From chemistry-request@server.ccl.net Thu Dec 2 16:24:23 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 QAA26455 for ; Thu, 2 Dec 1999 16:24:23 -0500 Received: from bratsche (bratsche.nist.gov [129.6.194.154]) by email.nist.gov (8.9.3/8.9.3) with SMTP id PAA20038 for ; Thu, 2 Dec 1999 15:17:25 -0500 (EST) Message-Id: <4.1.19991202145210.00b12c70@mailserver3.nist.gov> X-Sender: irikura@mailserver3.nist.gov X-Mailer: QUALCOMM Windows Eudora Pro Version 4.1 Date: Thu, 02 Dec 1999 15:10:53 -0500 To: CHEMISTRY@ccl.net From: Karl Irikura Subject: postdoctoral fellowships: NRC(US) deadline approaching Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Throughout the US government, an increasing number of the NRC postdoctoral opportunities are in computational science. A major application deadline is approaching (January). If you're interested, please see the following website for further information: http://www.national-academies.org/rap ---------------------------------------------- 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 Thu Dec 2 18:19:51 1999 Received: from bioc1.msi.com (bioc1.msi.com [146.202.0.2]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id SAA27423 for ; Thu, 2 Dec 1999 18:19:50 -0500 Received: from jnauss1-pc (jnauss-pc.msi.com [146.202.26.50]) by bioc1.msi.com (8.9.3/8.9.3) with SMTP id EAA29536 for ; Thu, 2 Dec 1999 04:13:06 -0800 Message-Id: <3.0.3.32.19991202140945.0099f9b0@146.202.6.217> X-Sender: jnauss@146.202.6.217 X-Mailer: QUALCOMM Windows Eudora Pro Version 3.0.3 (32) X-Priority: 4 (Low) Date: Thu, 02 Dec 1999 14:09:45 -0800 To: CHEMISTRY@ccl.net From: "Jeffrey L. Nauss" Subject: Homology Based Protein Design Workshop, Jan 13-14, 2000 at Rutgers University, New Brunswick, NJ Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Molecular Simulations Inc. will be holding a 2-day "Homology Based Protein Design" workshop on January 13-14,2000 at Rutgers University, New Brunswick, NJ. This workshop is relevant to any of our customers who are interested in predicting protein structure and 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 a primary amino acid sequence will be covered step-by-step. The prerequisite for the course is a working knowledge of Insight II. Fees for the 2-day course are $1000 commercial, $500 government, and $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. Thank you very much. -- Jeffrey L. Nauss, PhD Phone: (858) 799-5555 Senior Scientist, Training 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 From chemistry-request@server.ccl.net Fri Dec 3 06:23:37 1999 Received: from huygens.rijnh.nl (huygens.rijnh.nl [192.42.124.30]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id GAA30412 for ; Fri, 3 Dec 1999 06:23:36 -0500 Received: from [192.42.124.238] (pcmoldyn3.rijnh.nl [192.42.124.238]) by huygens.rijnh.nl (980427.SGI.8.8.8/980728.SGI.AUTOCF) via ESMTP id LAA21925 for ; Fri, 3 Dec 1999 11:14:34 +0100 (MET) X-Sender: gertvh@pop-srv.sci.kun.nl Message-Id: Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Fri, 3 Dec 1999 12:21:16 +0100 To: CHEMISTRY@ccl.net From: Gert von Helden Subject: IR properties of metal oxides,carbides.. Dear all, We would like to estimate infrared line positions and line strength of small to medium size ( <100 atoms) metal oxide, carbide and nitride clusters. Ab-initio methods are for most of them out of the question. However, for some of the species, force fields from solid state studies are available. My question: Which force-field programs can calculate both, normal modes and infrared intensities? Also, do we have other