From chemistry-request@server.ccl.net Wed Jul 18 02:56:16 2001 Received: from unlserve.unl.edu ([129.93.1.130]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f6I6uG505557 for ; Wed, 18 Jul 2001 02:56:16 -0400 Received: from localhost (rrashid@localhost) by unlserve.unl.edu (8.9.1a/8.9.2) with SMTP id BAA45724; Wed, 18 Jul 2001 01:38:43 -0500 Date: Wed, 18 Jul 2001 01:38:43 -0500 (CDT) From: Ali N Rashid To: Benjamin.Moritz@asu.edu cc: chemistry@ccl.net, help@gaussian.com Subject: Re: CCL:Route Line In-Reply-To: <995409747.3b54bf538805d@webmail2.asu.edu> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Benjamin, I think your problem is with the length of the first line. I think Gausian only take line with 70 some characters everything else gets lost. > From what I know, Gaussian only recognizes empty lines as separators. So you can take your long line and split it into tow lines or three lines of smaller sises as long as there is no empty line it will understad it as the job input. Hope this helps. Ali On Tue, 17 Jul 2001 Benjamin.Moritz@asu.edu wrote: > Dear All, > > I'm trying to run a G98 problem and I have a long list of keywords in my route > section, which in turn causes G98 to break the line into two lines causing a > syntax error. Is there a way to correct for this? The input file is below, and > the error occurs in the second job. Thanks in advance. > > > %chk=cuOO > %mem=3gb > > # HF/3-21G* stable(ruhf,opt) scf=maxcycle=500 > > cuOO optimization > > 1 3 > Cu > O,1,R2 > O,1,R3,2,A3 > O,1,R4,2,A4,3,D4,0 > O,4,R5,1,A5,2,D5,0 > H,3,R6,1,A6,2,D6,0 > H,2,R7,1,A7,3,D7,0 > H,2,R8,1,A8,7,D8,0 > H,3,R9,1,A9,6,D9,0 > Variables: > R2=1.804 > R3=1.88504075 > R4=1.85527981 > R5=1.244 > R6=0.96673229 > R7=0.96674287 > R8=0.96615526 > R9=0.96616383 > A3=110.27970585 > A4=124.81858691 > A5=125.97567183 > A6=122.29814425 > A7=122.37407004 > A8=128.33421827 > A9=128.43244722 > D4=179.88894814 > D5=-80.69663424 > D6=-170.33004164 > D7=-167.17453856 > D8=-176.29123573 > D9=-176.66185433 > > --Link1-- > %chk=cuOO > %mem=3gb > > #uhf/3-21G* opt(maxcycle=200) freq=noraman geom=allcheck guess=read > scf=maxcycle=500 gfprint pop=full > > > > > ******************************************************************************** > Benjamin J. Moritz Work: 480-965-8509 > College of Engineering and Applied Sciences Mailto:bmoritz@asu.edu > Dept. of Chemical & Materials Engineering > PO Box 876006 > Tempe, AZ > 85287-6006 > ******************************************************************************** > > -= 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 Wed Jul 18 03:25:09 2001 Received: from c2bapps9 ([193.113.154.18]) by server.ccl.net (8.11.0/8.11.0) with SMTP id f6I7P8506095 for ; Wed, 18 Jul 2001 03:25:08 -0400 Received: from patriot (actually host host217-32-161-43.hg.mdip.bt.net) by c2bapps9 with SMTP (XT-PP); Wed, 18 Jul 2001 08:24:55 +0100 From: "Roma Oakes" To: "ccl" Subject: addition of downloaded basis set help! Date: Wed, 18 Jul 2001 08:20:41 +0100 Message-ID: MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit X-Priority: 3 (Normal) X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook IMO, Build 9.0.2416 (9.0.2911.0) Importance: Normal X-MimeOLE: Produced By Microsoft MimeOLE V5.50.4133.2400 Dear all I am fairly new to computational chem. (6 months). I use Gaussian 98 on both a Linux and a windows system. Can someone explain, (in very simple terms) and one step at a time, how to get g98 to use a basis set that I have downloaded from http://www.dl.ac.uk/emsl_pnl/basisform.html It downloaded as a .rtf. I have located where the basis sets are stored on Linux (can't find them at all in the windows version!) I know that I need to use additional keywords but I can't figure out exactly what they ought to be - and where they should be put. All help gratefully received Roma Oakes r.oakes@qub.ac.uk From chemistry-request@server.ccl.net Wed Jul 18 03:25:36 2001 Received: from lancelot.imb-jena.de ([192.124.248.76]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f6I7PZ506130 for ; Wed, 18 Jul 2001 03:25:36 -0400 Received: (from pineda@localhost) by lancelot.imb-jena.de (SGI-8.9.3/8.8.8) id JAA32268 for chemistry@ccl.net; Wed, 18 Jul 2001 09:25:35 +0200 (CEST) From: