From chemistry-request@server.ccl.net Wed Aug 1 10:16:39 2001 Received: from mh1-cam.cam.accelrys.com ([192.190.183.254]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f71EGc531155 for ; Wed, 1 Aug 2001 10:16:39 -0400 Received: from dhcp241.cam.accelrys.com ([172.27.65.241] helo=bonanza.accelrys.com) by mh1-cam.cam.accelrys.com with esmtp (Exim 3.12 #1 (Debian)) id 15Rwnb-0006ov-00 for ; Wed, 01 Aug 2001 15:16:35 +0100 Message-Id: <5.0.0.25.2.20010731160918.01c0ec20@mailhost.cam.msi-eu.com> X-Sender: phil_hastings@mailhost.cam.msi-eu.com X-Mailer: QUALCOMM Windows Eudora Version 5.0 Date: Wed, 01 Aug 2001 15:05:51 +0100 To: chemistry@ccl.net From: Phil Hastings Subject: Forthcoming Seminar Series/ Materials Studio 2.0 Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii"; format=flowed Dear CCL list members I would like to draw your attention to a forthcoming worldwide seminar series organized by Accelrys, on the subject of Predictive Atomistic Simulations of Reaction Mechanisms, Surfaces and Materials Properties. The theme of the seminars will be that developments in simulation software, coupled with exponential improvements in the performance of computer hardware, are enabling cost-effective and efficient computer experiments to improve the effectiveness of the R&D process. The seminars will take place in locations in the US, Europe and Japan, and are being run to coincide with the imminent release of Materials Studio 2.0. This release sees implementation of the QM codes, DMol3 and CASTEP on the PC for the first time, and includes improved transition state search methodologies, as well as advances in other modeling and visualization capabilities. For further information about the seminar series, including agendas, locations and lists of invited speakers, please visit: http://www.accelrys.com/seminars/mstudio2/ For further information about Materials Studio, please visit: http://www.accelrys.com/mstudio/ Sincerely Phil Hastings ****************************************** Dr Phil Hastings Senior Product Manager, Materials Studio Accelrys Website: http://www.accelrys.com MSI, GCG, Oxford Molecular, and Synopsys are now ACCELRYS ****************************************** From chemistry-request@server.ccl.net Wed Aug 1 07:57:05 2001 Received: from web12307.mail.yahoo.com ([216.136.173.105]) by server.ccl.net (8.11.0/8.11.0) with SMTP id f71Bv4527778 for ; Wed, 1 Aug 2001 07:57:04 -0400 Message-ID: <20010801115704.13497.qmail@web12307.mail.yahoo.com> Received: from [206.49.94.119] by web12307.mail.yahoo.com; Wed, 01 Aug 2001 04:57:04 PDT Date: Wed, 1 Aug 2001 04:57:04 -0700 (PDT) From: omar Deeb Subject: computational chemistry course - undergraduate To: chemistry@ccl.net MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Dear all, we are trying to give our undergraduate chemistry students a computational chemistry course. Any suggestions concerning outline, textbook, software and related material. Thanks in advance Dr. omar Deeb Chairman of the depart. of chemistry faculty of science and technology Alquds university jerusalem fax 972-2-2796960 e-mail deeb2000il@yahoo.com __________________________________________________ Do You Yahoo!? Make international calls for as low as $.04/minute with Yahoo! Messenger http://phonecard.yahoo.com/ From chemistry-request@server.ccl.net Wed Aug 1 01:56:18 