From mcbskt@leonis.nus.sg Wed Aug 27 03:20:20 1997 Received: from sable.nus.sg for mcbskt@leonis.nus.sg by www.ccl.net (8.8.3/950822.1) id CAA29516; Wed, 27 Aug 1997 02:55:46 -0400 (EDT) Received: from leonis.nus.sg (root@leonis.nus.sg [137.132.1.18]) by sable.nus.sg (8.8.4/8.6.9) with ESMTP id OAA09336 for ; Wed, 27 Aug 1997 14:55:12 +0800 (SST) Received: from [137.132.43.94] ([137.132.43.94]) by leonis.nus.sg (8.6.10/8.6.9/CNS-3.5) with ESMTP id OAA19190 for ; Wed, 27 Aug 1997 14:55:07 +0800 Message-Id: Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Wed, 27 Aug 1997 15:08:20 +1410 To: CHEMISTRY@www.ccl.net From: "Kah-Tong, Seow" Subject: Summary: :Searching thge PDB database using the 3D protein structures My previous request was: >I would appreciate any help in getting some references or review articles on >web servers which provide the service to search PDB database with the 3D >protein structure coordinates. The summary: 1) Accessing the PDB database http://www.pdb.bnl.gov/ there is a 3D browser, where you can search for structures based on their names, authors etc. Rolf-Dietrich Stigler e-mail: rolf@immunologie.charite.hu-berlin.de I know the web site "http://www2.ebi.ac.uk/pdb/" to find some data using the 3D protein structures Nathalie Vancampenhout, Ph.D. e-mail: nathalie@chbs.ciba.com 2) other databases From: Les Clowney To: mcbskt@leonis.nus.sg Subject: accessing pdb Hello, You might be interested in the "Protein Finder" available at http://ndb.rutgers.edu . Les 3) Journal articles Susman, Nature Structural Biology 4(7) 1997 p. 517 or better still Stampf et al., Nature 374 (1995) pp. 572-574. Ed E. Moret E-mail: E.E.Moret@far.ruu.nl To all who responded, thank you. one of the servers suggested by friends but not listed above is the Dali Server http://www.embl-heidelberg.de/dali/dali.html The Dali server is a network service for comparing protein structures in 3D. You submit the coordinates of a query protein structure and Dali compares them against those in the Protein Data Bank. Kah-Tong, Seow From gjlinker@geocities.com Wed Aug 27 08:20:22 1997 Received: from geocities.com for gjlinker@geocities.com by www.ccl.net (8.8.3/950822.1) id IAA00708; Wed, 27 Aug 1997 08:09:25 -0400 (EDT) Received: from m4ld351.sct.co.uk ([194.130.240.161]) by geocities.com (8.8.5/8.8.5) with ESMTP id FAA15265 for ; Wed, 27 Aug 1997 05:08:32 -0700 (PDT) Message-Id: <199708271208.FAA15265@geocities.com> From: "Gerrit-Jan's Geocities mail" To: Subject: Standard Color codes for atoms Date: Wed, 27 Aug 1997 13:06:52 +0100 X-MSMail-Priority: Normal X-Priority: 3 X-Mailer: Microsoft Internet Mail 4.70.1155 MIME-Version: 1.0 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Hello all, I am looking for the standard color codes for atoms. As far as I can remember the standard color for Carbon is black, the one for Oxigen is blue, Nitrogen is Green. But I am not sure, I am just guessing. Does anyone know where to get (a more complete) list of color codes for atoms ? I need this information for a molecule viewer I am developing. Kind regards, Gerrit-Jan Linker Analyst/Programmer @ SCT International, Manchester, UK web: http://members.aol.com/gjlinker email: gjlinker@geocities.com From jmartell@lyon.edu Wed Aug 27 10:20:23 1997 Received: from lorien for jmartell@lyon.edu by www.ccl.net (8.8.3/950822.1) id KAA01198; Wed, 27 Aug 1997 10:13:52 -0400 (EDT) Received: by lorien.lyon.edu (UCX V4.1-12, OpenVMS V6.0 VAX); Wed, 27 Aug 1997 09:08:34 -0500 X-Sender: jmartell@lorien.lyon.edu Message-Id: Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Wed, 27 Aug 1997 09:19:06 -0600 To: chemistry@www.ccl.net From: jmartell@lyon.edu (Jaime Martell) Subject: Digital Personal Workstations Dear CClers I am considering buying a Digital Personal Workstation, 500 au. I believe these have only been on the market a few months, so I am wondering if anyone has experience with them. Specifically, I want something that will run Gaussian and other ab initio