From chemistry-request@server.ccl.net Sat Aug 11 15:15:49 2001 Received: from web4903.mail.yahoo.com ([216.115.106.28]) by server.ccl.net (8.11.0/8.11.0) with SMTP id f7BJFnv22563 for ; Sat, 11 Aug 2001 15:15:49 -0400 Message-ID: <20010811191548.19877.qmail@web4903.mail.yahoo.com> Received: from [66.81.18.71] by web4903.mail.yahoo.com via HTTP; Sat, 11 Aug 2001 12:15:48 PDT Date: Sat, 11 Aug 2001 12:15:48 -0700 (PDT) From: Sengen Sun Subject: Cycloadditions & MOs To: chemistry@ccl.net MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Five people responded to my CCL positing of July 29, 2001. Two of them requested a summary, and three requested references. Therefore, I have nothing to summarize. The following three kinds of references were requested. I can only give a few examples for each kind. 1. References on experimental facts (or computational results) that are not consistent to the expectations of MO control theories. (a) Spino, C.; Crawford, J.; Cui, Y.; Gugelchuk, M. J. Chem. Soc., Perkin Trans. 2, 1998, 1499. (b) Haller, J.; Beno, B. R.; Houk, K. N. J. Am. Chem. Soc. 1998, 120, 6468. (c) THEOCHEM, 1989, 200, 301. Dewar gave some examples of failure of FMO. Note: The inconsistency between theories and facts has often been attributed to polar effects and/or Coulombic forces in MANY publications. The polar effects and Coulombic effects are usually not mentioned when the MO control theories fit experimental observations. 2. References on discussions of possible control factors: (a) Bader & MacDougall, JACS 1985, 107, 6788 (given in my posting of July 29, 01). (b) Sakata, K. J. Phys. Chem. A 2000,104, 10001-10008, and some references therein. (c) My preprint paper that a CCL member announced a few days ago: “Collision-induced electron reorganization as the general mechanism of concerted cycloadditions”. It can be found at http://preprint.chemweb.com/orgchem/0107002. This preprint paper is more of philosophical arguments on electron density control in concerted cycloadditions such as acrolein dimerization. I understand that many people don’t like it because some routines of computational chemistry are not followed. It attempts to address some “obfuscating phenomena” that chemical bonds are preferentially formed between two negative centers or between two positive centers, but not between compatible positive-negative centers in some thermal cycloadditions. I welcome any private or public comments on the philosophical points in the paper. 3. The particular remark "hypnotic effect" can be found in JACS 1984, 106, 209-219 (On page 209, the second column, the end of the first paragraph). Dewar’s remarks in his several publications imply that this highly ranked theoretical chemist did not fully understand the mechanisms of chemical reactions based on single MOs. I don’t think that I can understand a chemical reaction without knowing how and why electrons move along a reaction path (as argued by Sakata, 2(b) above). Aren’t there interacting forces via partial bonds in bond forming and breaking processes? Why don’t we try to describe these forces logically rather than just to believe quantum phenomena? Of course, you can argue that my mind is too classical to understand those quantum phenomena. I do have conflicts in my mind. I hope to see more research work by theoretical and computational chemists in this area. Thanks. __________________________________________________ Do You Yahoo!? Send instant messages & get email alerts with Yahoo! Messenger. http://im.yahoo.com/ From chemistry-request@server.ccl.net Sat Aug 11 19:09:43 2001 Received: from web14704.mail.yahoo.com ([216.136.224.121]) by server.ccl.net (8.11.0/8.11.0) with SMTP id f7BN9hv25089 for ; Sat, 11 Aug 2001 19:09:43 -0400 Message-ID: <20010811230942.53268.qmail@web14704.mail.yahoo.com> Received: from [128.100.13.59] by web14704.mail.yahoo.com; Sat, 11 Aug 2001 16:09:42 PDT Date: Sat, 11 Aug 2001 16:09:42 -0700 (PDT) From: Ron Chen Subject: RE: Motherboards and Linux question To: raeker@umich.edu, tsd@asus.com Cc: chemistry@ccl.net MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii http://www.keylabs.com/linux/results_server.html has the review of ASUS A7V and several others, but I could not find A7S-VM. The best thing for you to do is to ask the tech support of ASUS (ie. tsd@asus.com). The motherboard manufacters should tell us whether Linux is supported or not, this would save a lot of trouble. Also, if you want to run simulations over and over, you should install a batch system, which will schedule another job to the node where a job