From chemistry-request@server.ccl.net Wed May 24 06:13:07 2000 Received: from jivdhan.unipune.ernet.in (jivdhan.unipune.ernet.in [196.1.114.31]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id GAA25889 for ; Wed, 24 May 2000 06:13:00 -0400 From: quanta@chem.unipune.ernet.in Received: from chem.unipune.ernet.in (chem.unipune.ernet.in [196.1.114.10]) by jivdhan.unipune.ernet.in (8.9.0/UnipuneMailhubV1.3) with ESMTP id PAA14050 for ; Wed, 24 May 2000 15:31:13 +0530 Received: (from quanta@localhost) by chem.unipune.ernet.in (8.8.7/8.8.7) id QAA28015 for CHEMISTRY@www.ccl.net; Wed, 24 May 2000 16:07:01 +0530 Date: Wed, 24 May 2000 16:07:01 +0530 Message-Id: <200005241037.QAA28015@chem.unipune.ernet.in> To: CHEMISTRY@server.ccl.net Subject: Info. please !! May 24, 2000 Emil Fischer has proposed his famous term 'lock and key' in the paper quoted as: Fischer, E., Ber. Deutsch Chem. Gesell. (1894) 27, 2985 Can anyone please tell me the the exact page numbers of this paper? Thanks in advance. ANANT From chemistry-request@server.ccl.net Wed May 24 08:47:56 2000 Received: from donkeykong.gpcc.itd.umich.edu (smtp@donkeykong.gpcc.itd.umich.edu [141.211.2.163]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id IAA27367 for ; Wed, 24 May 2000 08:47:56 -0400 Received: from breakout.gpcc.itd.umich.edu (smtp@breakout.gpcc.itd.umich.edu [141.211.2.141]) by donkeykong.gpcc.itd.umich.edu (8.8.8/4.3-mailhub) with ESMTP id IAA02352; Wed, 24 May 2000 08:46:07 -0400 (EDT) Received: from localhost (brupalf@localhost) by breakout.gpcc.itd.umich.edu (8.8.8/5.1-client) with ESMTP id IAA13661; Wed, 24 May 2000 08:47:43 -0400 (EDT) Precedence: first-class Date: Wed, 24 May 2000 08:47:43 -0400 (EDT) From: Bruce Allan Palfey X-Sender: brupalf@breakout.gpcc.itd.umich.edu To: quanta@chem.unipune.ernet.in cc: CHEMISTRY@server.ccl.net Subject: Re: CCL:Info. please !! In-Reply-To: <200005241037.QAA28015@chem.unipune.ernet.in> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII The pages are 2985-2993. Bruce On Wed, 24 May 2000 quanta@chem.unipune.ernet.in wrote: > May 24, 2000 > > Emil Fischer has proposed his famous term 'lock and key' in the paper > quoted as: > > Fischer, E., Ber. Deutsch Chem. Gesell. (1894) 27, 2985 > > Can anyone please tell me the the exact page numbers of this paper? > Thanks in advance. > > ANANT > > > -= 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 Tue May 23 13:29:59 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 NAA21225 for ; Tue, 23 May 2000 13:29:58 -0400 Received: (from daemon@localhost) by mailhost.msi.com (980427.SGI.8.8.8/970903.SGI.AUTOCF) id KAA09696 for ; Tue, 23 May 2000 10:27:06 -0700 (PDT) Received: from jnauss-pc.msi.com(146.202.26.50) by mailhost via smap (V2.0) id xma009693; Tue, 23 May 00 10:26:42 -0700 Message-Id: <4.3.0.20000523102040.00b0aa10@146.202.6.217> X-Sender: jnauss@146.202.6.217 X-Mailer: QUALCOMM Windows Eudora Version 4.3 Date: Tue, 23 May 2000 10:21:57 -0400 To: chemistry@ccl.net From: Jeff Nauss Subject: MSI Customer Training Workshop on Cerius2 and Catalyst in Tel Aviv Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii"; format=flowed Molecular Simulations Inc. will be holding a combined Cerius2 and Catalyst workshop in Tel Aviv, Israel. This workshop will be hosted by the Bioinformatics Unit of the G.S. Wise Faculty of Life Sciences, Tel Aviv University Small Molecule and Drug Design with Cerius2 and Catalyst On June 27-28, the "Small Molecule and Drug Design with Cerius2 and Catalyst" workshop will be offered. This course provides an overview of molecular modeling techniques for applications in drug design. It is aimed at our customers in the pharmaceutical industry and involved in drug design who would like to make more effective use of modeling in their research. In the first day, attendees will be working with the Cerius2 user interface studying techniques in QSAR. The second day will cover pharmacophore hypotheses with Catalyst. Some basic understanding of molecular modeling is required for this course. Familiarity with the Cerius2 and Catalyst environments is also recommended but not required. Fees for this 2-day course are US$1000 commercial, US$500 government, and US$400 academic. 