2001 Received: from srv2.resnet.ohio-state.edu ([164.107.3.56]) by server.ccl.net (8.11.0/8.11.0) with SMTP id f715uI508221 for ; Wed, 1 Aug 2001 01:56:18 -0400 Received: (qmail 49624 invoked from network); 1 Aug 2001 05:56:18 -0000 Received: from rjot-84-236.resnet.ohio-state.edu (HELO wong) (164.107.84.236) by campbell.mps.ohio-state.edu with SMTP; 1 Aug 2001 05:56:18 -0000 Message-ID: <001f01c11a4e$c6671460$ec546ba4@255.resnet.ohiostate.edu> From: "Kiniu WONG \(Kin-Yiu\)" To: References: <3B672129.D70E2F78@lauca.usach.cl> Subject: GAUSSIAN: ERROR from Stable=(Opt, Symm) Date: Wed, 1 Aug 2001 01:56:58 -0400 Organization: Physics, OSU MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 5.50.4133.2400 X-MimeOLE: Produced By Microsoft MimeOLE V5.50.4133.2400 Dear CCLers, I have got an error message from GAUSSIAN 98 A.7 when Stable=(Opt, Symm) is employed. The hightlight of the error from the output could be found at the end of this email. But the strange point is that if I use Stable=(Opt) only, there's no problem (this is also attached at the end). So what's wrong with it? What should I do to solve it? I am a new to computational chemisty, any kind of suggetions or ideas would be helpful! Thank you very much in advance!! Wishes, Kiniu ---- Kiniu WONG (Kin-Yiu) Graduate Student Department of Physics The Ohio State University Email: kiniu@mps.ohio-state.edu or kyiwong@phy.cuhk.edu.hk error output: %rwf=/usr/tmp/temp %int=/usr/tmp/temp %d2e=/usr/tmp/temp %scr=/usr/tmp/temp %chk=/usr/tmp/temp %Mem=400MB ---------------------------------------------------------------------- #P UHF/6-31G(d) SCF=(Tight, direct, MaxCycle=128) Stable=(Symm, Opt) M axDisk=3GB Guess=CheckPoint Geom=AllCheck ---------------------------------------------------------------------- ........ ........ ....... Leave Link 202 at Sat Jul 28 07:57:49 2001, MaxMem= 52428800 cpu: 0.1 (Enter /usr/local/g98/l301.exe) Standard basis: 6-31G(d) (6D, 7F) There are 550 symmetry adapted basis functions of A symmetry. Crude estimate of integral set expansion from redundant integrals=1.000. Integral buffers will be 131072 words long. Raffenetti 2 integral format. Two-electron integral symmetry is turned on. 550 basis functions 1048 primitive gaussians 119 alpha electrons 119 beta electrons nuclear repulsion energy 3694.9943364774 Hartrees. Leave Link 301 at Sat Jul 28 07:57:51 2001, MaxMem= 52428800 cpu: 0.2 (Enter /usr/local/g98/l302.exe) One-electron integrals computed using PRISM. NBasis= 550 RedAO= T NBF= 550 NBsUse= 550 1.00D-04 NBFU= 550 Leave Link 302 at Sat Jul 28 07:58:06 2001, MaxMem= 52428800 cpu: 9.2 ....... ..... of initial guess= 0.0000 Leave Link 401 at Sat Jul 28 08:01:04 2001, MaxMem= 52428800 cpu: 165.2 (Enter /usr/local/g98/l503.exe) NBASIS 550 EXCEEDS MDIM 256 Error termination via Lnk1e in /usr/local/g98/l503.exe. No error: %rwf=/usr/tmp/temp %int=/usr/tmp/temp %d2e=/usr/tmp/temp %scr=/usr/tmp/temp %chk=/usr/tmp/temp %Mem=400MB ---------------------------------------------------------------------- #P UHF/6-31G(d) SCF=(Tight, Direct, MaxCycle=128) MaxDisk=3GB Stable=O pt ---------------------------------------------------------------------- ......... ....... of initial guess= 0.0000 Leave Link 401 at Fri Feb 2 01:20:54 2001, MaxMem= 52428800 cpu: 99.3 (Enter /usr/local/g98/l502.exe) IExCor= 0 DFT=F Ex=HF Corr=None ScaHFX= 1.0000 ScaDFX= 0.0000 0.0000 0.0000 0.0000 IRadAn= 0 IRanWt= -1 IRanGd= 0 ICorTp=0 Using DIIS extrapolation. UHF open shell SCF: ........ ...... From chemistry-request@server.ccl.net Wed Aug 1 04:39:54 2001 Received: from gensig.nibsc.ac.uk ([193.62.43.13]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f718dr507522 for ; Wed, 1 Aug 2001 04:39:53 -0400 Received: from nibsc.ac.uk (dlinmf3.nibsc.ac.uk [193.62.42.139]) by gensig.nibsc.ac.uk (980427.SGI.8.8.8/970903.SGI.AUTOCF) via ESMTP id JAA93096; Wed, 1 Aug 2001 09:41:11 +0100 (BST) Message-ID: <3B67C088.B595C568@nibsc.ac.uk> Date: Wed, 01 Aug 2001 09:40:40 +0100 From: Mark Forster X-Mailer: Mozilla 4.77 [en] (Win95; U) X-Accept-Language: en MIME-Version: 1.0 To: Danilo Gonzalez , chemistry@ccl.net Subject: Re: CCL:InsightII/UNIX References: <3B672129.D70E2F78@lauca.usach.cl> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear Danilo I am not sure if you can do it with a Unix command, but below is an insightII BCL script (get_frame.log) that extracts a single frame (number 51 in this example) from a history file and writes out a PDB file called frame.pdb. You will need to substitute in the names of your own molecule files. If you do not want graphics you can run insightII with the command insightII -at then type source get_frame.log at the command line. If you set a Unix environment variable as follows setenv INSIGHT_INIT_LOCAL get_frame.log Then when insightII starts up the script will be automatically run, the single frame extracted and insightII will exit. Hope this helps. Mark ---get_frame.log----- Get Molecule Archive Frame 1 bdglc0.car BDGLC0 -Reference_Object Analysis Get Trajectory bdglc0.his BDGLC0 -Load_Velocities -Load_Pressure -Load_Cell Range 1 end 1 Conformation Trajectory Frame 51 Put Molecule PDB BDGLC0 frame.pdb -Transformed -Displayed -Insight_Style -Write_PSF quit on -------------------- Danilo Gonzalez wrote: > Hi All! > > I'm working with InsightII and Discover. Anybody know how can I take > only one conformation from a history file (*.his) using only UNIX > command? (don't using display mode), if is possible > > Thanks a lot! > > Dr. Danilo Gonzalez > University of Santiago of Chile > Faculty of Chemistry and Biology > Casilla 40, Correo 33, CHILE. > > -= 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 -- Dr Mark J Forster Ph.D. Principal Scientist Informatics Laboratory National Institute for Biological Standards and Control Blanche Lane, South Mimms, Hertfordshire EN6 3QG, United Kingdom. Tel +44 (0)1707 654753 FAX +44 (0)1707 646730 E-mail mforster@nibsc.ac.uk From chemistry-request@server.ccl.net Wed Aug 1 06:25:11 2001 Received: from mlucom8.urz.uni-halle.de ([141.48.10.118]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f71AP9525492 for ; Wed, 1 Aug 2001 06:25:11 -0400 Received: from studcom (actually studcom.urz.Uni-Halle.DE) by mlucom8.urz.uni-halle.de with lsmtp with ESMTP; Wed, 1 Aug 2001 12:24:43 +0200 Received: from bathl ([141.48.223.39]) by studcom (8.9.3 (PHNE_22672)/8.9.3) with SMTP id MAA19189; Wed, 1 Aug 2001 12:25:13 +0200 (METDST) Content-Type: Multipart/Mixed; charset="iso-8859-1"; boundary="------------Boundary-00=_LWWD7P00BXQDT5S7700N" From: Bernd Schubert To: Ha-Yeon Cheong Subject: Re: CCL:Gaussian98 source code and facility of parallel implementation Date: Wed, 1 Aug 2001 12:24:21 +0200 X-Mailer: KMail [version 1.2] References: <000001c119e2$4b851240$b5848c8b@progeny> In-Reply-To: <000001c119e2$4b851240$b5848c8b@progeny> Cc: spiske@chemie.uni-halle.de, chemistry MIME-Version: 1.0 Message-Id: <01080112242101.03056@bathl> --------------Boundary-00=_LWWD7P00BXQDT5S7700N Content-type: text/plain; charset="iso-8859-1" Content-transfer-encoding: 8bit Hi, I had the same problem and asked the gaussian support about it. They send me a documentation how to change the shmmax parameter. I think the first thing you need is a kernel compiled with big memory support (we are using the 2.4.x kernels and I have enabled 64GB support). Before recompiling the kernel you can change the shmmax parameter in the kernel_source_dir/include/linux/shmmax (for 2.4.x kernels, for 2.2.x kernel see the attachment I'v got from gaussian support). But I'm not sure if this is neccessary because I did it but with a too small value. So gaussian still didn't run in parallel mode. After the following command gaussian run fine in parallel mode then: echo "2147483648" >/proc/sys/kernel/shmmax This enables 2GB shared memory support, a higher value can be specified but will be automatically reduced to 2GB. I hope it helps you, Bernd --------------Boundary-00=_LWWD7P00BXQDT5S7700N Content-type: text/plain; charset="iso-8859-1"; name="linux_shmmax.txt from gaussian support" Content-transfer-encoding: base64 Content-Disposition: attachment; filename="linux_shmmax.txt from gaussian support" SW5jcmVhc2luZyB0aGUgc2l6ZSBvZiB0aGUgTGludXggc2hhcmVkIG1lbW9yeSBzZWdtZW50CgpU aGUgc2l6ZSBvZiB0aGUgc2hhcmVkIG1lbW9yeSBzZWdtZW50IGlzIHNldCBieSB0aGUgcGFyYW1l dGVyClNITU1BWCwgaW4gL3Vzci9zcmMvbGludXgvaW5jbHVkZS9hc20vc2htcGFyYW0uaC4gIFRo ZSBkZWZhdWx0CnZhbHVlIGluIDIuMCBhbmQgMi4yIGtlcm5lbHMgaXMgMHgyMDAwMDAwLCBvciAz Mk1CLiAgVG8gaW5jcmVhc2UKdGhlIHZhbHVlIG9mIFNITU1BWCwgZWRpdCBzaG1wYXJhbS5oLCBy ZWJ1aWxkIHRoZSBrZXJuZWwsIGFuZCByZWJvb3QuCgpJZiB5b3UgYXJlIGNvbWZvcnRhYmxlIHdp dGggdGhlIHByb2Nlc3Mgb2YgYnVpbGRpbmcgdGhlIExpbnV4IGtlcm5lbCwKd2Ugc3VnZ2VzdCB5 b3UgdHJ5IHRoZSByZWNlbnRseSByZWxlYXNlZCAyLjIuMSBrZXJuZWwgKGdldCBpdCBmcm9tCmZ0 cC5rZXJuZWwub3JnIG9yIGEgbWlycm9yIHNpdGUpLiAgVGhlIDIuMiBrZXJuZWxzIGhhdmUgaW1w cm92ZWQgU01QCnBlcmZvcm1hbmNlIGFuZCB0aGUgYWJpbGl0eSB0byBjaGFuZ2UgdGhlIHNoYXJl ZCBtZW1vcnkgc2l6ZSBvbiB0aGUgZmx5LApieSBjaGFuZ2luZyB0aGUgdmFsdWUgaW4gL3Byb2Mv c3lzL2tlcm5lbC9zaG1tYXguICBGb3IgZXhhbXBsZSwKCiMgZWNobyAiNjcxMDg4NjQiID4vcHJv Yy9zeXMva2VybmVsL3NobW1heAoKd291bGQgc2V0IHRoZSBtYXhpbXVtIHNoYXJlZCBtZW1vcnkg c2VnbWVudCBzaXplIHRvIDY0TUIuCgpJZiB5b3UgYXJlIG5vdCBmYW1pbGlhciB3aXRoIHRoZSBw cm9jZWR1cmUgZm9yIGJ1aWxkaW5nIHRoZSBrZXJuZWwsCmFuZCB5b3UgYXJlIHVzaW5nIHRoZSBr ZXJuZWwgZGlzdHJpYnV0ZWQgd2l0aCBSZWQgSGF0IExpbnV4IDUuMiwKaGVyZSBpcyBhIHN0ZXAt Ynktc3RlcCBndWlkZSB0byByZWJ1aWxkaW5nIHRoZSBSZWQgSGF0IGtlcm5lbDoKCjEpIE1ha2Ug c3VyZSB0aGUga2VybmVsIHNvdXJjZSBhbmQgaGVhZGVycyBhcmUgaW5zdGFsbGVkLCBieSBkb2lu ZwoKJSBycG0gLXFhIHwgZ3JlcCBrZXJuCmtlcm5lbC0yLjAuMzYtMC43Cmtlcm5lbC1wY21jaWEt Y3MtMi4wLjM2LTAuNwprZXJuZWxjZmctMC41LTMKa2VybmVsLWhlYWRlcnMtMi4wLjM2LTAuNwpr ZXJuZWwtc291cmNlLTIuMC4zNi0wLjcKCklmIHlvdSBkbyBub3Qgc2VlCgprZXJuZWwtaGVhZGVy cy0yLjAuMzYtMC43Cmtlcm5lbC1zb3VyY2UtMi4wLjM2LTAuNwoKeW91IG11c3QgaW5zdGFsbCB0 aGVtIGZyb20gdGhlIFJlZCBIYXQgQ0QsIGJ5IGRvaW5nLCBhcyByb290CgojIHJwbSAtaSBrZXJu ZWwtaGVhZGVycy0yLjAuMzYtMC43LmkzODYucnBtCiMgcnBtIC1pIGtlcm5lbC1zb3VyY2UtMi4w