options like running MD calculations and doing an FT of some correlation function? Any information, hints or pointers are very welcome! Thanks in advance, Gert Gert von Helden Dept. of molecular and Laser Physics, University of Nijmegen, Netherlands e-mail: gertvh@sci.kun.nl, phone: (+31) 24 3652179, fax: (+31) 24 3653311 From chemistry-request@server.ccl.net Fri Dec 3 06:32:50 1999 Received: from mail-b.bcc.ac.uk (mail-b.bcc.ac.uk [144.82.100.22]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id GAA30506 for ; Fri, 3 Dec 1999 06:32:50 -0500 Received: from biochem.ucl.ac.uk (actually host bsmori1.biochem.ucl.ac.uk) by mail-b.bcc.ac.uk with SMTP (XT-PP) with ESMTP; Fri, 3 Dec 1999 10:23:53 +0000 Received: from bsmir18.biochem.ucl.ac.uk (bsmir18 [128.40.46.21]) by biochem.ucl.ac.uk (8.9.2/8.9.1) with ESMTP id KAA08393 for ; Fri, 3 Dec 1999 10:24:06 GMT Received: from localhost (nobeli@localhost) by bsmir18.biochem.ucl.ac.uk (8.9.3/8.9.3) with SMTP id KAA11746 for ; Fri, 3 Dec 1999 10:24:06 GMT X-Authentication-Warning: bsmir18.biochem.ucl.ac.uk: nobeli owned process doing -bs Date: Fri, 3 Dec 1999 10:24:06 +0000 ("GMT) From: Irene Nobeli X-Sender: nobeli@bsmir18 To: Computational Chemistry List Subject: DOCK: ligand moving out of grid Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear CCL readers Someone asked a couple of days ago how to stop a peptide moving out of the binding site in Autodock. I have a similar problem with DOCK. I have a sugar that moves completely out of the grid I have defined during the docking. All my spheres are well inside the grid with a comfortable margin around them, but I don't seem to be able to stop the molecule from moving out. Is there some parameter that can control this? Many thanks I. ------------------------------------------------ Irene (Irilenia) Nobeli Biomolecular Structure and Modelling Unit Department of Biochemistry and Molecular Biology University College London Darwin Building Gower Street London WC1E 6BT nobeli@biochem.ucl.ac.uk 0171-419 3890 0171 504 2171 >>> I wanted to go out and change the world but... I couldn't find a babysitter <<< From chemistry-request@server.ccl.net Fri Dec 3 11:46:59 1999 Received: from sirocco.cc.mcgill.ca (sirocco.CC.McGill.CA [132.206.27.12]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id LAA32543 for ; Fri, 3 Dec 1999 11:46:59 -0500 Received: from lansend.cc.mcgill.ca (lansend.CC.McGill.CA [132.206.37.4]) by sirocco.cc.mcgill.ca (8.9.1/8.9.1) with SMTP id KAA05279 for ; Fri, 3 Dec 1999 10:39:26 -0500 (EST) Message-Id: <199912031539.KAA05279@sirocco.cc.mcgill.ca> Received: by MicroMailer 3.72 (.Lan.McGill.CA) on Fri, 03 Dec 1999 10:23:11 -0500 From: "Balakrishnan Viswanathan" Organization: Chemistry Dept., McGill University To: chemistry@ccl.net Date: Fri, 3 Dec 1999 10:19:16 -0500 MIME-Version: 1.0 Content-type: text/plain; charset=US-ASCII Content-transfer-encoding: 7BIT Subject: Transition States for Reactions with no Activation Barrier Reply-to: viswana@chemistry.mcgill.ca X-Confirm-Reading-To: viswana@chemistry.mcgill.ca X-pmrqc: 1 Priority: normal X-mailer: Pegasus Mail for Win32 (v3.01d) Greetings to all members, I have been attempting to calculate reaction rates for gas phase radical reactions involving high atomic weight transition metals using Gaussian 98 for Windows. I observed that some of these reactions occur with no activation barrier, (ie) the potential curve obtained is the classic Morse curve. I would like to know how, in this case, the transition state is derived and where I can find more reading on such procedures. Thanking