From chemistry-request@server.ccl.net Tue Mar 5 12:47:47 2002 Received: from iris.chimfarm.unipg.it ([141.250.13.4]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g25Hlk505084 for ; Tue, 5 Mar 2002 12:47:47 -0500 Received: from apollo.chimfarm.unipg.it ([141.250.13.72] ident=mirco) by iris.chimfarm.unipg.it with esmtp (Exim 2.04 #2) id 16iKis-00010y-00 for CHEMISTRY@ccl.net; Tue, 5 Mar 2002 11:35:42 -0800 Date: Tue, 5 Mar 2002 18:47:52 +0100 (CET) From: Mirco Meniconi X-Sender: mirco@localhost.localdomain To: CHEMISTRY@ccl.net Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII #p CCSD/6-31G** AI-Quis.gzm 0 1 H N 1 r2 O 2 r3 1 a3 C 3 r4 2 a4 1 d4 N 4 r5 3 a5 2 d5 C 5 r6 4 a6 3 d6 O 4 r7 3 a7 2 d7 O 6 r8 5 a8 4 d8 H 5 r9 4 a9 3 d9 C 1 r10 2 a10 3 d10 C 10 r11 1 a11 2 d11 C 11 r12 10 a12 1 d12 O 12 r13 11 a13 10 d13 O 12 r14 11 a14 10 d14 N 11 r15 10 a15 1 d15 H 15 r16 11 a16 10 d16 H 15 r17 11 a17 10 d17 H 15 r18 11 a18 10 d18 H 10 r19 1 a19 2 d19 H 11 r20 10 a20 1 d20 .... ... .... ecc ecc dears CCL users, when I run the previous job in g98 I alwais obtain this error message: Range of M.O.s used for correlation: 14 230 NBasis= 230 NAE= 49 NBE= 49 NFC= 13 NFV= 0 NROrb= 217 NOA= 36 NOB= 36 NVA= 181 NVB= 181 Leave Link 801 at Tue Mar 5 18:28:02 2002, MaxMem= 16777216 cpu: 0.0 (Enter /usr/local/g98/l804.exe) Closed-shell transformation, MDV= 16777216 ITran=7 ISComp=1. Estimate disk for full transformation -42491378 words. Semi-Direct transformation. Erroneous write during file extend. write 57343 instead of 4096 Probably out of disk space. but I have 6GB of free space in my PC. The gaussian job die when I still have 3GB of free space in my PC. why? thanks in advance. -- Mirco Meniconi PhD candidate dip. chimica e tecnologia del farmaco via del liceo 1 06100 Perugia university of Perugia (ITALY) phone: +39 075 585 5114 e-mail: mirco.me@inwind.it e-mail: mirco@unipg.it RESISTERE RESISTERE RESISTERE ... From chemistry-request@server.ccl.net Wed Mar 6 10:59:36 2002 Received: from igcar.ernet.in ([202.141.82.2]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g26FxX517071 for ; Wed, 6 Mar 2002 10:59:35 -0500 Received: from igcar.ernet.in (localhost.localdomain [127.0.0.1]) by igcar.ernet.in (8.9.3/8.9.3) with ESMTP id VAA29932 for ; Wed, 6 Mar 2002 21:33:29 +0530 Received: from [203.199.205.25] ([203.199.205.25]) by igcar.ernet.in (8.9.3/8.9.3) with SMTP id VAA29917 for ; Wed, 6 Mar 2002 21:33:24 +0530 Received: from [10.1.1.100] by [203.199.205.25] via smtpd (for mail.igcar.ernet.in [202.141.82.2]) with SMTP; 6 Mar 2002 15:59:56 UT Received: (from Urcl@localhost) by igcmail.igcar.ernet.in (8.9.3+Sun/8.9.1) id VAA22047 for chemistry@ccl.net; Wed, 6 Mar 2002 21:29:23 -0500 (GMT) X-Authentication-Warning: igcmail.igcar.ernet.in: Urcl set sender to vvenkat@igcar.ernet.in using -f >Received: from localhost by rcl.igcar.ernet.in (8.9.1b+Sun/SMI-SVR4) id VAA03950; Wed, 6 Mar 2002 21:28:35 -0500 (GMT) Date: Wed, 6 Mar 2002 21:28:35 -0500 (GMT) From: "V.Venkatesan" X-Sender: vvenkat@rcl To: chemistry@ccl.net Subject: about NBO deletion procedure in G94W Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII HELLO ANYBODY CLARIFY THE DOUGHT THAT WHY NBODEL CALCULATION HAS ERROR TERMINATED? MY INPUT FORMAT --------------- %MEM=8000000 %CHK=E:\ch2ome2\opt\gghnbd2.chk #N HF/6-31++G** POP=NBODEL SCF=TIGHT NBO CALCULATION 0,1 | | $ DEL NOSTAR $ END OUTPUT FORMAT ------------- NtrOpn-Old failed. Error termination via Lnk1e