove.acs.unt.edu (8.8.8/8.8.8) with ESMTP id RAA20612 for ; Mon, 30 Oct 2000 17:17:25 -0600 (CST) Date: Mon, 30 Oct 2000 17:17:25 -0600 (CST) From: TREVOR D POWER To: chemistry@server.ccl.net Subject: Re: CCL:Dimer structures In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Frank, Gaussian 98 (Gaussian 94 as well) does a good job of finding stationary points for complexes that you are interested in. You may have to tool around with (perturb) the starting geometry to insure that you obtain the lowest energy coordination. A careful literature search, which you seem to have already done, may shed some light on possible coordinations. For the type of complexes you are interested in, you should expect to get pretty good qualitative results at the Hartree-Fock level with a reasonable sized basis set [say 6-31G(d,p)]. If you are interested in better geometrical results that one could compare with, say x-ray or the like, then you could later perform geometry optimizations at the MP2 level with that basis set. Obviously, your computational resourses will define how you proceed past the Hartree-Fock level. You can employ various methods (SCRF is quite popular and inexpensive to use) that will attempt to incorporate solvation, however, you will find few significant geometrical differences from the gas phase since these methods cannot account for direct H-bonding of the solvent molecule(s) to whatever you are optimizing. You would have to explicity add solvent molecules where they are expected to be; a task that is loads easier said than done. Believe me --- I work with lithium complexes!! With regard to calculating IR spectra, I would not be qualified to direct you further. I am hoping someone out there has some experience with this; I too am interested in their answer. Regards, David Power tdp0006@unt.edu On Fri, 27 Oct 2000, Frank J. Devlin wrote: > > Hi Trevor, > > Consider dimethylsulfoxide (DMSO). It is known experimentally > that DMSO forms dimers in solution i.e. IR bands for dimer can > be observed. Now I would like to model the dimer system to > determine the structure that exists in solution. > > Is it like this for example > > CH3 O CH3 > \ / \ / > S S > / \ / \ > CH3 O CH3 > > or are the DMSO molecules oriented in some other way? > > So, I want to optimize the geometries of likley dimer > structures and calculate their IR spectra. > > Regards, > > Frank. > > > > > > On Fri, 27 Oct 2000, TREVOR D POWER wrote: > > > Frank, > > What kind of dimeric structures are you interested in calculating? > > With symmetry constraints? > > > > Regards, > > David Power > > Department of Chemistry > > University of North Texas > > Nt Station, Box 305070 > > Denton, Texas 76203-5070 > > tdp0006@unt.edu > > > > > > > > On Fri, 27 Oct 2000, Frank J. Devlin wrote: > > > > > > > > Dear CCl, > > > > > > Is it possible to optimize dimeric structures using Gaussian? > > > Any pointers, references, etc. would be very helpful. > > > > > > I will summarize to the list. > > > > > > Thank you, > > > > > > Dr. Frank Devlin. > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > -= 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 Oct 30 18:51:53 2000 Received: from mercury.chem.nwu.edu (gwuxi@mercury.chem.nwu.edu [129.105.116.2]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id SAA18498 for ; Mon, 30 Oct 2000 18:51:53 -0500 Received: from localhost by mercury.chem.nwu.edu (8.9.1/8.9.1) with SMTP id RAA13951 for ; Mon, 30 Oct 2000 17:53:49 -0600 (CST) Date: Mon, 30 Oct 2000 17:53:49 -0600 (CST) From: Guosheng Wu To: ccl Subject: Summary: Help on force field for simplified "atoms" In-Reply-To: <000b01c04358$edc5cc40$1fe4fdcd@becky> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi, all, As the request of a few people, I am summarizing what I got on this topic. Sorry for those who are n't interested, but have to get it. :-) First of all, I recommend a new book by A. F. Sax(editor), "Potential energy surfaces" (Springer, 1999) ----- Lecture notes in Chemistry (71) and one reference in the book (page 204, ref h, missing for some reason). M. A. Bates & G. R. Luckhurst, J. Chem. Phys., 104(17), 6696, 1996 The book is very useful for those who are interested in potential energy surface and force field development. The paper is on "anisotropic version of a shifted LJ potential", with application in the simulation of liquid crystals. (This may be the most related reference.) Then, here are the responses I have got so far.