you. Sincerely, Balakrishnan Balakrishnan Viswanathan viswana@chemistry.mcgill.ca Lab: (514) 398-6920 Fax: (514) 398-2382 From chemistry-request@server.ccl.net Fri Dec 3 11:55:11 1999 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 LAA32601 for ; Fri, 3 Dec 1999 11:55:11 -0500 Received: from iaf.uquebec.ca ([198.168.44.40]) by lambda.inrs.uquebec.ca (Netscape Messaging Server 3.62) with ESMTP id 387 for ; Fri, 3 Dec 1999 10:46:00 -0500 Message-ID: <3847E7FC.6EC00D10@iaf.uquebec.ca> Date: Fri, 03 Dec 1999 10:55:41 -0500 From: "Jianhui Wu" X-Mailer: Mozilla 4.5 [en] (Win95; I) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net Subject: InsightII, PBC, counter ions Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit Dear all, I am trying to model ligand-protein interaction using discovery within InsightII (version 97). I would like to solvate the system by PBC water box. The protein has –12 charge (ligand is neutral). Is it essential to add the counter ions in the system to neutralize the net charge before a PBC discovery calculation (MM or MD) is performed? (Probably, yes) I find counter_ion.bcl in the $BIOSYM/gifts/insight/BCL/ directory. It is for DNA stuff. It seems that 12 Na+ ions have to be put into the 12 most negative charged position (somewhere in the protein, I guess), how can I find these position? Any help will be greatly appreciated. Yours sincerely, Jian Hui, Wu email : JianHui_Wu@IAF.Uquenebec.ca From chemistry-request@server.ccl.net Fri Dec 3 12:20:10 1999 Received: from prserv.net (out4.prserv.net [165.87.194.239]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id MAA00061 for ; Fri, 3 Dec 1999 12:20:09 -0500 From: jmmckel@attglobal.net Received: from schutz ([32.100.232.236]) by prserv.net (out4) with SMTP id <19991203161231239037emnae>; Fri, 3 Dec 1999 16:12:32 +0000 Message-ID: <3848F9BD.1228@attglobal.net> Date: Sat, 04 Dec 1999 11:23:41 +0000 Reply-To: jmmckel@attglobal.net X-Mailer: Mozilla 3.04 (WinNT; I) MIME-Version: 1.0 To: chemistry@ccl.net Subject: the BLAS Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hello... Can someone please remind me where I can find the source code for the BLAS? Thanks! John McKelvey From chemistry-request@server.ccl.net Fri Dec 3 12:32:36 1999 Received: from nucleus.harvard.edu (nucleus.harvard.edu [140.247.90.196]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id MAA00156 for ; Fri, 3 Dec 1999 12:32:36 -0500 Received: from localhost (daizadeh@localhost) by nucleus.harvard.edu (8.9.3/8.9.3) with ESMTP id LAA01690; Fri, 3 Dec 1999 11:27:31 -0500 (EST) Date: Fri, 3 Dec 1999 11:27:31 -0500 (EST) From: Iraj Daizadeh To: jmmckel@attglobal.net cc: chemistry@ccl.net Subject: Re: CCL:the BLAS In-Reply-To: <3848F9BD.1228@attglobal.net> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII netlib.org iraj On Sat, 4 Dec 1999 jmmckel@attglobal.net wrote: > Hello... > > Can someone please remind me where I can find the source code for the > BLAS? > > Thanks! > > John McKelvey > > -= 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 Fri Dec 3 12:58:51 1999 Received: from cuces.unisi.it (cuces.unisi.it [193.205.4.2]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id MAA00313 for ; Fri, 3 Dec 1999 12:58:50 -0500 Received: from neriserv.chim.unisi.it (picciuno.bio-mol.unisi.it [192.167.124.24]) by unisi.it (PMDF V5.2-32 #31247) with ESMTP id <01JJ2NU7QGXM00121L@unisi.it> for chemistry@www.ccl.net; Fri, 3 Dec 1999 17:51:15 MET Date: Fri, 03 Dec 1999 17:53:33 +0100 From: Andrea Bernini Subject: evaluation of intermolecular interactions To: Computational