programs, and to be able to do all the functions of a Unix workstation and a PC on one machine. I would appreciate comments from anyone on the list who has used anything in the au series. Thanks for all replies. Jaime Jaime Martell, Ph.D. Camille and Henry Dreyfus Fellow Division of Biology and Chemistry Lyon College Batesville, AR 72501 From JANET.CICARIELLO-COOK@roche.com Wed Aug 27 10:28:35 1997 Received: from gatekeeper.roche.com for JANET.CICARIELLO-COOK@roche.com by www.ccl.net (8.8.3/950822.1) id KAA01136; Wed, 27 Aug 1997 10:02:00 -0400 (EDT) Received: by gatekeeper.roche.com (5.65v3.2/fma-120691); id AA18062; Wed, 27 Aug 1997 10:00:09 -0400 Received: from rnuc01.nut.roche.com by mailgate.roche.com; (5.65v3.2/1.1.8.2/20Mar96-0227PM) id AA04728; Wed, 27 Aug 1997 10:02:02 -0400 Received: from mr.nut.roche.com by Roche.COM (PMDF V5.1-8 #22401) id <01IMXI4SM974019PVQ@Roche.COM> for chemistry@www.ccl.net; Wed, 27 Aug 1997 10:00:43 EDT Received: with PMDF-MR; Wed, 27 Aug 1997 09:55:48 -0400 (EDT) Mr-Received: by mta RNIS08; Relayed; Wed, 27 Aug 1997 09:55:48 -0400 Mr-Received: by mta RNUC01; Relayed; Wed, 27 Aug 1997 10:00:35 -0400 Alternate-Recipient: prohibited Date: Wed, 27 Aug 1997 09:55:48 -0400 (EDT) From: JANET CICARIELLO-COOK 57165 Subject: Standard Color Codes To: chemistry@www.ccl.net Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; CHARSET=US-ASCII Posting-Date: Wed, 27 Aug 1997 09:55:50 -0400 (EDT) Importance: normal Priority: normal Ua-Content-Id: E1793IZN25GZH X400-Mts-Identifier: [;84559072807991/803008@RNISD0] A1-Type: MAIL Hop-Count: 2 Hi, I think most major software packages use something like this: C=Black or White if background is Black N=Blue O=Red H=Cyan S=Yellow P=Orangish(?) or Yellow Halogens=Green Janet ********************************************* * Janet Cicariello-Cook, Ph.D. * * Hoffmann-LaRoche, Inc. * * 340 Kingsland St. * * Nutley, NJ 07110 * * ph: (201) 235-7165 * * fax: (201) 235-7292 * * e-mail: janet.cicariello-cook@roche.com * ********************************************* >>I am looking for the standard color codes for atoms. As far as I can >>remember the standard color for Carbon is black, the one for Oxigen is >>blue, Nitrogen is Green. But I am not sure, I am just guessing. >>Does anyone know where to get (a more complete) list of color codes for >>atoms ? >>I need this information for a molecule viewer I am developing. >>Kind regards, Gerrit-Jan Linker >>Analyst/Programmer @ SCT International, Manchester, UK >>web: http://members.aol.com/gjlinker >>email: gjlinker@geocities.com From newhoir@mail.auburn.edu Wed Aug 27 10:34:06 1997 Received: from mallard.duc.auburn.edu for newhoir@mail.auburn.edu by www.ccl.net (8.8.3/950822.1) id JAA01024; Wed, 27 Aug 1997 09:45:49 -0400 (EDT) Received: from localhost by mallard.duc.auburn.edu (SMI-8.6/SMI-SVR4) id IAA18278; Wed, 27 Aug 1997 08:45:29 -0500 Date: Wed, 27 Aug 1997 08:45:29 -0500 (CDT) From: Irene Newhouse X-Sender: newhoir@mallard To: "Jaime E. Combariza" cc: chemistry@www.ccl.net Subject: Re: CCL:G:G94 on SGI irix6.4 In-Reply-To: <199708261632.KAA17510@pecos.rc.arizona.edu> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII We have an o2k here & have G94 on it. We did not mess with with Gaussian INc's flags & used f77 -mp, but no -pfa. G94 does itsown autotasking & Gaussian Inc would probably tell you not to change their flags. The code is so baroque slight changes can tangle it up hopelessly [don't quote this to a general audience -- I need to keep Gaussian Inc talking to me!!!] We do get a lot of warnings aoubt weak definitions, but it compiles. We do not get duplicate object messages; there seems to be some problem with with your files to get that. Good luck! Irene Newhouse On Tue, 26 Aug 1997, Jaime E. Combariza wrote: > Has anyone attempted to compile Gaussian 94 on an Origin2000 running > Irix 6.4 and the power compilers? > > I am getting a lot of warnings mainly due to duplication of objects > in different libraries