LjM2LTAuNy5pMzg2LnJwbQoKMikgTm93LCBhcyByb290LCBlZGl0IC91c3Ivc3JjL2xpbnV4L2lu Y2x1ZGUvYXNtL3NobXBhcmFtLmggYW5kCmNoYW5nZSB0aGUgdmFsdWUgb2YgU0hNTUFYIHRvIGFu IGFwcHJvcHJpYXRlIHZhbHVlICgzLzQgb2YgdGhlIGFtb3VudCBvZgpwaHlzaWNhbCBtZW1vcnkg d291bGQgYmUgcmVhc29uYWJsZSkuCgozKSBOb3cgZG8sIGFzIHJvb3QKCiMgY2QgL3Vzci9zcmMv bGludXgKIyBtYWtlIG1wcm9wZXIKIyBtYWtlIGNvbmZpZwoKbWFrZSBjb25maWcgd2lsbCBhc2sg YSBzZXJpZXMgb2YgY29uZmlndXJhdGlvbiBxdWVzdGlvbnMsIGl0IHdpbGwgbG9vayBsaWtlOgoK IyBtYWtlIGNvbmZpZwpybSAtZiBpbmNsdWRlL2FzbQooIGNkIGluY2x1ZGUgOyBsbiAtc2YgYXNt LWkzODYgYXNtKQovYmluL3NoIHNjcmlwdHMvQ29uZmlndXJlIGFyY2gvaTM4Ni9jb25maWcuaW4K IwojIFVzaW5nIGRlZmF1bHRzIGZvdW5kIGluIGFyY2gvaTM4Ni9kZWZjb25maWcKIwoqCiogQ29k ZSBtYXR1cml0eSBsZXZlbCBvcHRpb25zCioKUHJvbXB0IGZvciBkZXZlbG9wbWVudCBhbmQvb3Ig aW5jb21wbGV0ZSBjb2RlL2RyaXZlcnMgKENPTkZJR19FWFBFUklNRU5UQUwpIFtZL24vP10gCgph bmQgc28gb24uICBUbyBldmVyeSBxdWVzdGlvbiwgVEFLRSBUSEUgREVGQVVMVCBWQUxVRSBCWSBI SVRUSU5HIEVOVEVSLgpXaGVuIHlvdSBhcmUgZG9uZSwgZG86CgojIG1ha2UgZGVwOyBtYWtlIGJv b3QKCkEgZ3JlYXQgZGVhbCBvZiBvdXRwdXQgd2lsbCBzY3JvbGwgYnkgYXMgYSBuZXcga2VybmVs IGlzIGNvbXBpbGVkLiAgV2hlbgp0aGUgYnVpbGQgaXMgY29tcGxldGUsIHRoZSBuZXcga2VybmVs IHdpbGwgYmUgaW4gdGhlIGZpbGUKL3Vzci9zcmMvbGludXgvYXJjaC9pMzg2L2Jvb3QvekltYWdl LgoKNCkgIE5vdyB5b3UgbWF5IHRlc3QgdGhlIG5ldyBrZXJuZWwgYnkgYm9vdGluZyBpdCBmcm9t IGEgZmxvcHB5LiAgUHV0IGEgYmxhbmsKZGlza2V0dGUgaW4geW91IGZsb3BweSBkcml2ZSBhbmQg ZG8sIGFzIHJvb3Q6CgojIGRkIGlmPS91c3Ivc3JjL2xpbnV4L2FyY2gvaTM4Ni9ib290L3pJbWFn ZSBvZj0vZGV2L2ZkMAoKNSkgIE5vdyByZWJvb3QgZnJvbSB0aGlzIGZsb3BweS4gIElmIGFsbCBz ZWVtcyB3ZWxsIHlvdSBtYXkgY29uZmlndXJlIExJTE8KdG8gYm9vdCB0aGUgbmV3IGtlcm5lbCwg b3IgY29udGludWUgdG8gYm9vdCBmcm9tIGZsb3BweS4KClRoZSBSZWQgSGF0IExpbnV4IDUuMiBt YW51YWwgZGlzY3Vzc2VzIGJ1aWxkaW5nIGEgY3VzdG9tIGtlcm5lbCwgYW5kIHVzaW5nCkxJTE8g dG8gYm9vdCBpdCBpbiBTZWN0aW9uIDExLjYsIHBwIDE5Ny0yMDAsIHRvIHdoaWNoIHdlIHJlZmVy IHlvdSBmb3IKZnVydGhlciBkZXRhaWxzLg== --------------Boundary-00=_LWWD7P00BXQDT5S7700N-- From chemistry-request@server.ccl.net Wed Aug 1 06:09:02 2001 Received: from chim02.chin.unipd.it ([147.162.52.1]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f71A8x525339 for ; Wed, 1 Aug 2001 06:09:00 -0400 Received: from Fregona (volfre.chin.unipd.it [147.162.52.31]) by chim02.chin.unipd.it (8.8.7/8.8.7) with ESMTP id MAA27071 for ; Wed, 1 Aug 2001 12:10:56 GMT Message-Id: <5.1.0.14.0.20010801121023.009e8be0@chin.unipd.it> X-Sender: ronconi@chin.unipd.it X-Mailer: QUALCOMM Windows Eudora Version 5.1 Date: Wed, 01 Aug 2001 12:12:58 +0200 To: chemistry@ccl.net From: Luca Ronconi Subject: MOPAC parameters for Au. Mime-Version: 1.0 Content-Type: multipart/alternative; boundary="=====================_9713323==_.ALT" --=====================_9713323==_.ALT Content-Type: text/plain; charset="iso-8859-1"; format=flowed Content-Transfer-Encoding: quoted-printable Dear Collegues, I am looking for Au parameters for MOPAC. I really appreciate any information. Thanks in advance. Regards. ---------- Dr. Luca Ronconi Universit=E0 di Padova - Dip. CIMA Via Loredan n=B04, 35131, Padova (ITALY) Tel.: +39.(0)49.08275159 Mobile: +39.349.8645706 Fax: +39.(0)2.700538450 e-mail: ronconi@chin.unipd.it --=====================_9713323==_.ALT Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Dear Collegues,

    I am looking for Au parameters for MOPAC.
    I really appreciate any information.
    Thanks in advance.

    Regards.