Chemistry list Message-id: <3847F58D.7F522311@neriserv.chim.unisi.it> Organization: Diparttimento Biologia Molecolare MIME-version: 1.0 X-Mailer: Mozilla 4.5 [it] (WinNT; I) Content-type: text/plain; charset=us-ascii Content-transfer-encoding: 7bit X-Accept-Language: en, it Dear CCL'ers I'm searching for free software that, giving in input a pdb file of a two or more protein complex, can give an evaluation of all intermolecular interactions of any kind as output, have you suggestions? Thanks, Andrea. From chemistry-request@server.ccl.net Fri Dec 3 13:03:06 1999 Received: from postoffice.npac.syr.edu (postoffice.npac.syr.edu [128.230.7.230]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id NAA00363 for ; Fri, 3 Dec 1999 13:03:06 -0500 Received: from snake.npac.syr.edu (snake.npac.syr.edu [128.230.162.60]) by postoffice.npac.syr.edu (8.9.3/8.9.3) with ESMTP id LAA14444; Fri, 3 Dec 1999 11:55:31 -0500 (EST) Received: from npac.syr.edu (bernhold@localhost) by snake.npac.syr.edu (8.9.3/8.9.3) with ESMTP id LAA08533; Fri, 3 Dec 1999 11:55:30 -0500 (EST) Message-Id: <199912031655.LAA08533@snake.npac.syr.edu> X-Authentication-Warning: snake.npac.syr.edu: bernhold owned process doing -bs Reply-to: bernhold@npac.syr.edu To: jmmckel@attglobal.net cc: chemistry@ccl.net cc: bernhold@npac.syr.edu Subject: Re: CCL:the BLAS In-reply-to: Message from jmmckel@attglobal.net of "Sat, 04 Dec 1999 11:23:41 GMT." <3848F9BD.1228@attglobal.net> MIME-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Content-ID: <8551.944240129.1@npac.syr.edu> Date: Fri, 03 Dec 1999 11:55:30 -0500 From: "David E. Bernholdt" John, www.netlib.org is the cannonical location for a large body of numerical linear algebra software, including BLAS, LAPACK, and much more. -- David E. Bernholdt | Email: bernhold@npac.syr.edu Northeast Parallel Architectures Center | Phone: +1 315 443 3857 111 College Place, Syracuse University | Fax: +1 315 443 1973 Syracuse, NY 13244-4100 | URL: http://www.npac.syr.edu From chemistry-request@server.ccl.net Fri Dec 3 13:31:29 1999 Received: from igor.wag.caltech.edu (igor.wag.caltech.edu [131.215.33.3]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id NAA00564 for ; Fri, 3 Dec 1999 13:31:29 -0500 Received: from wag.caltech.edu (octane2 [131.215.33.125]) by igor.wag.caltech.edu (8.9.3/8.9.3) with ESMTP id JAA14646 for ; Fri, 3 Dec 1999 09:23:54 -0800 (PST) Sender: rpm@wag.caltech.edu Message-ID: <3847FCA9.36C353FB@wag.caltech.edu> Date: Fri, 03 Dec 1999 09:23:54 -0800 From: "Richard P. Muller" X-Mailer: Mozilla 4.6 [en] (X11; U; IRIX64 6.4 IP30) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net Subject: BLAS Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Unknown wrote: > > From owner-chemistry@server.ccl.net Fri Dec 3 08:59:41 1999 > Received: from server.ccl.net (server.ccl.net [192.153.40.39]) > by igor.wag.caltech.edu (8.9.3/8.9.3) with ESMTP id IAA14294 > for ; Fri, 3 Dec 1999 08:59:41 -0800 (PST) > Received: (from root@localhost) > by server.ccl.net (8.8.7/8.8.7) id MAA00093 > for ccl4; Fri, 3 Dec 1999 12:22:39 -0500 > Received: from prserv.net (out4.prserv.net [165.87.194.239]) > by server.ccl.net (8.8.7/8.8.7) with ESMTP id MAA00061 > for ; Fri, 3 Dec 1999 12:20:09 -0500 > From: jmmckel@attglobal.net > Received: from schutz ([32.100.232.236]) by prserv.net (out4) with SMTP > > Hello... > > Can someone please remind me where I can find the source code for the > BLAS? > > Thanks! > > John McKelvey The netlib repository is a good place to find BLAS, as well as LAPACK and many other math libraries. You can access them