pineda@imb-jena.de (Felipe Pineda) Message-Id: <10107180925.ZM32306@lancelot.imb-jena.de> Date: Wed, 18 Jul 2001 09:25:34 +0000 In-Reply-To: Jordi Villa "CCL:PhD fellowship on 3D-QSAR in Barcelona" (Jul 17, 11:31am) References: <3B5405FA.97F0C9ED@imim.es> X-Mailer: Z-Mail (3.2.3 08feb96 MediaMail) To: chemistry@ccl.net Subject: moloc Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii dear CCLers, i will very appreciate any opinion from the modeling/simulation community (small molecules/biomolecules) about the software package MOLOC, especially in comparison with other commercial and academic software (insight/sybyl suites, amber, charmm; cost/performance ratio etc.). Any pointer to relevant sources of information (benchmark information if it exists) would be also very helpful. thanks in advance & best regards felipe -- ********************************************************************** * Felipe Pineda,PhD * * Institut fuer Molekulare Biotechnologie * * AG Theoretische Biophysik * * Beutenbergstrasse 11, Jena Vox: +49-3641-65-6491 * * Postfach 100 813, D-07708 Jena, Germany Fax: -6495 * * web: www.imb-jena.de/~pineda * ********************************************************************** ********************************************************************** * DISCLAIMER: Unless indicated otherwise, everything in this note is * * my personal opinion, not an official statement of my employer * ********************************************************************** From chemistry-request@server.ccl.net Wed Jul 18 03:20:42 2001 Received: from mh1-munich.munich.accelrys.com ([192.190.183.254]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f6I7Kf506007 for ; Wed, 18 Jul 2001 03:20:41 -0400 Received: from woernitz.munich.accelrys.com ([172.29.64.178] helo=woernitz.munich.msi-eu.com) by mh1-munich.munich.accelrys.com with esmtp (Exim 3.12 #1 (Debian)) id 15MldN-0006gI-00 for ; Wed, 18 Jul 2001 09:20:37 +0200 Received: (from jxh@localhost) by woernitz.munich.msi-eu.com (8.8.8/8.8.8) id JAA28611 for CHEMISTRY@ccl.net; Wed, 18 Jul 2001 09:20:37 +0200 (MEST) From: "Joerg-Ruediger Hill" Message-Id: <10107180920.ZM28607@woernitz.munich.msi-eu.com> Date: Wed, 18 Jul 2001 09:20:36 +0200 X-Mailer: Z-Mail (3.2.3 08feb96 MediaMail) To: CHEMISTRY@ccl.net Subject: Re: CCL:GLw - GL Widget toolkit for Linux ? Mime-Version: 1.0 Content-Type: multipart/mixed; boundary="PART-BOUNDARY=.110107180920.ZM28607.munich.msi-eu.com" --PART-BOUNDARY=.110107180920.ZM28607.munich.msi-eu.com Content-Description: Text Content-Type: text/plain ; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable X-Zm-Decoding-Hint: mimencode -q -u > I am in the process of rewriting an old molecular graphics toolkit and > would like it to be both portable and flexible. > > OpenGL is an obvious chice for the molecule display, a number of > integrations of OpenGL into the X windows system are available. Some > integrations are smooth and use the GLU toolkit, but limited in user > control. The other option is GLX which allows low level control, but > does require a substantial amount of programming. A good solution > appears to be the GLw or GL Widget library supplied by SGI and as far a= s > I recall it is also avalable for IBM platforms. > > I have not seen any public domain GLw libraries - is anybody aware of > the existence of such a toolkit for Linux ? and if so does it work with= > Mesa ? There exists two versions of the GLw libraries. SGI has released the source code to its version and Mesa has its own enhanced version. If you download the Mesa source code you will get both versions in the directories widgets-sgi and widgets-mesa. You need to compile them separately from Mesa. J=F6rg-R=FCdiger Hill -- = -------------------------------------------------------------------------= ----- Dr. J=F6rg-R=FCdiger Hill | Phone +49 89 61459-413 | The opinions exp= ressed in Accelrys GmbH | Fax +49 89 61459-400 | this message are my= per- Inselkammerstrasse 1 | E-mail jxh@accelrys.com | sonal opinions an= d no D-82008 Unterhaching | | offical statements= of Germany | http://www.accelrys.com/ | Accelrys Inc. -------------------------------------------------------------------------= ----- --PART-BOUNDARY=.110107180920.ZM28607.munich.msi-eu.com-- From