Dr. Luca Ronconi
Universit=E0 di Padova - Dip. CIMA
Via Loredan n=B04, 35131, Padova (ITALY)
Tel.: +39.(0)49.08275159
Mobile: +39.349.8645706
Fax: +39.(0)2.700538450
e-mail: ronconi@chin.unipd.it
--=====================_9713323==_.ALT-- From chemistry-request@server.ccl.net Wed Aug 1 13:14:36 2001 Received: from juliet.schrodinger.com ([192.156.98.102]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f71HEZ503530 for ; Wed, 1 Aug 2001 13:14:35 -0400 Received: from localhost (jshelley@localhost) by juliet.schrodinger.com (8.9.3/8.9.3) with ESMTP id KAA18494; Wed, 1 Aug 2001 10:14:31 -0700 X-Authentication-Warning: juliet.schrodinger.com: jshelley owned process doing -bs Date: Wed, 1 Aug 2001 10:14:31 -0700 (PDT) From: John Shelley To: omar Deeb cc: chemistry@ccl.net Subject: Re: CCL:computational chemistry course - undergraduate In-Reply-To: <20010801115704.13497.qmail@web12307.mail.yahoo.com> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear Dr. Deeb, Text books: I'd recommend: 1. Andrew R. Leach's book: Molecular Modelling: Principles and Applications It offers very broad practical coverage of molecular modelling in an understandable style. The perspective that it provides (practicality) is uncommon. This most applicable to drug design. For simulations: I like: 1. D. Frenkel and B. Smit's: Understanding Molecular Simulation 2. M.P. Allen and D. J. Tildesley's: Computer Simulation of liquids John C. Shelley Schrodinger, Inc. On Wed, 1 Aug 2001, omar Deeb wrote: > Dear all, > > we are trying to give our undergraduate chemistry > students a computational chemistry course. > Any suggestions concerning outline, textbook, software > and related material. > > Thanks in advance > > Dr. omar Deeb > Chairman of the depart. of chemistry > faculty of science and technology > Alquds university > jerusalem > > fax 972-2-2796960 > > e-mail deeb2000il@yahoo.com > > __________________________________________________ > Do You Yahoo!? > Make international calls for as low as $.04/minute with Yahoo! Messenger > http://phonecard.yahoo.com/ > > > -= 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 Aug 1 10:42:55 2001 Received: from web11907.mail.yahoo.com ([216.136.172.191]) by server.ccl.net (8.11.0/8.11.0) with SMTP id f71Egt532016 for ; Wed, 1 Aug 2001 10:42:55 -0400 Message-ID: <20010801144254.35959.qmail@web11907.mail.yahoo.com> Received: from [150.161.5.236] by web11907.mail.yahoo.com; Wed, 01 Aug 2001 07:42:54 PDT Date: Wed, 1 Aug 2001 07:42:54 -0700 (PDT) From: Sidney Ramos Subject: MPI libraries for Solaris To: chemistry@ccl.net, dalton-users@kjemi.uio.no MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Dear CCLers and Dalton Users, I get the last Dalton 1.2 version and I wish I compiled the parallel version in the Sun Entreprise(4 nodes). Anybody knows where can I get MPI libraries for Solaris? Thanks for any help! Best Regards, Sidney Ramos LQTC - DQF - CCEN - UFPE __________________________________________________ Do You Yahoo!? Make international calls for as low as $.04/minute with Yahoo! Messenger http://phonecard.yahoo.com/ From chemistry-request@server.ccl.net Wed Aug 1 12:22:40 2001 Received: from narnia2.rutgers.edu ([165.230.180.158]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f71GMd502035 for ; Wed, 1 Aug 2001 12:22:39 -0400 Received: from eden.rutgers.edu (molly.envsci.rutgers.edu [165.230.5.148]) by narnia2.rutgers.edu (8.8.8/8.8.8) with ESMTP id MAA14762 for ; Wed, 1 Aug 2001 12:22:39 -0400 (EDT) Message-ID: <3B682EAA.F2335A9A@eden.rutgers.edu> Date: Wed, 01 Aug 2001 12:30:34 -0400 From: "Mary O'Connor" X-Mailer: Mozilla 4.08 [en] (Win98; I) MIME-Version: 1.0 To: chemistry@ccl.net Subject: PES of water. Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit I wish to thank everyone who offered answers regarding my question about finding the energies of the water molecule at different geometries: 1.) Li Guohui: 2 published PES of water up to dissociation : one by Rabitz of Princeton and another by Schwenke ( NASA). The Schwenke results gets the better rating. Search JCP for papers. 2.) Pierre Vitorge said that my basis set was probably too small, but that I could scan in the Z-matrix (after the geometry) data to be scanned with the key code "S". My basis set would be far too small to calculate the dissociation equilibrium. 3.)Ned C. Haubein: start with right angle water and move one of the H in 0.5 A increments using the modredundant keyword, and scanning the atoms 4 times. 