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 me should you have any questions. You may also contact our Paris office at +33 1 69 35 32 32. Thank you very much. Jeffrey L. Nauss MSI Training Programs -- 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 Tue May 23 13:59:45 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 NAA21410 for ; Tue, 23 May 2000 13:59:45 -0400 Received: (from daemon@localhost) by mailhost.msi.com (980427.SGI.8.8.8/970903.SGI.AUTOCF) id KAA10680 for ; Tue, 23 May 2000 10:56:52 -0700 (PDT) Received: from jnauss-pc.msi.com(146.202.26.50) by mailhost via smap (V2.0) id xmaa10673; Tue, 23 May 00 10:56:43 -0700 Message-Id: <4.3.0.20000523103940.00af8690@146.202.6.217> X-Sender: jnauss@146.202.6.217 X-Mailer: QUALCOMM Windows Eudora Version 4.3 Date: Tue, 23 May 2000 10:40:08 -0400 To: chemistry@ccl.net From: Jeff Nauss Subject: MSI Advanced Training Workshops 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. On July 25-26, the "CHARMm Workshop" will be offered. This course provides an overview of molecular modeling techniques for life sciences applications with CHARMm. The workshop will emphasize hands-on experience with command line usage but use of InsightII will be made for visualization of results. Prior modeling experience is not assumed making this course a great place to start molecular modeling with CHARMm. On July 27-28, the "Structure-Based Drug Design with InsightII" workshop will be offered. This course offers an in-depth examination of receptor-based drug design using the InsightII graphical user interface. This workshop is our capstone course in InsightII covering a variety of modules and their integration. It is aimed at our customers in the pharmaceutical industry and involved in drug design who would like to be more efficient with InsightII. Extensive understanding of molecular modeling and InsightII is required. 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 me should you have any questions. Thank you very much. Jeffrey L. Nauss MSI Training Programs (858) 799-5555 -- 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 Tue May 23 19:37:02 2000 Received: from tahoe.orconet.com (tahoe.orconet.com [216.98.227.70]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id TAA23202 for ; Tue, 23 May 2000 19:37:01 -0400 Received: from molecules.com (adsl-87-228-98-216.dsl.orconet.com [216.98.228.87]) by tahoe.orconet.com (8.9.3/8.9.3) with ESMTP id QAA01495; Tue, 23 May 2000 16:39:03 -0700 (PDT) Message-ID: <392B1715.D0DA9F9D@molecules.com> Date: Tue, 23 May 2000 16:41:09 -0700 From: James Givens Reply-To: jamesg@molecules.com Organization: Molecular Arts Corp - http://www.molecules.com X-Mailer: Mozilla 4.6 [en] (Win95; I) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net CC: Richard Gillilan Subject: Re: CCL:stable Ih ice References: <001001bfc142$515cc5e0$0200a8c0@pavilion> <392AAF8A.E53B9175@tc.cornell.edu> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Richard Gillilan wrote (in part): > > I was recently asked to generate an animation sequence of > a solid melting into a fluid and then vaporizing. Since it > was for purposes of illustration only (a low-level > educational film) we did not need a great deal of > accuracy in the model, just the basic behavior. There is a nice Quicktime animation on H20 transitions at: http://www.molecules.com/movies.shtml This only applies to your project in general, but I thought it may help your efforts as background/example material. Sincerely, -- James Givens ---------------------------------------------------------------- Molecular Arts Corporation | ---------------------------------------------------------------- From chemistry-request@server.ccl.net Wed May 24 04:14:08 2000 Received: from jivdhan.unipune.ernet.in (jivdhan.unipune.ernet.in [196.1.114.31]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id EAA25464 for ; Wed, 24 May 2000 04:14:01 -0400 Received: from chem.unipune.ernet.in (chem.unipune.ernet.in [196.1.114.10]) by jivdhan.unipune.ernet.in (8.9.0/UnipuneMailhubV1.3) with ESMTP id NAA13077 for ; Wed, 24 May 2000 13:32:13 +0530 Received: from localhost (quanta@localhost) by chem.unipune.ernet.in (8.8.7/8.8.7) with SMTP id OAA27134 for ; Wed, 24 May 2000 14:08:05 +0530 Date: Wed, 24 May 2000 14:08:05 +0530 (IST) From: QUANTA To: CHEMISTRY@server.ccl.net Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear all, I am studying the hydration of a NaCl(100) cluster and also its interactions with various diatomic, triatomic and linear molecules such as H2, N2, CO2, CO, etc. I would like to know if any work has been done, theoretical as well as experimetal, on this topic. Kindly let me know the appropriate references and if possible the abstracts of the same. Thanks in advance. Vishal Barge. From chemistry-request@server.ccl.net Wed May 24 05:04:52 2000 Received: from earth.ox.ac.uk (darwin.earth.ox.ac.uk [163.1.22.6]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id FAA25671 for ; Wed, 24 May 2000 05:04:51 -0400 Received: from metropolis.earth.ox.ac.uk (metropolis [163.1.22.59]) by earth.ox.ac.uk (8.9.3+Sun/8.9.1) with ESMTP id KAA08074; Wed, 24 May 2000 10:04:42 +0100 (BST) From: Keith Refson MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Message-ID: <14635.39728.282077.29619@gargle.gargle.HOWL> Date: Wed, 24 May 2000 10:04:48 +0100 (BST) To: Richard Gillilan CC: chemistry@ccl.net, ccp4bb@dl.ac.uk Subject: CCL:stable Ih ice and P63/mmc space group In-Reply-To: <392AAF8A.E53B9175@tc.cornell.edu> References: <001001bfc142$515cc5e0$0200a8c0@pavilion> <392AAF8A.E53B9175@tc.cornell.edu> X-Mailer: VM 6.75 under 21.1 (patch 3) "Acadia" XEmacs Lucid Richard Gillilan writes: > I constructed a slab of Ih ice from the crystal structure. > Because the structure is space and time averaged, or perhaps > because the protons hop around a lot, the P63/mmc space group > symmetry operators place 24 water molecules in the unit cell in > 4 overlapping groups of 6. There are only 4 unique Oxygen positions, > but each has 4 unique protons, so there appear to be clashes between > neighboring protons. Sorry, this is hard to describe in words. That's not too bad a discription of the proton disorder characteristic of Ice Ih. Pauling expressed it a little more concisely with his "ice rules" 1. H2O Molecules are intact, neglecting the small fraction of ionized molecules. 2. Each H2O molecule is oriented so that its two O-H bonds are directed approximately towards two of the four nearest neighbouring oxygen atoms. 3. The orientation of adjacent water molecules are such that only one hydrogen atom lies approximately along the axis between adjacent oxygen atoms. > I can simply choose four unique H2O molecules per unit cell > and get a nice lattice with no clashes, which is what I did. You have made an ordered variant of the ice Ih lattice. It will have a large dipole moment so don't expect to get the melting temperature too accurately as the dipole energy will cause significant bias depending on your electrostatic boundary conditions. Since you have more than one unit cell, it may be worth creating more