in C:\G94W\l607.exe. Job cpu time: 0 days 0 hours 47 minutes 42.0 seconds. File lengths (MBytes): RWF= 21 Int= 0 D2E= 0 Chk= 1 Scr= 1 anybody help me thanking you ******************************************************************************* NAME:V.VENKATESAN ADDRESS:MATERIALS CHEMISTRY DIVISION RADIOCHEMICAL LABORATORY INDIRA GANDHI CENTRE FOR ATOMIC RESEACH KALPAKKAM-603102 TAMILNADU INDIA E-MAIL ID:vvenkat@igcar.ernet.in ******************************************************************************* From chemistry-request@server.ccl.net Wed Mar 6 07:20:30 2002 Received: from mailrelay1.lrz-muenchen.de ([129.187.254.101]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g26CKT506589 for ; Wed, 6 Mar 2002 07:20:30 -0500 Received: from sun4.lrz-muenchen.de by mailrelay1.lrz-muenchen.de with ESMTP; Wed, 6 Mar 2002 13:19:56 +0100 Received: from localhost (ui22204@localhost) by sun4.lrz-muenchen.de (8.8.8+Sun/8.8.8) with ESMTP id NAA04461; Wed, 6 Mar 2002 13:19:53 +0100 (MET) X-Authentication-Warning: sun4.lrz-muenchen.de: ui22204 owned process doing -bs Date: Wed, 6 Mar 2002 13:19:53 +0100 (MET) From: Eugene Leitl X-X-Sender: ui22204@sun4.lrz-muenchen.de To: nano , cc: je@infochem.de, , Subject: Use of SVG in Chemistry and xml2svg Transformations (fwd) Message-Id: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII -- Eugen* Leitl leitl ______________________________________________________________ ICBMTO: N48 04'14.8'' E11 36'41.2'' http://www.leitl.org 57F9CFD3: ED90 0433 EB74 E4A9 537F CFF5 86E7 629B 57F9 CFD3 ---------- Forwarded message ---------- Date: Wed, 6 Mar 2002 11:59:56 +0000 From: "Rzepa, Henry" To: chemweb@ic.ac.uk Subject: Use of SVG in Chemistry and xml2svg Transformations Some discussion on another list (the SVG developers) has prompted me (and others) to summarise progress in the "XML" solution to handling and in particular displaying of chemical content. Unlike HTML, which is predominantly a display and text-based format where chemical content has to be included via "legacy" formats such as eg Molfiles, or via images, XML is designed for essentially complete semantic markup of content. Because no browser could easily handle such a broad scope, the concept is that XML documents will be displayed by appropriate transformation of the content into a small set of generic display formats which the browser CAN handle. The pre-eminent XML-based graphical format is SVG (scalable vector graphics) and hence the issue now resolves to how to transform any particular XML component to eg SVG, generically referred to here as xml2svg (although this does not preclude transformation to older non-XML formats such as Molfile and hence use of eg Chime). Listed below are some useful sites which cover issues of handling XML, and converting it to SVG 1. http://www.adobe.com/svg/demos/main.html which has an XSLT-based cml2svg converter 2. http://www.xml-cml.org/jumbo3/jumbo3-JS/ being a JavaScript based dynamic cml2svg converter. The http://www.xml-cml.org/ site has much other information about XML and CML. Also there you will find XACE (eXtensible annotating chemical editor), based on JME, but with "XML" wrappers. Work on XACE Mk II is well under way. 3. The cml2xbl2svg concept, originally part of Croczilla (http://www.croczilla.com/svg/), now part of one of the builds of Mozilla 0.9.8, and expected to be a permanent part of the Mozilla 1.0 release. 