finishes execution. (So that you don't need to do this by hand) SGE 5.2.3 binary: www.sun.com/gridware SGE 5.3 source+binary: gridengine.sunsource.net PBS: www.openpbs.com PBSPro: www.pbspro.com Both are free, and come with source! -Ron > I will be building a 16 node Linux cluster for ab >initio calculations and >MD simulations from scratch and have narrowed down my >choice of micro >ATX >motherboards to two options. They are the ASUS A7S-VM >and the Shuttle >MS21N. >Does anyone have any experience with either of these? >I have no >experience >with either board and other people I have talked to >only the ASUS ATX >boards. > >Thanks > >Todd. > >-- >Todd Raeker >Department of Chemistry >University of Michigan __________________________________________________ Do You Yahoo!? Send instant messages & get email alerts with Yahoo! Messenger. http://im.yahoo.com/ From chemistry-request@server.ccl.net Sat Aug 11 13:29:36 2001 Received: from p2.fhp.bsunet ([217.21.43.20]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f7BHT4v20077 for ; Sat, 11 Aug 2001 13:29:35 -0400 Received: from localhost (sa@localhost) by p2.fhp.bsunet (8.9.3/8.9.3/my hands 8.9.3-0.1) with ESMTP id UAA11720 for ; Sat, 11 Aug 2001 20:28:54 +0300 Date: Sat, 11 Aug 2001 20:28:54 +0300 (EEST) From: Alexander Kulak To: Subject: 1,5-Diaminotetrazole aminogroup structure Message-ID: Organization: Inst. Phys. Chem. problems of BSU X-Mailer: Pine (LNX) MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hello, All. "N6" ------> NH2 | // \ N N - NH2 <------ "N5" | | N = N X-ray investigation of this compound shows that N6 aminogroup is planar (angles = 118,118,119) and lies in the tetrazole plane. But MP2/6-31G(d,p) calculation gives the non-planar structure of that aminogroup (112,113,114 degrees), although H atoms lie close to the ring plane, in contrast with N5, where they lie at the different sides of the plane. The HOMO is combined from p(z)-AO of ring's nitrogens and p(z) of N6, confirming common assumpion about Pi-conjugation of ring and N6. At the same time localization (Boys or Pipek-Mezey) gives a clear picture of lone-pair at N6. Could anyone please answer the QUESTIONS: 1) Why calculated N6 is not planar while nature says it is planar? 2) Why it CAN be planar? b.w., Alexander Kulak [ http://i.am/kulak ] From chemistry-request@server.ccl.net Sat Aug 11 12:51:10 2001 Received: from sd.accelrys.com ([146.202.0.242]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f7BGpAv19537 for ; Sat, 11 Aug 2001 12:51:10 -0400 Received: (from jnauss@localhost) by sd.accelrys.com (8.11.0/8.11.0) id f7BGpxT14872 for chemistry@ccl.net; Sat, 11 Aug 2001 09:51:59 -0700 Received: from JNAUSS-PC.accelrys.com (dhcp101.sd.accelrys.com [172.30.200.101]) by sd.accelrys.com (8.11.0/8.11.0) with ESMTP id f7BGpoq14863 for ; Sat, 11 Aug 2001 09:51:51 -0700 Message-Id: <5.1.0.14.0.20010811094137.00b17048@sparky2.sd.accelrys.com> X-Sender: jnauss@sparky2.sd.accelrys.com X-Mailer: QUALCOMM Windows Eudora Version 5.1 Date: Sat, 11 Aug 2001 09:44:45 -0700 To: chemistry@ccl.net From: Jeff Nauss Subject: Accelrys Customer Training on InsightII in Paris Mime-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1"; format=flowed Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id f7BGpAv19538 Accelrys will be holding a pair of 2-day workshops at the Université Pierre et Marie Curie, Paris, France, in October. Both workshops will use the InsightII interface. On 16-17 October, 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 18-19 October, 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 FRF 7700 commercial, FRF 3850 government/non-profit, FRF 3080 academic (excl VAT) if payment is by check or purchase order. If payment is made through a credit card, the fees are US$1000 commercial, US$500 government, and US$400 academic (excl VAT). However, register for both courses and receive a 25% discount for the second workshop. Please note that on June 1, MSI, Synopsys, Oxford Molecular, and GCG became the single company named Accelrys. Further detailed information about this and other Accelrys training workshops, as well as on-line course registration, can be found at the Accelrys website (http://www.accelrys.com/training/lifesci/schedule.html). Please do not hesitate to contact us should you have any questions. Thank you very much. Tien Luu +44 1223 402 895 Chris Arzt +1-858-799-5340 -- Jeffrey L. Nauss, PhD Phone: (858) 799-5555 Life Science Customer Training Fax: (858) 799-5100 Accelrys E-mail: jnauss@accelrys.com 9685 Scranton Road http://www.accelrys.com/training/lifesci/ San Diego, CA 92121-3752 On June 1, MSI, Synopsys, Oxford Molecular, and GCG became Accelrys. Accelrys is a subsidiary of Pharmacopeia, Inc. From chemistry-request@server.ccl.net Sat Aug 11 12:51:00 2001 Received: from sd.accelrys.com ([146.202.0.242]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f7BGoxv19525 for ; Sat, 11 Aug 2001 12:50:59 -0400 Received: (from jnauss@localhost) by sd.accelrys.com (8.11.0/8.11.0) id f7BGpmU14852 for chemistry@ccl.net; Sat, 11 Aug 2001 09:51:48 -0700 Received: from JNAUSS-PC.accelrys.com (dhcp101.sd.accelrys.com [172.30.200.101]) by sd.accelrys.com (8.11.0/8.11.0) with ESMTP id f7BGpiq14833 for ; Sat, 11 Aug 2001 09:51:45 -0700 Message-Id: <5.1.0.14.0.20010811093800.00b173d8@sparky2.sd.accelrys.com> X-Sender: jnauss@sparky2.sd.accelrys.com X-Mailer: QUALCOMM Windows Eudora Version 5.1 Date: Sat, 11 Aug 2001 09:40:24 -0700 To: chemistry@ccl.net From: Jeff Nauss Subject: Accelrys Customer Training on NMR in Paris Mime-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1"; format=flowed Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id f7BGp0v19526 Accelrys Inc. will be holding a pair of workshops focusing on NMR techniques at the Université Pierre et Marie Curie, Paris, France. On 9-10 October, the "Biomolecular NMR: Processing and Analysis Workshop" will be held. This is an introductory course that addresses processing, display, and analysis of NMR data, culminating in the generation of specific NMR-based restraints using FELIX. No prior experience with FELIX is necessary for this workshop. On 11-12 October, the "Biomolecular NMR: Structure Determination Workshop" will be given. This course addresses the generation, refinement, and evaluation of structures based upon NMR data predominantly using NMR X-PLOR in InsightII and CNX. Different methods of structure generation using NMR restraints are discussed, as well as methods for evaluating the quality of structures. Knowledge of routine NMR data collection and analysis techniques is required. Attendees of the Structure Determination Workshop should have either taken the "Introduction to Life Science Modeling with Insight II Workshop" or have general experience with the Insight II interface. Fees for each 2-day course are FRF 7700 commercial, FRF 3850 government/non-profit, FRF 3080 academic (excl VAT) if payment is by check or purchase order. If payment is made through a credit card, the fees are US$1000 commercial, US$500 government, and US$400 academic (excl VAT). However, register for both courses and receive a 25% discount for the second workshop. Further detailed information about this and other Accelrys life science training workshops, as well as on-line course registration, can be found at the Accelrys website (http://www.accelrys.com/training/lifesci/schedule.html). Please do not hesitate to contact us should you have any questions. Please note that on 1 June, MSI, Synopsys, Oxford Molecular, and GCG became Accelrys Inc. Thank you very much. Tien Luu +44 1223 402 895 Chris Arzt +1-858-799-5340 -- Jeffrey L. Nauss, PhD Phone: (858) 799-5555 Life Science Customer Training Fax: (858) 799-5100 Accelrys E-mail: jnauss@accelrys.com 9685 Scranton Road http://www.accelrys.com/training/lifesci/ San Diego, CA 92121-3752 On June 1, MSI, Synopsys, Oxford Molecular, and GCG became Accelrys. Accelrys is a subsidiary of Pharmacopeia, Inc. From chemistry-request@server.ccl.net Sat Aug 11 13:13:18 2001 Received: from sd.accelrys.com ([146.202.0.242]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f7BHDHv19814 for ; Sat, 11 Aug 2001 13:13:17 -0400 Received: (from jnauss@localhost) by sd.accelrys.com (8.11.0/8.11.0) id f7BHE6e15494 for chemistry@ccl.net; Sat, 11 Aug 2001 10:14:06 -0700 Received: from JNAUSS-PC.accelrys.com (dhcp101.sd.accelrys.com [172.30.200.101]) by sd.accelrys.com (8.11.0/8.11.0) with ESMTP id f7BHDwq15485 for ; Sat, 11 Aug 2001 10:14:00 -0700 Message-Id: <5.1.0.14.0.20010811095539.026233c0@sparky2.sd.accelrys.com> X-Sender: jnauss@sparky2.sd.accelrys.com X-Mailer: QUALCOMM Windows Eudora Version 5.1 Date: Sat, 11 Aug 2001 09:57:19 -0700 To: chemistry@ccl.net From: Jeff Nauss Subject: Accelrys Customer Training on Cerius2 in Italy Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii"; format=flowed Accelrys will be holding a pair of workshops in Modena, Italy, at CICAIA, Universita` di Modena e Reggio Emilia from 11 to 14 September. On 11-12 September, the "Introduction to Cerius2 for Life Sciences Workshop" will be offered. This course provides an overview of molecular modeling techniques for life