disorder between the cells, or at least constructing an ordered state with no dipole. > When I minimize a block of ice, I was surprised to find that the > the crystal structure appears to collapse .... or at least there is > no minimum near the ice structure. I'm using a simple pairwise > VDW+point charge model. Is this something like the TIP4P or SPC/E models? Either of those should give a good ice structure, and be suitable for your movie. > > Q1: Is a more advanced potential model (say with explicit H bonds) > needed to have stable Ih ice, or is there a good set of point > charges and VDW parameters that will work? Both TIP4P, SPC/E and a number of simple variants are rigid-body models with point charges and Lennard-Jones interactions between the oxygens. You can't easily simulate any of the TIP4P family using a constraints MD program because one of the charge sites has no mass, but a true rigid body code will have no problems with this. > > Q2: The 24 symmetry operators fall into 4 groups of 6, each of which > has the same z-value in common. For example: > > -x+y, -x, -z+1/2 > -y , -x, -z+1/2 > -x+y, -y, -z+1/2 > x , x-y, -z+1/2 > x , y, -z+1/2 > -y , x-y, -z+1/2 > > I would have expected these operators to produce the six possible > orientations of a single water molecule at a given lattice site. > Instead, > they seem to produce a doubly redundant set in which one OH bond is > always fixed on the z axis. Am I missing something here? There is no crystallographic requirement that the symmetry group operators generate a non-redundant set of co-ordinates from the basis. In general if an atom is at a site of high symmetry there will be multiple operations generating that site. Reduced symmetry lists for special positions are listed in the International Tables for Crystallography. Keith Refson -- Dr Keith Refson, "Paradigm is a word too often used by those who would Dept of Earth Sciences like to have a new idea but cannot think of one." Parks Road, -- Mervyn King, Deputy Governor, Bank of England Oxford OX1 3PR, UK Keith.Refson@ Tel: 01865 272026 earth.ox.ac.uk Fax: 01865 272072 From chemistry-request@server.ccl.net Wed May 24 08:52:34 2000 Received: from mail.ceniai.inf.cu (ceniai.net.cu [169.158.128.142]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id IAA27420 for ; Wed, 24 May 2000 08:52:25 -0400 Received: from uucp.ceniai.inf.cu ([169.158.128.157]) by mail.ceniai.inf.cu (8.9.3/8.9.3) with ESMTP id JAA24920 for ; Wed, 24 May 2000 09:16:42 -0500 (EST) Received: (from uucp@localhost) by uucp.ceniai.inf.cu (8.9.3/8.9.3) with UUCP id IAA61211 for chemistry@ccl.net; Wed, 24 May 2000 08:53:14 -0500 (EST) Received: from ceinpet.inf.cu ([192.168.1.188]) by hermes.ceinpet.inf.cu (8.8.7/8.8.7) with ESMTP id DAA01255 for ; Wed, 24 May 2000 03:15:09 -0500 Message-ID: <392BD211.8BFFDC27@ceinpet.inf.cu> Date: Wed, 24 May 2000 07:58:57 -0500 From: Ricardo Grau Crespo X-Mailer: Mozilla 4.61 [en] (Win95; I) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net Subject: cracking energy of n-heptane References: <37E8CAA8.F404E67E@ceinpet.inf.cu> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear all, Can anyone point me to some references on theoretical calculations of craking energies of n-heptane in a zeolite acid site? Thanks in advance, Ricardo. Ricardo Grau Crespo From chemistry-request@server.ccl.net Wed May 24 15:47:09 2000 Received: from lambda.inrs.uquebec.ca (lambda.inrs.uquebec.ca [207.162.3.13]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id PAA29884 for ; Wed, 24 May 2000 15:47:08 -0400 Received: from iaf.uquebec.ca ([198.168.44.40]) by lambda.inrs.uquebec.ca (Netscape Messaging Server 3.62) with ESMTP id 317 for ; Wed, 24 May 2000 15:43:55 -0400 Message-ID: <392C33E4.367FCE35@iaf.uquebec.ca> Date: Wed, 