4. http://www.schemasoft.com/MathML/ which is a mathml2svg converter based on XSLT 5. See http://www.web3d.org/TaskGroups/source/xj3d.html being an XML version of VRML, and for which a viewer is now available. ( http://www.adobe.com/svg/demos/main.html also does 3D rotations) 6. http://www.ch.ic.ac.uk/rzepa/xml/ where the process of converting cml2svg, and in general then on to PDF using FOP, is described A XSLT stylesheet for the conversion is at http://www.ch.ic.ac.uk/rzepa/xml/fop.html The above article was published as G. V. Gkoutos, P. Murray-Rust, H. S. Rzepa, and M. Wright, Internet J. Chemistry, 2001, article 13. 7. Jiri.Jirat has written a custom CML2SVG converter (XSLT), the results can be viewed at: http://zvon.org/xxl/CML1.0/Output/index.html 8. Marvin outputs SVG, and reads, inter alia, CML http://www.chemaxon.com/marvin/ There is no doubt much more out there. This collection also illustrates one very powerful aspect of XML, which is the re-usability of various generic tools in a chemical context, a phenomenon that is largely new (previously the chemical community had to pretty much write its own tools!). If anyone in their travels comes across other interesting examples of xml2xml (in the generic sense) tools, and interesting examples say > from the bio-informatics and other physical sciences, do please let this list know. -- Henry Rzepa. +44 (0870) 132 3747 (eFax) http://www.ch.ic.ac.uk/rzepa/ Dept. Chemistry, Imperial College, London, SW7 2AY, UK. chemweb: A list for Chemical Applications of the Internet. To post to list: mailto:chemweb@ic.ac.uk Archived as: http://www.lists.ic.ac.uk/hypermail/chemweb/ To (un)subscribe, mailto:majordomo@ic.ac.uk the following message; (un)subscribe chemweb List coordinator, Henry Rzepa (mailto:rzepa@ic.ac.uk) From chemistry-request@server.ccl.net Wed Mar 6 07:31:15 2002 Received: from dux1.tcd.ie ([134.226.1.23]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g26CVD507031 for ; Wed, 6 Mar 2002 07:31:14 -0500 Received: from wallaceiwork (chy108098.phy.tcd.ie [134.226.108.98]) by dux1.tcd.ie (Postfix) with SMTP id 714BC58E for ; Wed, 6 Mar 2002 12:30:37 +0000 (GMT) Message-ID: <001401c1b09c$6f710870$626ce286@wallaceiwork> From: "Iain Wallace" To: Subject: CCL: Gaussian Question Date: Fri, 8 Feb 2002 12:30:47 -0000 MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_0011_01C1B09C.6F5D0B40" X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 5.00.2919.6700 X-MimeOLE: Produced By Microsoft MimeOLE V5.00.2919.6700 This is a multi-part message in MIME format. ------=_NextPart_000_0011_01C1B09C.6F5D0B40 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Hi all,=20 I am running am1 optimisation in G98 on a few molecules. It works fine = most times.=20 Occasionally it crashes out with the error: Incomplete coordinate system. Try restarting with Geom=3DCheck Guess=3DRead Opt=3D(ReadFC,NewRedundant) Incomplete coordinate system. Error termination via Lnk1e in /usr/support/g98/l103.exe. Does any one know why this happens, and how I can avoid it in future?=20 Thanks=20 Iain=20 ------=_NextPart_000_0011_01C1B09C.6F5D0B40 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable
Hi all,
 
I am running am1 optimisation in G98 on = a few=20 molecules. It works fine most times.
Occasionally it crashes out with the=20 error:
 
 Incomplete coordinate = system.  Try=20 restarting with
 Geom=3DCheck Guess=3DRead=20 Opt=3D(ReadFC,NewRedundant)
 Incomplete coordinate = system.
 Error=20 termination via Lnk1e in /usr/support/g98/l103.exe.