(only 4, :-) --(1)------------------------------------------------------------------------- Date: Tue, 24 Oct 2000 11:22:18 +1000 From: "Kieran F Lim (Lim Pak Kwan)" groups like CH2 and CH3 are *relatively* (not perfectly) spherically symmetric so the unified atom (simplified "atom") approach is justified. however, groups like C6H5 (phenyl) or molecules like C6H6 (benzene) have a big orientation dependence (ie anisotropy) and cannot be modelled satisfactorily by a distance-dependent LJ(R) form without additional orientation (angle-dependent) terms. the best *simple* approach is to use atom-atom terms. we have looked at benzene-atom interactions in the context of atom-molecule collision dynamics. the calculations, etc of the potential function may help you in your thoughts T. Lenzer, K. Luther, J. Troe, R. G. Gilbert and K. F. Lim, "Trajectory simulations of collisional energy transfer in highly excited benzene and hexafluorobenzene", Journal of Chemical Physics, 1995, 103 (2), 626-641. Kieran ---(2)------------------------------------------------------------------------ From: Keith Glassford Subject: Re: Fwd: Re: Fwd: CCL:Help on force field for simplified Date: 10/24/00 4:41 PM What he wants to do is coarse grain the potentials and yes MSI does have experience in this and we have a product called Dissipative Particle Dynamics or DPD. One can use the COMPASS force field, blends, amorphous builder, dynmics etc, to get the interaction parameters needed for these simulations. Please direct him to the DPD site: http://www.msi.com/materials/cerius2/DPD.html and especially the following example which illustrates an oil water interface: http://www.msi.com/materials/cases/oilwater.html The usefulness of DPD will depend upon what type of system he wants to investigate and the chemistry and physics he is after. Best wishes, Keith ***(3)************************************************************************ Date: Tue, 31 Oct 2000 10:36:45 -0600 From: Rebecca Rone Your approach will probably not work in most cases. The C6H6 group needs to be able to stack in order to create correct interactions. There are several examples of this in the literature on x-ray structures. The most famous is the herringbone arrangement of benzene and there are several similar interactions for drugs with proteins. I cannot recommend this approach. Please see the Momany & Rone paper on force field development : "Validation of the General Purpose QUANTA 3.2/CHARMm Force Field," J. Comp. Chem. 13 (7), 888-900 (1992). Also check the MSI web site for other related information. This forcefield is currently in use for QUANTA and their CNX product. Friends inform me that it currently provides extensive coverage for drugs interacting with proteins. Becky Dr. Rebecca Rone Rone Biotechnology Consulting 773-646-2585 Chicago, IL. Boston, MA. ****(4)************************************************************************* Date: Mon, 30 Oct 2000 19:12:12 +0100 From: Harald Svedung I think this question i very interesting. Indeed there is a need for simple "V(R)-functions" in various contexts. (is there not?... tell me.) The problem with C6H6 and pairwise atom-atom interactions is that the C6H6 molecule shows some quite "non-atomic" or "molecular" qualities (aromatic interaction, anisotropic polarizabilities etc). Theese features are averaged out only at large distances using any atomic potential. Atom-atom LJ(rij) contributions can be taken from the literature as a first-aid in building a potential function. These parameters are not able to represent (in general) the specific qualities of, e.g., C6H6. LJ(12-6) potentials often over-estimate the repulsive hardness of the atom-atom interactions and there is no explicit treatment of the electrostatics. Therefore the mapping of ab-initio potential energy to such a potential must be done with care taken to the energies of interest and also to the angle of approach. Maby a single center angular dependent Buckingham-type (exp-6) potential would do as a first approximation, perhaps with the hydrogens interacting explicitly (...any other suggestions) all yours :-) /Harald ****************************************************************************** Finally, thanks a lot to those who responsed, gave reference or suggestion. More discussion is highly appreciated. Best regards! Guosheng -------------------------------------------- Guosheng Wu Dept. of Chem., Northwestern Univ. 2145 Sheridan Road, Evanston, IL, 60208-3113 -------------------------------------------- From chemistry-request@server.ccl.net Mon Oct 30 19:54:22 2000 Received: from mailhost.msi.com (fire.msi.com [146.202.0.242]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id TAA18709 for ; Mon, 30 Oct 2000 19:54:21 -0500 Received: (from daemon@localhost) by mailhost.msi.com (980427.SGI.8.8.8/970903.SGI.AUTOCF) id QAA20863 for ; Mon, 30 Oct 2000 16:53:50 -0800 (PST) Received: from jnauss-pc.msi.com(146.202.26.50) by mailhost.msi.com via smap (V2.0) id xma020859; Mon, 30 Oct 00 16:53:48 -0800 Message-Id: <4.3.2.7.0.20001030164855.00b135f0@146.202.6.217> X-Sender: jnauss@146.202.6.217 X-Mailer: QUALCOMM Windows Eudora Version 4.3.2 Date: Mon, 30 Oct 2000 16:52:08 -0500 To: chemistry@ccl.net From: Jeff Nauss Subject: MSI Workshops on InsightII in San Diego Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii"; format=flowed Molecular Simulations Inc. will be holding a pair of 2-day workshops at the San Diego Supercomputer Center, La Jolla, CA, in December. On December 5-6, the workshop "Introduction to Life Science Modeling with InsightII" will be offered. This course provides an overview of molecular modeling techniques for life sciences applications in the InsightII graphical user environment. Prior modeling experience is not assumed making this course a great place to start molecular modeling. On December 7-8, the "Homology-Based Protein Design" training will be offered. This workshop is relevant to any of our customers who are interested in predicting protein structure and who would like to make more effective use of modeling in their work. During the two-day workshop, the process of producing a three-dimensional model from an amino acid sequence will be covered step-by-step. Both manual and automatic methodologies will be discussed. Prerequisites for this course are the "Introduction to Life Science Modeling with InsightII" workshop or extensive experience with InsightII. Fees for each 2-day course are $1000 commercial, $500 government, and $400 academic. However, register for both courses and receive a 25% discount for the second course. Further detailed information about this and other MSI training workshops, as well as on-line course registration, can be found at MSI's website (http://www.msi.com/about/events/training). Please do not hesitate to contact us should you have any questions. Thank you very much. Jeffrey L. Nauss 858-799-5555 Chris Arzt 858-799-5340 -- Jeffrey L. Nauss, PhD Phone: (858) 799-5555 Customer Training Programs Fax: (858) 458-0136 Molecular Simulations Inc. E-mail: jnauss@msi.com 9685 Scranton Road http://www.msi.com/about/events/training San Diego, CA 92121-3752 From chemistry-request@server.ccl.net Mon Oct 30 21:13:22 2000 Received: from web2104.mail.yahoo.com (web2104.mail.yahoo.com [128.11.68.248]) by server.ccl.net (8.8.7/8.8.7) with SMTP id VAA18951 for ; Mon, 30 Oct 2000 21:13:21 -0500 Received: (qmail 26387 invoked by uid 60001); 31 Oct 2000 02:13:13 -0000 Message-ID: <20001031021313.26386.qmail@web2104.mail.yahoo.com> Received: from [63.97.7.140] by web2104.mail.yahoo.com; Mon, 30 Oct 2000 18:13:13 PST Date: Mon, 30 Oct 2000 18:13:13 -0800 (PST) From: Jianxin Guo Subject: binding conformations of small molecules. To: chemistry@ccl.net MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Hello, Can anyone provide the information about the binding conformation of the small molecules compared with the QC/MM minimized structures in the viewpoint of statistic by looking the available x-ray binding complexes structure? I am curious how much energy has been generally changed. That would give us an rough concept about the conformation range if the binding structure is unavailable. Thanks, Jianxin __________________________________________________ Do You Yahoo!? Yahoo! Messenger - Talk while you surf! It's FREE. http://im.yahoo.com/