and a few about dependences and even a couple > of warnings due to division by zero!!! > > This is what I am getting when I try to run the program: > > 25689:/scr2/jaimeco/g94/g94: rld: Fatal Error: cannot successfully map soname 'u > til.so' under any of the filenames /usr/lib64/util.so:/lib64/util.so:/usr/lib/64 > bit/util.so:/lib/64bit/util.so: > > > Please reply directly to me and I will send a summary to the list. > > > jaime Combariza > jaimeco@arizona.edu > > > -------This is added Automatically by the Software-------- > -- Original Sender Envelope Address: jaimeco@pecos.rc.arizona.edu > -- Original Sender From: Address: jaimeco@pecos.rc.arizona.edu > CHEMISTRY@www.ccl.net: Everybody | CHEMISTRY-REQUEST@www.ccl.net: Coordinator > MAILSERV@www.ccl.net: HELP CHEMISTRY or HELP SEARCH | Gopher: www.ccl.net 73 > Anon. ftp: www.ccl.net | CHEMISTRY-SEARCH@www.ccl.net -- archive search > Web: http://www.ccl.net/chemistry.html > > From anh@chm.ulaval.ca Wed Aug 27 11:20:25 1997 Received: from cerberus.ulaval.ca for anh@chm.ulaval.ca by www.ccl.net (8.8.3/950822.1) id LAA01454; Wed, 27 Aug 1997 11:02:16 -0400 (EDT) Received: from fluor.chm.ulaval.ca (fluor.chm.ulaval.ca [132.203.70.9]) by cerberus.ulaval.ca (8.7.5/8.7.3) with ESMTP id LAA07506; Wed, 27 Aug 1997 11:15:01 -0400 (EDT) Received: (from anh@localhost) by fluor.chm.ulaval.ca (8.6.12/8.6.12) id KAA07737; Wed, 27 Aug 1997 10:40:23 -0400 From: "Nguyen N. Anh" Message-Id: <9708271040.ZM7735@fluor.chm.ulaval.ca> Date: Wed, 27 Aug 1997 10:40:20 -0400 In-Reply-To: "Dr. Heinz Schiffer" "CCL:Breakdown of Born-Oppenheimer approx." (Aug 26, 9:11am) References: <3402818D.41C6@h1tw0036.hoechst.com> X-Mailer: Z-Mail (3.2.1 6apr95 MediaMail) To: "Dr. Heinz Schiffer" Subject: Re: CCL:Breakdown of Born-Oppenheimer approx. Cc: chemistry@www.ccl.net Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii > But I am not aware of > any recent calculations using adiabatic or non-adiabatic corrections > to the BO potential energy surface of molecules. May be some one else > know something about that. It would be interessting to hear about it > on the list. One of the good papers I've read is Y.Marechal J. Chem. Phys. 83, 247 (1985) The author introduces a phase shift between the response of the electronic wave function to changes in the nuclear configuration. This response is considered instantaneous in the BO approximation. The IR paradox disappears in this treatment. Futhermore it allows us to deal with systems whose ratios of energies or masses are not favorable. Ragards -- Nguyen Nam Anh Quebec, Canada E-mail: anh@chm.ulaval.ca WWW: http://promethium.chm.ulaval.ca/~anh/ From intsim.com!haun@news.cts.com Wed Aug 27 13:20:25 1997 Received: from mailhub.cts.com for intsim.com!haun@news.cts.com by www.ccl.net (8.8.3/950822.1) id MAA01963; Wed, 27 Aug 1997 12:54:25 -0400 (EDT) Received: from donews.cts.com(really [192.188.72.21]) by mailhub.cts.com via smail with smtp id for ; Wed, 27 Aug 97 09:54:24 -0700 (PDT) (Smail-3.1.92 1996-Mar-19 #3 built 1996-Apr-21) Received: from intsim.com by donews.cts.com with uucp (Smail3.1.29.1 #5) id m0x3lMN-00003EC; Wed, 27 Aug 97 09:54 PDT Received: from topi.intsim.com by zebra.intsim.com via SMTP (931110.SGI/930416.SGI.AUTO) for CHEMISTRY@www.ccl.net id AA29858; Wed, 27 Aug 97 09:48:57 -0700 Message-Id: <2.2.32.19970827165449.00693e40@zebra.intsim.com> X-Sender: haun@zebra.intsim.com X-Mailer: Windows Eudora Pro Version 2.2 (32) Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Wed, 27 Aug 1997 09:54:49 -0700 To: "Kah-Tong, Seow" From: Dan Haun Subject: Re: CCL:Summary: :Searching thge PDB database using the 3D protein structures Cc: CHEMISTRY@www.ccl.net Dear Kah-Tong, You may also visit Interactive Simulation's web site where you can access MDL's ChemScape Chime where you can search for PDB coordinates. http://www.intsim.com. Cheers, Dan Haun At 03:08 PM 8/27/97 +1410, Kah-Tong, Seow wrote: >My previous request was: > >>I would appreciate any