Does any one know why this happens, and = how I can=20 avoid it in future?
 
Thanks
 
Iain
 
------=_NextPart_000_0011_01C1B09C.6F5D0B40-- From chemistry-request@server.ccl.net Wed Mar 6 14:41:11 2002 Received: from email02.aon.at ([195.3.96.115]) by server.ccl.net (8.11.6/8.11.0) with SMTP id g26JfB502568 for ; Wed, 6 Mar 2002 14:41:11 -0500 Received: (qmail 133142 invoked from network); 6 Mar 2002 19:40:26 -0000 Received: from n771p010.adsl.highway.telekom.at (HELO pc1) ([62.47.40.74]) (envelope-sender ) by qmail2.highway.telekom.at (qmail-ldap-1.03) with SMTP for ; 6 Mar 2002 19:40:26 -0000 To: chemistry@ccl.net Subject: calculations of mean residence times From: Hannes Loeffler Date: 06 Mar 2002 20:42:17 +0100 Message-ID: <873czdfppi.fsf@uibk.ac.at> Lines: 20 User-Agent: Gnus/5.0808 (Gnus v5.8.8) XEmacs/21.4 (Common Lisp) MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Hello, the following paper describes the calculations of mean residence times of H2O molecules in the first shell of ions @Article(Impey:JPhysChem-87-25-5071, author = "R. W. Impey and P. A. Madden and I. R. McDonald", title = "Hydration and Mobility of Ions in Solution", journal = jpc, year = 1983, volume = 87, number = 25, pages = "5071--5083" ) since we do not fully understand how to do such calculations ourselves we would like to ask if somebody wants to share the code with us. Hannes. From chemistry-request@server.ccl.net Wed Mar 6 17:13:42 2002 Received: from mtiwmhc23.worldnet.att.net ([204.127.131.48]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g26MDg505192 for ; Wed, 6 Mar 2002 17:13:42 -0500 Received: from dopetec ([138.23.156.82]) by mtiwmhc23.worldnet.att.net (InterMail vM.4.01.03.27 201-229-121-127-20010626) with ESMTP id <20020306221308.OEDQ11836.mtiwmhc23.worldnet.att.net@dopetec> for ; Wed, 6 Mar 2002 22:13:08 +0000 Message-ID: <004501c1c55d$221b00f0$529c178a@dopetec> From: "Donald Keidel" To: Subject: video cards for RedHat 7.2 Date: Wed, 6 Mar 2002 14:20:31 -0800 MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_0042_01C1C51A.12A48D00" X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 6.00.2600.0000 X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2600.0000 This is a multi-part message in MIME format. ------=_NextPart_000_0042_01C1C51A.12A48D00 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Hello all, I am thinking of buying a new video card for my redhat linux 7.2 and = windows 2000 dual boot system. I need to limit the card type to 2x AGP. = I am wondering if anyone can recommend a good video card. I know I can = look at the hardware compatibility lists, but I want to know what CCLers = feel are good graphics cards when considering the needs of the software = we use. Thanks for any help. Don --------------------------------------------------- Donald J. Keidel University of California, Riverside Department of Biochemistry and Molecular Biology Riverside, CA 92521 phone: (909) 787-5493 fax: (909) 787-4434 dkeidel397@att.net webpage: www.biochemistry.ucr.edu/gru/gradstudents/don_keidel/index.htm ------=_NextPart_000_0042_01C1C51A.12A48D00 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable
Hello all,
 
I am thinking of buying a new video = card for my=20 redhat linux 7.2 and windows 2000 dual boot system.  I need to = limit the=20 card type to 2x AGP.  I am wondering if anyone can recommend a good = video=20 card.  I know I can look at the hardware compatibility lists, but I = want to=20 know what CCLers feel are good graphics cards when considering the needs = of the=20 software we use.  Thanks for any help.