4.) Stefan Fau: suggested much of the same approach, using the "s" keyword and modredundant to increase the variable 0.1 A per scan. 5.) Wang Dongqi: Optimize a water molecule, move a hydrogen in predefined increments, and get the enrgy of the modified system. Thank you all very much for your help, and I am trying out all of your suggestions. Mary O'Connor Doctoral Candidate Rutgers University New Brunswick, NJ 08903 USA From chemistry-request@server.ccl.net Wed Aug 1 13:21:28 2001 Received: from ozone.umsl.edu ([134.124.105.185]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f71HLR503758 for ; Wed, 1 Aug 2001 13:21:27 -0400 Received: from ozone.umsl.edu (localhost [127.0.0.1]) by ozone.umsl.edu (SGI-8.9.3/8.9.3) with ESMTP id MAA46141 for ; Wed, 1 Aug 2001 12:24:45 -0700 (PDT) Sender: siva@ozone.umsl.edu Message-ID: <3B68577D.2A949B3D@ozone.umsl.edu> Date: Wed, 01 Aug 2001 12:24:45 -0700 From: Sivanesan Dakshanamurthy Organization: University of Missouri-St. Louis X-Mailer: Mozilla 4.51 [en] (X11; I; IRIX64 6.5 IP27) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net Subject: CVFF parameters for Zn Content-Type: multipart/alternative; boundary="------------0969D9B00F5B191CF2A2D584" --------------0969D9B00F5B191CF2A2D584 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear CCLers, I am looking for Zn parameters for CVFF forcefield (as to how we can externally provide the parameters) to do docking calculations on Enzyme-Substrate interactions. I will summarize all replies. I would really appreciate any information. Thanks in advance. Sincerely, D.Sivanesan -- ( @ @ ) -------------------------------------------o00o----(_)----o00o---------------------- D. Sivanesan, Post Doctoral Fellow, Department of Chemistry, Computational Chemistry Group, University of Missouri, St. Louis, Missouri-63121. USA Phone: 314-516-6882 (Office) 314-389-4777 (Home) sivanesan15@hotmail.com and chedsiva@jinx.umsl.edu Fax : 314-516-5342 ------------------------------------------------------------------------------------ --------------0969D9B00F5B191CF2A2D584 Content-Type: text/html; charset=us-ascii Content-Transfer-Encoding: 7bit Dear CCLers,
I am looking for Zn parameters for CVFF forcefield (as to how we can externally provide the parameters) to do docking calculations on Enzyme-Substrate interactions. I will summarize all replies.
I would really appreciate any information.
Thanks in advance.
Sincerely,
D.Sivanesan 
-- 
                                                 ( @ @ )
-------------------------------------------o00o----(_)----o00o----------------------
D. Sivanesan,                        
Post Doctoral Fellow,            
Department of Chemistry,               
Computational Chemistry Group,       
University of Missouri,                             
St. Louis, Missouri-63121. USA                      
Phone: 314-516-6882 (Office)                         
       314-389-4777 (Home)                         
       sivanesan15@hotmail.com and  chedsiva@jinx.umsl.edu                        
Fax : 314-516-5342                                     
------------------------------------------------------------------------------------
  --------------0969D9B00F5B191CF2A2D584-- From chemistry-request@server.ccl.net Wed Aug 1 15:47:11 2001 Received: from hotmail.com ([64.4.37.25]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f71JlB507121 for ; Wed, 1 Aug 2001 15:47:11 -0400 Received: from mail pickup service by hotmail.com with Microsoft SMTPSVC; Wed, 1 Aug 2001 12:47:06 -0700 Received: from 66.81.51.229 by pv2fd.pav2.hotmail.msn.com with HTTP; Wed, 01 Aug 2001 19:47:06 GMT X-Originating-IP: [66.81.51.229] From: "Yuan-Yuan chen" To: chemistry@ccl.net Subject: Pericyclic additions Date: Wed, 01 Aug 2001 15:47:06 -0400 Mime-Version: 1.0 Content-Type: text/plain; format=flowed Message-ID: X-OriginalArrivalTime: 01 Aug 2001 19:47:06.0861 (UTC) FILETIME=[BEB539D0:01C11AC2] Hi, every one There are two recent papers of contradictory opinions on the mechanism of Diels-Alder reactions if you are interested: 1. Tetrahedron Lett. 2001, 42, 5077. “Merging of 4+2 and 2+4 cycloadditon paths in the regiospecific dimerization of methacrolein. A case of concerted crypto-diradical cycloaddition” 2. http://preprint.chemweb.com/orgchem/0107002 “Collision-induced electron reorganization as the general mechanism of concerted cycloaddition reactions”. Yuan-Yuan _________________________________________________________________ Get your FREE download of MSN Explorer at http://explorer.msn.com/intl.asp From chemistry-request@server.ccl.net Wed Aug 1 23:40:53 2001 Received: from cascara.uvic.ca (root@[142.104.5.28]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f723er517683 for ; Wed, 1 Aug 2001 23:40:53 -0400 Received: from pinc226.pinc.com (pinc226.pinc.com [199.60.118.226]) by cascara.uvic.ca (8.11.3/8.11.3) with SMTP id f723ep122924 for ; Wed, 1 Aug 2001 20:40:51 -0700 From: Roy Jensen To: chemistry@ccl.net Subject: SUMMARY: G98W on multi-processor computers Date: Wed, 01 Aug 2001 20:41:43 -0700 Message-ID: References: In-Reply-To: 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 f723er517684 Thanks to those who responded to my question. Roy Jensen ORIGINAL MESSAGE ================ > 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. SUMMARY ======= Gaussian 98W cannot use more than one processor but you can install several copies of Gaussian in