24 May 2000 15:56:20 -0400 From: "Jianhui Wu" X-Mailer: Mozilla 4.5 [en] (Win95; I) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net Subject: Large loop modelling Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear all, I am building a protein with a big loop (around 55 residues). Experimentally, the loop was found to involve with ligand binding (that is, some of the loop residues are in the ligand binding sites). Moreover, the conformation change on ligand binding involve at least 10 residues. My objective is to get a model of the complex. Obviously, to get a good model of the loop is the key step. What is the best method to model the big loop that involve with ligand binding? By the way, the template has similar loop but the X-ray structure do not have coordinates for that since the loop is too flexible. I read somewhere that people are developing method to model this kind of loop. I just can not find it now. Can you point me to some related references? Thanks a lot, Jian Hui Wu Institute Armand-Frappier Laval, Quebec email: JianHui_Wu@IAF.Uquebec.ca From chemistry-request@server.ccl.net Wed May 24 16:54:35 2000 Received: from jaibana.udea.edu.co (jaibana.udea.edu.co [200.24.21.239]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id QAA30169 for ; Wed, 24 May 2000 16:54:09 -0400 Received: from localhost by jaibana.udea.edu.co (8.9.3/8.9.3) with SMTP id PAA21948 for ; Wed, 24 May 2000 15:44:58 +0500 (GMT) Date: Wed, 24 May 2000 15:44:57 +0500 (GMT) From: Juan David Henao Lopez To: chemistry@ccl.net Subject: Zeolite A Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hello. My name is Juan D. Henao. I work in the Environmental Catalysis Laboratory at Universidad de Antioquia (Medellin-Colombia). At the moment, I am begining to work with the Gaussian 98 software, but I am an inexpert user of any computational methods. I am interested in building the unit cell of zeolite A and positioning some cobalt atoms into it and refining the resultant structure. About this, I have one question: - Among the methods available into the Gaussian 98 software, what is the best to refine this structure ? Note: I have a machine with only two Intel Pentium III processors. Thank you very much. Juan D. Henao L. From chemistry-request@server.ccl.net Wed May 24 17:27:58 2000 Received: from goshen.rutgers.edu (0@goshen.rutgers.edu [165.230.180.150]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id RAA30547 for ; Wed, 24 May 2000 17:27:57 -0400 Received: from email.eden.rutgers.edu (lsm003.rutgers.edu [165.230.84.141]) by goshen.rutgers.edu (8.8.8/8.8.8) with ESMTP id RAA04961; Wed, 24 May 2000 17:27:52 -0400 (EDT) Message-ID: <392C48C9.6B3BAA24@email.eden.rutgers.edu> Date: Wed, 24 May 2000 17:25:29 -0400 From: jianquan Organization: Rutgers University X-Mailer: Mozilla 4.61 [en] (Win95; U) X-Accept-Language: en MIME-Version: 1.0 To: Xiao-Ping Zhang CC: "chemistry@ccl.net" Subject: Re: CCL:Autodock 3 - non-integral charge References: <00051711562700.01636@dhcp-242.biokemi.su.se> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit make sure the total charge is integral before you use autotors to merge hydrogen atoms to C atoms. jianquan chen Xiao-Ping Zhang wrote: > Dear Autodock users, > > I would appreciate very much if somebody allow me to share > his experience on fixing the "Non-integral charge" of molecule > (especially the ligand). > > Thank you for your help! > > Sincerely yours, > > Xiao-Ping > > ****************************** > Xiao-Ping Zhang > Department of Biochemistry > Arrhenius Laboratories of Natural Sciences > Stockholm Universities > 106 91 Stockholm > Sweden > > Phone: 046-08-162472 /162582 > Fax: 046-08-153679 > e-mail: zhang@biokemi.su.se > > -= 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