help in getting some references or review articles on >>web servers which provide the service to search PDB database with the 3D >>protein structure coordinates. > >The summary: > >1) Accessing the PDB database > >http://www.pdb.bnl.gov/ > >there is a 3D browser, where you can search for structures based on >their names, authors etc. > >Rolf-Dietrich Stigler >e-mail: rolf@immunologie.charite.hu-berlin.de > > >I know the web site "http://www2.ebi.ac.uk/pdb/" to find some data using the 3D >protein structures > > >Nathalie Vancampenhout, Ph.D. > e-mail: nathalie@chbs.ciba.com > >2) other databases > >From: Les Clowney >To: mcbskt@leonis.nus.sg >Subject: accessing pdb > >Hello, > You might be interested in the "Protein Finder" available at >http://ndb.rutgers.edu . >Les > > >3) Journal articles > >Susman, Nature Structural Biology 4(7) 1997 p. 517 or better still >Stampf et al., Nature 374 (1995) pp. 572-574. > >Ed E. Moret >E-mail: E.E.Moret@far.ruu.nl > > >To all who responded, thank you. > >one of the servers suggested by friends but not listed above is the Dali Server >http://www.embl-heidelberg.de/dali/dali.html >The Dali server is a network service for comparing protein structures in >3D. You submit the >coordinates of a query protein structure and Dali compares them against >those in the Protein Data >Bank. > >Kah-Tong, Seow > > > >-------This is added Automatically by the Software-------- >-- Original Sender Envelope Address: mcbskt@leonis.nus.sg >-- Original Sender From: Address: mcbskt@leonis.nus.sg >CHEMISTRY@www.ccl.net: Everybody | CHEMISTRY-REQUEST@www.ccl.net: Coordinator >MAILSERV@www.ccl.net: HELP CHEMISTRY or HELP SEARCH | Gopher: www.ccl.net 73 >Anon. ftp: www.ccl.net | CHEMISTRY-SEARCH@www.ccl.net -- archive search > Web: http://www.ccl.net/chemistry.html > > Daniel P. Haun Tel: (619) 658-9462 Interactive Simulations Inc. Toll Free: (888) 272-8578 5330 Carroll Canyon Rd. Email: haun@intsim.com San Diego, CA 92121 Fax: (619) 658-9463 Web site http://www.intsim.com From bausch@chem.vill.edu Wed Aug 27 15:20:25 1997 Received: from rs6chem.chem.vill.edu for bausch@chem.vill.edu by www.ccl.net (8.8.3/950822.1) id OAA02554; Wed, 27 Aug 1997 14:45:56 -0400 (EDT) Received: from [153.104.73.18] (bausch.chem.vill.edu [153.104.73.18]) by rs6chem.chem.vill.edu (8.8.5/8.8.5) with SMTP id OAA13629 for ; Wed, 27 Aug 1997 14:52:24 -0400 Message-Id: Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Wed, 27 Aug 1997 02:46:41 -0500 To: CHEMISTRY@www.ccl.net From: bausch@chem.vill.edu (Joseph W. Bausch) Subject: cache size affecting G94 calcs With the help of some on the ccl, I (well, my students!) have succeeded in getting G94 up and running on a DualPentiumPro operating with linux. For those of you out there that may be thinking about going this route with the cheapness of the pentiums these day, it isn't too hard to set up and get going, and this was my groups first attempt at setting up a linux box from scratch. It is nice to see that the speed with which this machine runs the seven G94 test jobs frequently quoted in this group is pretty impressive. However, on the few calculations that I have done of interest to me, it seems the performance of my system drops significantly when a larger molecule is calculated. I base this on the same calcs I do on an rs6000, which run much faster. However, on the seven G94 test jobs, this linux box is faster than the rs6000. So I am curious as the reason for this, and wonder if anyone out there running G94 on a PentiumPro running linux has noticed the same thing. Is there any solutions to this problem? Is it related to having a 256K L2 cache on the Pentium? Would performance increase dramatically with a 512K cache? (Note: I am giving these jobs plenty of memory and according to the top command, they are getting full cpu power on the linux box, with little or no swapping going on). Thanks in advance (and I'll summarize if there is suitable interest), Joe bausch@chem.vill.edu -------