From chemistry-request@server.ccl.net Thu Nov 16 08:06:50 2000 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 IAA22345 for ; Thu, 16 Nov 2000 08:06:49 -0500 Received: from dale.ri.ac.uk by mail-b.bcc.ac.uk with SMTP (Mailer) with ESMTP; Thu, 16 Nov 2000 13:06:31 +0000 Received: from ri.ac.uk (davy.ri.ac.uk) by dale.ri.ac.uk (Content Technologies SMTPRS 4.1.5) with SMTP id for ; Thu, 16 Nov 2000 13:05:13 +0000 Received: from faraday.ri.ac.uk by ri.ac.uk (5.x/SMI-SVR4) id AA25090; Thu, 16 Nov 2000 13:06:30 GMT Received: from localhost by faraday.ri.ac.uk (980427.SGI.8.8.8) id NAA75011; Thu, 16 Nov 2000 13:06:29 GMT Date: Thu, 16 Nov 2000 13:06:29 +0000 (WET) From: Stefan Bromley X-Sender: stefan@faraday Reply-To: Stefan Bromley To: chemistry@ccl.net Subject: Analysing DMOL dos files in Cerius2 Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi all, For anyone having also having trouble with analysing *.dos files in Cerius2 I have had been informed of the following solution: The current vesion of the Cerius2 does not actually support reading/analysing DOS files from DMOL3. To do so you have to look for "Displaying DMol partial density of states" at: http://www.msi.com/user/consortia/catalysis/Script/scipts.html Here a program can be found "pdos" which converts *.dos files into *.grf files which can then be read by Cerius2 in 'Tables and Graphs'. Stefan ********************************************************************** This email and any files transmitted with it are confidential and intended solely for the use of the individual or entity to whom they are addressed. If you have received this email in error please notify the system manager. This footnote also confirms that this email message has been swept by MIMEsweeper for the presence of computer viruses. www.mimesweeper.com ********************************************************************** From chemistry-request@server.ccl.net Thu Nov 16 08:30:17 2000 Received: from vytautas.vdu.lt (mail@vytautas.vdu.lt [193.219.38.33]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id IAA22446 for ; Thu, 16 Nov 2000 08:29:56 -0500 Received: from vaidila.vdu.lt ([193.219.38.52] ident=root) by vytautas.vdu.lt with esmtp for CHEMISTRY@ccl.net id 13wP5i-0002cY-00; Thu, 16 Nov 2000 15:28:38 +0200 Received: from vaidila.vdu.lt (vejas.vdu.lt [193.219.38.82]) by vaidila.vdu.lt (8.9.3/8.9.3) with ESMTP id PAA17617 for ; Thu, 16 Nov 2000 15:28:39 +0200 (GMT) Message-ID: <3A13C486.16D2BA1D@vaidila.vdu.lt> Date: Thu, 16 Nov 2000 03:27:03 -0800 From: "art'" X-Mailer: Mozilla 4.7 [en] (Win98; I) X-Accept-Language: en MIME-Version: 1.0 CC: CCL Subject: CCL: UHF vs. ROHF ??? References: Content-Type: text/plain; charset=koi8-r Content-Transfer-Encoding: 7bit Hello CCL'ers, Can anyone say something about the difference of UHF and ROHF theory, when I want to examine electronic structure of compound. In my opinion, ROHF is better to produce MO energies. But, is there any differences between UHF and ROHF when we are talking about the distribution of MO (e.g. HOMO) over the whole molecule? If Yes, then what they are ? Thank you all in advance. The answers will be summarized on CCL. A.Ziemys From chemistry-request@server.ccl.net Thu Nov 16 10:04:10 2000 Received: from gpo.cam.msi-eu.com (cam.msi-eu.com [192.190.183.254]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id KAA23032 for ; Thu, 16 Nov 2000 10:04:09 -0500 Received: from coriander (dhcp45.munich.msi-eu.com [172.29.65.45]) by gpo.cam.msi-eu.com (8.9.3/8.9.3/Debian/GNU) with SMTP id PAA25484; Thu, 16 Nov 2000 15:01:47 GMT Message-Id: <3.0.32.20001116150448.00998e90@mailhost.munich.msi-eu.com> X-Sender: kstark@mailhost.munich.msi-eu.com X-Mailer: Windows Eudora Pro Version 3.0 (32) Date: Thu, 16 Nov 2000 15:04:49 -0600 To: Stefan Bromley From: "Dr. Klaus Stark" Subject: Re: CCL:Analysing DMOL dos files in Cerius2 Cc: chemistry@ccl.net Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Dear All, please note that this is a web page for members of MSI's Catalysis2000 Consortium only. It is password protected and not generally accessible. Best regards Klaus Stark At 01:06 PM 11/16/00 +0000, Stefan Bromley wrote: >Hi all, > >For anyone having also having trouble with analysing *.dos files in >Cerius2 I have had been informed of the following solution: > >The current vesion of the Cerius2 does not actually support >reading/analysing DOS files from DMOL3. To do so you have to look for >"Displaying DMol partial density of states" at: > >http://www.msi.com/user/consortia/catalysis/Script/scipts.html > >Here a program can be found "pdos" which converts *.dos files into *.grf >files which can then be read by Cerius2 in 'Tables and Graphs'. > >Stefan > > > >********************************************************************** >This email and any files transmitted with it are confidential and >intended solely for the use of the individual or entity to whom they >are addressed. If you have received this email in error please notify >the system manager. > >This footnote also confirms that this email message has been swept by >MIMEsweeper for the presence of computer viruses. > >www.mimesweeper.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 > > > > > -- Dr. Klaus Stark Application Scientist Molecular Simulations Inc. Inselkammerstr. 1 82 008 Unterhaching Germany Phone : ++49-89-61459-420 Mobile : ++49-172-936-3380 Fax : ++49-89-61459-400 E-Mail : kstark@msi.de Web Page : http://www.msi.com From chemistry-request@server.ccl.net Thu Nov 16 04:09:20 2000 Received: from mailserver.unimi.it (mailserver.unimi.it [159.149.10.1]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id EAA20665 for ; Thu, 16 Nov 2000 04:09:19 -0500 Received: from vega (vega.farma.unimi.it [159.149.79.32]) by mailserver.unimi.it (8.9.3/8.9.3) with SMTP id KAA22557; Thu, 16 Nov 2000 10:09:07 +0100 (MET) Message-ID: <004d01c04fac$c19f84c0$204f959f@farma.unimi.it.farma.unimi.it> From: "Giulio Vistoli" To: "Anselm Horn" , "CCL" References: <3A12DB39.DC7EDB55@ccc.uni-erlangen.de> Subject: Re: CCL:Sybyl atom types Date: Thu, 16 Nov 2000 10:07:58 +0100 Organization: Ist. Chimica Farmaceutica MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 5.50.4522.1200 X-MimeOLE: Produced By Microsoft MimeOLE V5.50.4522.1200 Dear Anselm Horn Our software VEGA can assign correctly sybyl atom types to any molecules (macromolecules or small compounds). Moreover VEGA can convert several molecular file formats and it can assign not only sybyl atom types, but also CVFF, AMBER, CHARMM atom types. Finally VEGA calculates molecular surfaces and analyzes molecular dynamic trajectories. You can free download VEGA at our website http://users.unimi.it/~ddl Hope it helps, Giulio -- Dr. Giulio Vistoli Ist. di Chimica Farmaceutica e Tossicologica Viale Abruzzi, 42 I-20131 Milano (Italy) Tel. +39-02-29502230 Fax +39-02-29514197 E-Mail: giulio.vistoli@unimi.it WWW: http://users.unimi.it/~ddl From chemistry-request@server.ccl.net Thu Nov 16 13:26:29 2000 Received: from dont.csc.cuhk.edu.hk (root@dont.csc.cuhk.edu.hk [137.189.6.34]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id NAA23889 for ; Thu, 16 Nov 2000 13:26:27 -0500 Received: from l (dialup2-075.csc.cuhk.edu.hk [137.189.209.75]) by dont.csc.cuhk.edu.hk (8.9.3/8.9.3) with SMTP id CAA25984 for ; Fri, 17 Nov 2000 02:26:10 +0800 (HKT) Message-ID: <006e01c04ffa$c66fae00$c4ba40ca@l> Reply-To: "Kiniu WONG Kin-Yiu" From: "Kiniu WONG Kin-Yiu" To: Subject: energy of a singlet state in which HOMO wavefunction is substituted by LUMO wavefunction Date: Fri, 17 Nov 2000 02:26:34 +0800 Organization: Physics CUHK MIME-Version: 1.0 Content-Type: text/plain; charset="big5" 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 all, I want to find the excitation energy from a singlet ground state to another singlet state (excited). I know CIS in Gaussian is able to calculate it, however, the disk space of the CIS computation required for our molecule (Alq3) exceeds the upper limit (~25GB) of Gaussian. Therefore, instead of calculating a whole CI with a number of Slater determinants, I want to find out the energy of a singlet state in which HOMO wavefunction is substituted by LUMO wavefunction, and treat it as the energy of the first excited state. But I don't know how to use Gaussian to compute it, can anybody teach me? Thank you in advance! Wishes, Kiniu ---- Kiniu WONG Kin-Yiu Undergraduate student Department of Physics The Chinese University of Hong Kong Email: kiniu@cuhk.edu.hk or kyiwong@phy.cuhk.edu.hk From chemistry-request@server.ccl.net Thu Nov 16 14:01:54 2000 Received: from abello.unab.cl (abello.unab.cl [200.27.72.3]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id OAA24163 for ; Thu, 16 Nov 2000 14:01:47 -0500 Received: from quimanche ([200.27.72.154]) by abello.unab.cl (8.9.3/8.9.3) with SMTP id PAA18465 for ; Thu, 16 Nov 2000 15:01:12 -0300 From: "Ramiro Arratia-Perez" To: Subject: Re2X8 Date: Thu, 16 Nov 2000 15:58:35 -0400 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 (9.0.2910.0) X-MimeOLE: Produced By Microsoft MimeOLE V5.00.2919.6700 Importance: Normal Dear CClers, I would like to receive information regarding the Re2F8(2-) and Re2I8(2-) anions. I am looking for references dealing with their structural parameters and spectroscopic properties. I'll summarize the answer Thanks, Ramiro Arratia-Perez,Ph.D. Director Area Ciencias Quimicas Universidad Nacional Andres Bello Republica 217, Santiago de Chile Phone: (562)-689-5919 Ext. 383 Fax: (562)-671-1936 From chemistry-request@server.ccl.net Thu Nov 16 14:16:15 2000 Received: from postoffice.mail.cornell.edu (postoffice.mail.cornell.edu [132.236.56.7]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id OAA24277 for ; Thu, 16 Nov 2000 14:16:15 -0500 Received: from cornell.edu (carbo2.foodsci.cornell.edu [132.236.147.61]) by postoffice.mail.cornell.edu (8.9.3/8.9.3) with ESMTP id OAA22589 for ; Thu, 16 Nov 2000 14:16:15 -0500 (EST) Sender: dwood@cornell.edu Message-ID: <3A1432DB.E0C8CB44@cornell.edu> Date: Thu, 16 Nov 2000 14:17:47 -0500 From: "Dr. Richard Wood" Organization: Cornell University X-Mailer: Mozilla 4.7C-SGI [en] (X11; I; IRIX 6.5 IP32) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net Subject: Thank you for your help and suggestions Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi all I would like that thank Dorina Kosztin, Rick Venable, Don Gregory and eugene Leitl for their help, suggestions, files, and URL's to aid in my building of the wheel, in this case a bigger water box. I solved the problem when I realized that in my update image command my image cutoff (cutim) was too small. When I increased it, I was able to build a box of over 10000 waters. Again, thank you to all that offered their help. I appreciate it. Richard -- Richard L. Wood, Ph. D. Physical/Computational Chemist Post-doctoral Associate Cornell University, Ithaca, NY 14853 From chemistry-request@server.ccl.net Thu Nov 16 14:48:13 2000 Received: from cougar.it.wsu.edu (root@cougar.it.wsu.edu [134.121.1.10]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id OAA24446 for ; Thu, 16 Nov 2000 14:48:13 -0500 Received: from ucis (ucis.chem.wsu.edu [134.121.41.180]) by cougar.it.wsu.edu (8.9.3/8.9.3) with SMTP id LAA06286; Thu, 16 Nov 2000 11:48:05 -0800 (PST) Message-ID: <000f01c05006$20ecce70$b4297986@chem.wsu.edu> From: "Phillip D. Matz" To: "Kiniu WONG Kin-Yiu" , References: <006e01c04ffa$c66fae00$c4ba40ca@l> Subject: Re: CCL:energy of a singlet state in which HOMO wavefunction is substituted by LUMO wavefunction Date: Thu, 16 Nov 2000 11:48:01 -0800 MIME-Version: 1.0 Content-Type: text/plain; charset="big5" Content-Transfer-Encoding: 7bit X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 5.00.3018.1300 X-MimeOLE: Produced By Microsoft MimeOLE V5.00.3018.1300 Hello Kiniu, > calculate it, however, the disk space of the CIS computation required for > our molecule (Alq3) exceeds the upper limit (~25GB) of Gaussian. Therefore If you still want to use CIS then you can specify CIS(Direct) and then you will find that the calculation will proceed correctly. Respectfully, Phillip Matz matz@wsunix.wsu.edu ----- Original Message ----- From: "Kiniu WONG Kin-Yiu" To: Sent: Thursday, November 16, 2000 10:26 AM Subject: CCL:energy of a singlet state in which HOMO wavefunction is substituted by LUMO wavefunction > Dear all, > > I want to find the excitation energy from a singlet ground state to > another singlet state (excited). I know CIS in Gaussian is able to > calculate it, however, the disk space of the CIS computation required for > our molecule (Alq3) exceeds the upper limit (~25GB) of Gaussian. Therefore, > instead of calculating a whole CI with a number of Slater determinants, I > want to find out the energy of a singlet state in which HOMO wavefunction is > substituted by LUMO wavefunction, and treat it as the energy of the first > excited state. But I don't know how to use Gaussian to compute it, can > anybody teach me? Thank you in advance! > > Wishes, > Kiniu > > ---- > Kiniu WONG Kin-Yiu > Undergraduate student > Department of Physics > The Chinese University of Hong Kong > Email: kiniu@cuhk.edu.hk or kyiwong@phy.cuhk.edu.hk > > > > -= 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 Thu Nov 16 18:25:29 2000 Received: from day.its.uiowa.edu (day.its.uiowa.edu [128.255.56.107]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id SAA25999 for ; Thu, 16 Nov 2000 18:25:28 -0500 Received: from [128.255.72.43] (his.chem.uiowa.edu [128.255.72.43]) by day.its.uiowa.edu (8.9.3/8.9.1/ns-mx-1.11) with ESMTP id RAA16436 for ; Thu, 16 Nov 2000 17:25:26 -0600 Message-Id: Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Thu, 16 Nov 2000 17:28:49 -0500 To: chemistry@ccl.net From: "Jan H. Jensen" Subject: HyperChem Hi, I am contemplating buying a copy of HyperChem, but I have a few questions about its capabilities. 1) Is it possible to automatically add hydrogens to a crystallographically determined geometry of a protein? 2) Is it possible to optimize (with AMBER) the positions of these hydrogens while keeping the heavy atoms fixed at their crystallographically determined positions? 3) HyperChem is supposed to have a sophisticated scripting language that allows for interfaces to other programs. Has anyone interfaced HyperChem to GAMESS US? Thanks, Jan Jensen =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=- Jan H. Jensen Assistant Professor Department of Chemistry jan-jensen@uiowa.edu University of Iowa Phone:(319) 335-1108 Iowa City, IA 52242 FAX: (319) 335-1270 http://www.uiowa.edu/~chemdept/faculty/jensen/ =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-