sciences applications using Cerius2. The workshop will focus on basic skills for use of the interface and will explore various modules in the areas of rational-drug design, structure-based drug design, and combinatorial chemistry. Prior modeling experience is not assumed making this course a great place to learn molecular modeling with Cerius2. On 13-14 September, the "Small Molecule and Drug Design with Cerius2" workshop will be offered. This workshop is aimed at our customers who are involved in drug design or the development of other bioactive compounds and who would like to make more effective use of modeling in their research. The course will focus on QSAR techniques and methodologies as well as structure-based ligand design. Attendees should possess knowledge of basic UNIX commands and have a basic understanding of QSAR theory. Familiarity with the Cerius2 environment is required for attendance to this workshop. Both suggested prerequisites can be met by attending the introductory workshop. Fees for each 2-day course are 2,125,000 ITL commercial, 1,062,500 ITL government, and 850,000 ITL academic (excl VAT) if paid by check or purchase order. If payment is made through a credit card, the fees are US$1000 commercial, US$500 government, and US$400 academic. However, register for both courses and receive a 25% discount for the second workshop. Further detailed information about this and other Accelrys training workshops, as well as on-line course registration, can be found at the Accelrys website (http://www.accelrys.com/training/lifesci/schedule.html). In addition, feel free to call your Account Manager or the Paris office (tel no +33 1 69 35 32 32) should you have any questions: Industrial Customers: Katie Valentine (kvalentine@accelrys.com) Academic Customers: Severine Capely (severine@accelrys.com) Thank you very much. Tien Luu +44 1223 402 895 Chris Artz +1 858 799 5340 -- Jeffrey L. Nauss, PhD Phone: (858) 799-5555 Life Science Customer Training Fax: (858) 799-5100 Accelrys E-mail: jnauss@accelrys.com 9685 Scranton Road http://www.accelrys.com/training/lifesci/ San Diego, CA 92121-3752 On June 1, MSI, Synopsys, Oxford Molecular, and GCG became Accelrys. Accelrys is a subsidiary of Pharmacopeia, Inc. From chemistry-request@server.ccl.net Sun Aug 12 23:03:00 2001 Received: from ozone.umsl.edu ([134.124.105.185]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f7D330v06210 for ; Sun, 12 Aug 2001 23:03:00 -0400 Received: from ozone.umsl.edu (localhost [127.0.0.1]) by ozone.umsl.edu (SGI-8.9.3/8.9.3) with ESMTP id WAA71085 for ; Sun, 12 Aug 2001 22:06:35 -0700 (PDT) Sender: siva@ozone.umsl.edu Message-ID: <3B77605A.E6C0D8AF@ozone.umsl.edu> Date: Sun, 12 Aug 2001 22:06:34 -0700 From: Sivanesan Dakshanamurthy Organization: University of Missouri-St. Louis X-Mailer: Mozilla 4.51 [en] (X11; I; IRIX64 6.5 IP27) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net Subject: help Content-Type: multipart/alternative; boundary="------------966CEE37A1D6390594CC812A" --------------966CEE37A1D6390594CC812A Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear CCLers, I did minimization calculation on Enzyme-inhibitor complex using DISCOVER. I am getting Positive Total Energy for all of the following: Enzyme-Inhibitor Complex, protein & inhibitor. Resultant Interaction Energy in turn be positive. Actually this is not the case (I.E. should be negative) for any system which tightly binds, if my assumption is correct. I also note in my Summary of calculation, it seems van der Waals Repulsive contribution is higher than vdW Attractive. I also need to know the quantitative relationship between Binding energy and Interaction energy for this type of calculation. Thanks in advance, Sincerely, D.Sivanesan --------------966CEE37A1D6390594CC812A Content-Type: text/html; charset=us-ascii Content-Transfer-Encoding: 7bit Dear CCLers,
I did minimization calculation on Enzyme-inhibitor complex using DISCOVER. I am getting Positive Total Energy for all of the following: Enzyme-Inhibitor Complex, protein & inhibitor. Resultant Interaction Energy in turn be positive. Actually this is not the case (I.E. should be negative) for any system which tightly binds, if my assumption is correct. I also note in my Summary of calculation, it seems van der Waals Repulsive contribution is higher than vdW Attractive.  I also need to know the quantitative relationship between Binding energy and Interaction energy for this type of calculation.
Thanks in advance,
Sincerely,
D.Sivanesan 

 

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