 
Don
---------------------------------------------------
Donald = J.=20 Keidel
University of California, Riverside
Department of = Biochemistry and=20 Molecular Biology
Riverside, CA 92521
phone:  (909)=20 787-5493
fax:  (909) 787-4434
dkeidel397@att.net
webpage: www.biochemistry.ucr.edu/gru/gradstudents/don_keidel/index.htm<= BR>
------=_NextPart_000_0042_01C1C51A.12A48D00-- From chemistry-request@server.ccl.net Wed Mar 6 16:37:35 2002 Received: from web13401.mail.yahoo.com ([216.136.175.59]) by server.ccl.net (8.11.6/8.11.0) with SMTP id g26LbZ504710 for ; Wed, 6 Mar 2002 16:37:35 -0500 Message-ID: <20020306213659.27129.qmail@web13401.mail.yahoo.com> Received: from [67.17.165.31] by web13401.mail.yahoo.com via HTTP; Wed, 06 Mar 2002 13:36:59 PST Date: Wed, 6 Mar 2002 13:36:59 -0800 (PST) From: quch quch Subject: Re: CCL:calculations of mean residence times To: Hannes Loeffler , chemistry@ccl.net In-Reply-To: <873czdfppi.fsf@uibk.ac.at> MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii since you only care the residue time in the first shell, one simple direct solution is to look at the numbering of water in the first shell at each snapshot (suppose the number is fixed for each molecule and atom in the whole trajectory), then trace down how the numbering chang with time. you could get residual time for each water. sum and average the residue time for whole water molecules in the first shell and whole trajectories, the final value is what you want. If you look at the residual time of water to an specific atoms or molecules, the similar idea could be apply. you may need to add the angle restriction in this case. qc --- Hannes Loeffler wrote: > Hello, > > the following paper describes the calculations of > mean residence times of H2O > molecules in the first shell of ions > > @Article(Impey:JPhysChem-87-25-5071, > author = "R. W. Impey and P. A. Madden and I. > R. McDonald", > title = "Hydration and Mobility of Ions in > Solution", > journal = jpc, > year = 1983, > volume = 87, > number = 25, > pages = "5071--5083" > ) > > since we do not fully understand how to do such > calculations ourselves we would > like to ask if somebody wants to share the code with > us. > > > Hannes. > > > > -= 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 > > > > > __________________________________________________ Do You Yahoo!? Try FREE Yahoo! Mail - the world's greatest free email! http://mail.yahoo.com/ From chemistry-request@server.ccl.net Wed Mar 6 21:02:43 2002 Received: from ks.uiuc.edu ([130.126.120.73]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g2722g513650 for ; Wed, 6 Mar 2002 21:02:42 -0500 Received: from verdun.ks.uiuc.edu (verdun.ks.uiuc.edu [130.126.120.129]) by ks.uiuc.edu (8.11.2/8.11.2) with ESMTP id g2722B713623; Wed, 6 Mar 2002 20:02:11 -0600 (CST) Received: from localhost (jim@localhost) by verdun.ks.uiuc.edu (8.10.2+Sun/8.9.1) with ESMTP id g2722Bq10450; Wed, 6 Mar 2002 20:02:11 -0600 (CST) X-Authentication-Warning: verdun.ks.uiuc.edu: jim owned process doing -bs Date: Wed, 6 Mar 2002 20:02:11 -0600 (CST) From: Jim Phillips To: Donald Keidel cc: chemistry@ccl.net Subject: Re: CCL:video cards for RedHat 7.2 In-Reply-To: <004501c1c55d$221b00f0$529c178a@dopetec> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi, See http://www.ks.uiuc.edu/Research/vmd/current/accelerators.html For real 3D acceration under Linux you want an NVidia GeForce something. -Jim On Wed, 6 Mar 2002, Donald Keidel wrote: > Hello all, > > I am thinking of buying a new video card for my redhat linux 7.2 and windows 2000 dual boot system. I need to limit the card type to 2x AGP. I am wondering if anyone can recommend a good video card. I know I can look at the hardware compatibility lists, but I want to know what CCLers feel are good graphics cards when considering the needs of the software we use. Thanks for any help. > > Don > --------------------------------------------------- > Donald J. Keidel > University of California, Riverside > Department of Biochemistry and Molecular Biology > Riverside, CA 92521 > phone: (909) 787-5493 > fax: (909) 787-4434 > dkeidel397@att.net > webpage: www.biochemistry.ucr.edu/gru/gradstudents/don_keidel/index.htm > >