at: http://netlib2.cs.utk.edu/ Rick -- Richard P. Muller, Ph.D. rpm@wag.caltech.edu http://www.wag.caltech.edu/home/rpm From chemistry-request@server.ccl.net Fri Dec 3 13:52:56 1999 Received: from smtpsrv0.isis.unc.edu (smtpsrv0.isis.unc.edu [152.2.1.139]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id NAA00732 for ; Fri, 3 Dec 1999 13:52:56 -0500 Received: from email.unc.edu (viggan@login2.isis.unc.edu [152.2.25.132]) by smtpsrv0.isis.unc.edu (8.9.3/8.9.1) with ESMTP id MAA00793 for ; Fri, 3 Dec 1999 12:45:31 -0500 (EST) Received: (from viggan@localhost) by email.unc.edu (8.9.3/8.9.3) id MAA102644; Fri, 3 Dec 1999 12:45:21 -0500 Date: Fri, 3 Dec 1999 12:45:21 -0500 (EST) From: Ganesh Ethiraj X-Sender: viggan@login2.isis.unc.edu To: chemistry@ccl.net Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hello, Could somebody please comment on performance of FlexiDock module avaiable in Sybyl. Is there published literature available using FlexiDock. Thanks Ganesh From chemistry-request@server.ccl.net Fri Dec 3 13:50:34 1999 Received: from smtpsrv0.isis.unc.edu (smtpsrv0.isis.unc.edu [152.2.1.139]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id NAA00709 for ; Fri, 3 Dec 1999 13:50:33 -0500 Received: from email.unc.edu (viggan@login2.isis.unc.edu [152.2.25.132]) by smtpsrv0.isis.unc.edu (8.9.3/8.9.1) with ESMTP id MAA00353 for ; Fri, 3 Dec 1999 12:43:08 -0500 (EST) Received: (from viggan@localhost) by email.unc.edu (8.9.3/8.9.3) id MAA85722; Fri, 3 Dec 1999 12:42:57 -0500 Date: Fri, 3 Dec 1999 12:42:56 -0500 (EST) From: Ganesh Ethiraj X-Sender: viggan@login2.isis.unc.edu To: chemistry@ccl.net Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hello, Is anybody aware of any references regarding database searching for DHFR.If there is please let me know. Thanks Ganesh From chemistry-request@server.ccl.net Fri Dec 3 14:19:59 1999 Received: from caliper-server3.calipertech.com (seven.calpr.com [206.86.242.7]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id OAA00881 for ; Fri, 3 Dec 1999 14:19:59 -0500 Received: by seven.calpr.com with Internet Mail Service (5.5.2448.0) id ; Fri, 3 Dec 1999 10:03:07 -0800 Message-ID: <7CDB70B0AC00D3119ECF00105A12745C0E0CFE@seven.calpr.com> From: Nick Hodge To: "'chemistry@server.ccl.net'" Subject: Extinction Coefficients Date: Fri, 3 Dec 1999 10:03:05 -0800 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2448.0) Content-Type: text/plain Dear CCL, Does anyone know of a table (preferably in digital form) of extinction coefficients and lamda(max) for organic molecules? The CRC Index has a reasonable collection but is there anything more extensive? Thanks, Nick Hodge C. Nicholas Hodge, Ph.D. Director, Drug Discovery Technologies Caliper Technologies Corporation 605 Fairchild Drive Mountain View, CA 94043-2234 nick.hodge@calipertech.com www.calipertech.com (650) 623-0761 (650) 623-0500 (fax) From chemistry-request@server.ccl.net Fri Dec 3 17:50:38 1999 Received: from harvey.caam.rice.edu (harvey.caam.rice.edu [128.42.17.97]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id RAA01835 for ; Fri, 3 Dec 1999 17:50:37 -0500 Received: (from zdenko@localhost) by harvey.caam.rice.edu (8.8.8/8.8.8) id PAA22037; Fri, 3 Dec 1999 15:42:45 -0600 (CST) Date: Fri, 3 Dec 1999 15:42:45 -0600 (CST) Message-Id: <199912032142.PAA22037@harvey.caam.rice.edu> From: Zdenko Tomasic To: jmmckel@attglobal.net CC: chemistry@ccl.net In-reply-to: <3848F9BD.1228@attglobal.net> (jmmckel@attglobal.net) Subject: Re: CCL:the BLAS 1) your computer vendor for machine optimized blas 2) www.netlib.org for generic blas ZT