different directories, with different scratch directories, and run them individually. The Windows Operating System dynamically assigns jobs to the processors on the basis of usage; each job should go to a different processor. One person was concerned that this may violate the Gaussian license. Doug Fox responded with an alternate method for starting multiple Gaussian jobs (command line from a DOS prompt similar to Unix). Although no definitive, I think it resolves this issue. From chemistry-request@server.ccl.net Wed Aug 1 15:34:46 2001 Received: from wodc7-1.uucp-gw.mail.uu.net ([199.171.54.178]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f71JYk506926 for ; Wed, 1 Aug 2001 15:34:46 -0400 Received: from wodc7uc0.ffx.ops.us.uu.net by wodc7ug0.ffx.ops.us.uu.net with SMTP (peer crosschecked as: wodc7-1.uucp.uu.net [199.171.54.179]) id QQlafu21063 for ; Wed, 1 Aug 2001 19:34:46 GMT Message-Id: Received: from m10.UUCP by wodc7uc0.ffx.ops.us.uu.net with UUCP/RMAIL ; Wed, 1 Aug 2001 19:34:46 +0000 Received: by m10.gaussian.com; Wed, 1 Aug 2001 15:30:07 -0400 Received: by mousse.gaussian.com; Wed, 1 Aug 2001 15:37:17 -0400 From: gaussian.com!moses@gaussian.com (David Moses) Subject: Upcoming Gaussian Workshops To: chemistry@ccl.net Date: Wed, 1 Aug 2001 15:37:16 -0400 (EDT) X-Mailer: ELM [version 2.4 PL25] MIME-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Gaussian, Inc. is pleased to announce two upcoming workshops INTRODUCTION TO GAUSSIAN: THEORY AND PRACTICE ____________________________________________________________________ UNITED STATES, in conjunction with IBM and NCSC. Date: October 9-12, 2001 Location: North Carolina Supercomputing Center MCNC 3021 Cornwallis Road Research Triangle Park, NC 27709-2889 Registration Fee: $250 Application deadline: September 28, 2001 ____________________________________________________________________ CHILE, in conjunction with COMPAQ and Pontificia Universidad Catolica (PUC) Date: November 13-16, 2001 Location: Pontificia Universidad Catolica Facultad de Quimica Avda. Vicuna Mackenna #4860 Santiago, Chile Registration Fee: $350 Registration Deadline: November 2, 2001 ____________________________________________________________________ "Introduction to Gaussian: Theory and Practice." will be presented by representatives of Gaussian, Inc. The workshops will cover the full range of methods available in the Gaussian 98 package with emphasis on new methods and features which make Gaussian 98 applicable to an ever-widening spectrum of research applications. The workshop is structured to provide an introduction to electronic structure theory as well as a hands-on review for researchers active in the field. The workshop is open to researchers at all levels of academic, government and industrial research. Preliminary Topic List: Independent Particle Methods Model Chemistries: A Framework for Understanding Electronic Structure Theory Results Using ONIOM MCSCF Methods and Applications Geometry Optimization Techniques Electron Correlation Methods Density Functional Theory Methods Methods for Excited Electronic States Interpretation of Gaussian Results Prediction of Molecular Properties Solvent Effects via Electronic Structure Methods Estimating Resource Requirements There will be hands-on sessions each day between the morning and afternoon lectures. Additional hands-on sessions will be available until the building closes. Workshop participants will be provided with use of a workstation to complete exercises, experiment and/or conduct short research topics. The GaussView user interface will be used to perform visualization of results and to facilitate calculation setup. Each workshop participant will also be provided a copy of the lecture notes, a copy of Exploring Chemistry with Electronic Structure Methods, 2nd Edition, and a Gaussian 98 User's Reference. For an Application please contact (Please specify which workshop): Workshop Coordinator Gaussian, Inc. Carnegie Office Park, Bldg. 6 Pittsburgh, PA 15106 Additional information can be obtained from: Telephone: 412 279 6700 Fax: 412 279 2118 email: info@gaussian.com Hotel Accommodations: A list of hotel accommodations in the vicinity of the the workshop location will be made available to all registrants. Hotel accommodations will be the responsibility of each participant. Meals: Meals will be the responsibility of each participant. DEADLINES: Receipt of Registration Materials along with the registration fee must be received by the specified deadlines. **************************************************************************** This notice is sent without warranty of any kind, expressed or implied by Gaussian Inc., IBM or COMPAQ. Gaussian is a registered trademark of Gaussian, Inc. ---- David J. Moses, Ph.D. Vice President, C.O.O. Gaussian, Inc. Carnegie Office Park Building Six Pittsburgh, PA 15106 412-279-6700 (Voice) 412-279-2118 (FAX) moses@gaussian.com http://www.gaussian.com