chemistry-request@server.ccl.net Wed Jul 18 08:16:14 2001 Received: from mta4.263.net ([202.96.44.46]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f6ICGD525467 for ; Wed, 18 Jul 2001 08:16:13 -0400 Received: by mta4.263.net (Postfix, from userid 60001) id 3B99B1C5DD830; Wed, 18 Jul 2001 20:17:40 +0800 (CST) Message-Id: <3B557E64.24239@mta4> Date: Wed, 18 Jul 2001 20:17:40 +0800 (CST) From: "chyhw" To: chemistry@ccl.net Subject: A question X-Priority: 3 X-Originating-IP: [202.38.82.74] X-Mailer: COREMAIL Dear CCL, For Gaussian 98,SCF=QC is only suitable for RHF and UHF,but not for complex or ROHF.When we use the keyword Complex or ROHF and encount convergence problems,how to solve the trouble? Sincerely yours, Chy. __________________________________________ IP卡、上网卡全线跳水价 http://shopping.263.net/category08.htm 古埃及订情饰物订做 http://shopping.263.net/category11.htm From chemistry-request@server.ccl.net Wed Jul 18 06:53:19 2001 Received: from server.mldnet.com (root@[212.56.192.20]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f6IArG524286 for ; Wed, 18 Jul 2001 06:53:16 -0400 Received: from spu (ppp-212.56.193.232.mldnet.com [212.56.193.232]) by server.mldnet.com (8.9.3/8.9.3) with SMTP id NAA24463 for ; Wed, 18 Jul 2001 13:52:54 +0300 Received: from SPU3 (192.168.1.3) by spu with MERCUR-SMTP/POP3/IMAP4-Server (v3.20.01 HS-0040000) for ; Wed, 18 Jul 2001 14:02:25 +0300 Date: Wed, 18 Jul 2001 14:02:17 +0300 From: Mike Peleah X-Mailer: The Bat! (v1.53d) Reply-To: Mike Peleah X-Priority: 3 (Normal) Message-ID: <810638867.20010718140217@spu.mldnet.com> X-Confirm-Reading-To: MikePeleah@yahoo.com Disposition-Notification-To: MikePeleah@yahoo.com To: CHEMISTRY@server.ccl.net Subject: Basis set(s) for Al and Cr MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear CHEMISTRY, Could somebody advice me good/best basis set to use for calculation of Al and Cr compounds? Best regards, Mike mailto:MikePeleah@yahoo.com From chemistry-request@server.ccl.net Wed Jul 18 02:45:07 2001 Received: from cascara.uvic.ca (root@[142.104.5.28]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f6I6j7504908 for ; Wed, 18 Jul 2001 02:45:07 -0400 Received: from pinc229.pinc.com (pinc229.pinc.com [199.60.118.229]) by cascara.uvic.ca (8.11.3/8.11.3) with SMTP id f6I6j5p44536 for ; Tue, 17 Jul 2001 23:45:05 -0700 From: Roy Jensen To: chemistry@ccl.net Subject: G98W on multi-processor computers Date: Tue, 17 Jul 2001 23:45:55 -0700 Message-ID: X-Mailer: Forte Agent 1.8/32.548 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 f6I6j7504909 It was recently discussed and agreed that Gaussian for Windows was compiled for a single processor. One suggestion was to run two jobs at once to make use of the second processor. How does one do this? I presume the method also works on quad-processor PCs. Thanks, Roy Jensen From chemistry-request@server.ccl.net Wed Jul 18 11:32:50 2001 Received: from physics.lsu.edu ([130.39.182.96]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f6IFWn530064 for ; Wed, 18 Jul 2001 11:32:49 -0400 Received: from localhost (vani@localhost) by physics.lsu.edu (8.9.2/8.9.2) with ESMTP id KAA14109 for ; Wed, 18 Jul 2001 10:32:09 -0500 (CDT) Date: Wed, 18 Jul 2001 10:32:08 -0500 (CDT) From: Vemparala Satyavani To: chemistry@ccl.net Subject: atom names in PDB files Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Iam new to PDB files. Iam having problems trying to correlate between the atom names in the file and the atoms in the actual structure of amino acids. for example the first three lines of glutamine acid in a protein are: ATOM 1 N GLN A 1 63.870 -23.035 -4.001 1.00 2.09 MCP1 N ATOM 2 CA GLN A 1 65.000 -22.112 -3.695 1.00 1.89 MCP1 C ATOM 3 C GLN A 1 64.534 -20.647 -3.880 1.00 1.67 MCP1 C my question is there are 2 Nitrogens, 5 carbons etc.,..in Glutamine residue. how would i know which corresponds to what? Thanks vani From chemistry-request@server.ccl.net Wed Jul 18 12:32:34 2001 Received: from mailhub1.shef.ac.uk ([143.167.1.9]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f6IGWX531431 for ; Wed, 18 Jul 2001 12:32:33 -0400 Received: from ramsley.shef.ac.uk ([143.167.103.254]) by mailhub1.shef.ac.uk with esmtp (Exim 3.22 #4) id 15MuFU-0005pP-00; Wed, 18 Jul 2001 17:32:32 +0100 Received: from RAMSLEY/SpoolDir by ramsley.shef.ac.uk (Mercury 1.48); 18 Jul 01 17:33:28 +0100 Received: from SpoolDir by RAMSLEY (Mercury 1.48); 18 Jul 01 17:33:27 +0100 From: "Nick Rhodes" To: chemistry@ccl.net, Vemparala Satyavani Date: Wed, 18 Jul 2001 17:33:23 +0100 MIME-Version: 1.0 Content-type: text/enriched; charset=US-ASCII Content-transfer-encoding: 7BIT Subject: Re: CCL:atom names in PDB files X-Confirm-Reading-To: "Nick Rhodes" X-pmrqc: 1 Priority: normal In-reply-to: X-mailer: Pegasus Mail for Win32 (v3.12a) Message-Id: 7F00,0000,0000> Iam new to PDB files. Iam having problems trying to correlate between the > atom names in the file and the atoms in the actual structure of amino > acids. for example the first three lines of glutamine acid in a protein > are: > > ATOM 1 N GLN A 1 63.870 -23.035 -4.001 1.00 2.09 > MCP1 N > ATOM 2 CA GLN A 1 65.000 -22.112 -3.695 1.00 1.89 > MCP1 C > ATOM 3 C GLN A 1 64.534 -20.647 -3.880 1.00 1.67 > MCP1 C > > my question is there are 2 Nitrogens, 5 carbons etc.,..in Glutamine > residue. how would i know which corresponds to what? The following URL should provide all the information you need: http://pdb.ccdc.cam.ac.uk/pdb/docs/format/pdbguide2.2/guide2.2_frame.html Nick ***************************************************************** Nick Rhodes, Computational Information Systems Research Group, Department of Information Studies, University of Sheffield, Regent Court, 211 Portobello Street, Sheffield, South Yorkshire, S1 4DP, United Kingdom. From chemistry-request@server.ccl.net Wed Jul 18 10:43:32 2001 Received: from mailrelay1.lrz-muenchen.de ([129.187.254.101]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f6IEhV528904 for ; Wed, 18 Jul 2001 10:43:31 -0400 Received: from sun1.lrz-muenchen.de by mailrelay1.lrz-muenchen.de with ESMTP for chemistry@ccl.net; Wed, 18 Jul 2001 16:43:30 +0200 Received: from localhost (ui22204@localhost) by sun1.lrz-muenchen.de (8.8.8+Sun/8.8.8) with ESMTP id QAA15032 for ; Wed, 18 Jul 2001 16:43:28 +0200 (MET DST) X-Authentication-Warning: sun1.lrz-muenchen.de: ui22204 owned process doing -bs Date: Wed, 18 Jul 2001 16:43:28 +0200 (MET DST) From: Eugene Leitl X-X-Sender: To: Subject: Re: [No Subject Given By The Author (fwd)] (fwd) Message-Id: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII -- Eugen* Leitl leitl ______________________________________________________________ ICBMTO : N48 10'07'' E011 33'53'' http://www.lrz.de/~ui22204 57F9CFD3: ED90 0433 EB74 E4A9 537F CFF5 86E7 629B 57F9 CFD3 ---------- Forwarded message ---------- Date: 18 Jul 2001 10:05:14 EDT From: Joey Raheb To: Eugene Leitl , Beowulf@beowulf.org Subject: Re: [No Subject Given By The Author (fwd)] Boris, >We are just about to buy computer configuration with AMD Thunderbird >1.4GHz processor and 512 MB DDR RAM with ASUS A7A266 motherboard. We plan >to use it for quantum chemistry programs (Gaussian, Gammes). >Here are my questions: does anybody have any experience with this >motherboard, and can anybody recommend me any other suitable >motherboard (for example A7M266)? I currently have one of these at home, it offers you the ability to choose between SD and DDR RAM. I currently work for a group in quantum chem and built a beowulf for the group. We just purchased 50 more PCs using the EPOX AMD boards with AMDs 761 chipset. There has been talk that the ALi 1 chipset is not as efficient as the AMDs new 761 chipset which is a revision of the 760 chipset. We found that the differences between the two boards were minimal, but the 761 did outperform the ALi chip. So, I guess as far as what to get, go with whatever gives you the best price. >Then, is it better to use DDR RAM or SDRAM? DDR is much better that SDRAM if we compare them strictly together, however, the question you should be asking is do my applications require DDR or can I get away with SDRAM? We do some G98 and GAMESS calculations here to and found that DDR does improve performance. >I'm also interested to find out may I use Portland compiler on this AMD >based configuration? Of course!, thats what we use! Joey ____________________________________________________________________ Get free email and a permanent address at http://www.amexmail.com/?A=1