From chemistry-request@server.ccl.net Fri Nov 10 02:09:16 2000 Received: from web9608.mail.yahoo.com (web9608.mail.yahoo.com [216.136.129.187]) by server.ccl.net (8.8.7/8.8.7) with SMTP id CAA09440 for ; Fri, 10 Nov 2000 02:09:16 -0500 Message-ID: <20001110070707.46959.qmail@web9608.mail.yahoo.com> Received: from [161.142.4.9] by web9608.mail.yahoo.com; Thu, 09 Nov 2000 23:07:07 PST Date: Thu, 9 Nov 2000 23:07:07 -0800 (PST) From: sohail qamar Subject: hi friends! To: chemistry@ccl.net Cc: chemistry@ccl.net MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii hi ccl friends! again...... I am in search of a database (compounds).I will use DOCK for screening purpose.Any reliable(free) database other then AVAILABLE CHEMICALS DIRECTORY. Any suggestion would be greatly appreciated.... with the best of luck for u good future plans. sohail university sains malaysia. __________________________________________________ Do You Yahoo!? Thousands of Stores. Millions of Products. All in one Place. http://shopping.yahoo.com/ From chemistry-request@server.ccl.net Fri Nov 10 05:33:36 2000 Received: from mail-d.bcc.ac.uk (mail-d.bcc.ac.uk [144.82.100.24]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id FAA10497 for ; Fri, 10 Nov 2000 05:33:35 -0500 Received: from ucl.ac.uk (actually host chlorine.chem.ucl.ac.uk) by mail-d.bcc.ac.uk with SMTP (Mailer) with ESMTP; Fri, 10 Nov 2000 10:33:06 +0000 Sender: mb@ucl.ac.uk Message-ID: <3A0BDC00.53B05EBD@ucl.ac.uk> Date: Fri, 10 Nov 2000 11:29:04 +0000 From: Michael Brunsteiner Organization: University College London X-Mailer: Mozilla 4.7C-SGI [en] (X11; I; IRIX64 6.5 IP30) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net Subject: Gaussian98 won't give me a WFN-file Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear all, I run a small job on a simple molecule with Gaussian98 (example input script below) ... and i'd like to have Gaussian to write a WFN-file at the end of the run for further analysis, however, it seems just to ignore the OUTPUT keyword given. I can find no wfn-file in the working nor in the scratch directory and there is no according message in the output ... i'd be very grateful if anybody could tell me what i made wrong thanks in advance mic --------------------------------------------- # HF/6-31G** OPT=VERYTIGHT OUTPUT=WFN co optimization 0, 1 C 0.000000 0.000000 -0.636408 O 0.000000 0.000000 0.477306 HF.631++.wfn --------------------------------------------- =================================================== The Golden Rule of Arts and Sciences: He who has the gold makes the rules. "Why should we subsidize intellectual curiosity?" -Ronald Reagan --------------------------------------------------- Michael Brunsteiner Centre for Theoretical and Computational Chemistry University College London mailto:m.brunsteiner@ucl.ac.uk, http://www.ucl.ac.uk/~uccambr/ --------------------------------------------------- From chemistry-request@server.ccl.net Fri Nov 10 05:26:47 2000 Received: from muguet.saclay.cea.fr (muguet.saclay.cea.fr [132.166.192.6]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id FAA10449 for ; Fri, 10 Nov 2000 05:26:47 -0500 Received: from drfmc.ceng.cea.fr (drfmc.ceng.cea.fr [132.168.10.1]) by muguet.saclay.cea.fr (8.9.1a/8.9.1/CEAnet-relay-5.2.D20+Y2K) with ESMTP id LAA15517; Fri, 10 Nov 2000 11:26:33 +0100 (MET) Received: from drfmc.ceng.cea.fr (localhost [127.0.0.1]) by drfmc.ceng.cea.fr (8.9.3/8.8.8) with ESMTP id LAA18357; Fri, 10 Nov 2000 11:26:31 +0100 Message-ID: X-Mailer: XFMail 1.4.4 on Solaris X-Priority: 3 (Normal) Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit MIME-Version: 1.0 In-Reply-To: <200011091031.eA9AV7b06713@lgsx01.lg.ehu.es> Date: Fri, 10 Nov 2000 11:26:31 +0100 (MET) From: Valentina Vetere To: Pablo Vitoria Subject: RE: CCL:Change basis set in G98 Cc: CCL , fan@mail.chem.tamu.edu Content-Transfer-Encoding: 8bit Hi Pablo, can you write an example of your method? I'd like to understand if in the first input, with the small basis set, you are using vshift, alter, etc.. And for the second one? What kind of basis set are you using on transition Metals (the small one)? Thank you valentina On 09-Nov-2000 Pablo Vitoria wrote: > Hi Huajun, > > You can use guess=read with DFT and HF methods when changing basis set, > geometry of the molecule and even if you add some atoms to your molecule, > for example calculating a dimer after the monomer as long as you keep the > order of the atoms. (It works!) > > In fact, I use this method very often in calculations involving transition > metal elements, which have convergence problems. I run a calculation with a > "small" basis set, faster and easier to converge, check if it converged to > the correct electronic state, and then I run a final calculation with a > bigger basis set using guess=read. > > I am not an expert in G98 internals, but as far as I know, the program reads > the orbitals from the checkpoint file, and then proyects them to the new > basis set. > > Best regards > > Pablo > > ----------------------------------------- > Pablo Vitoria Garcia > Dpto. Quimica Inorganica, Facultad de Ciencias > Universidad del Pais Vasco (UPV/EHU) > Aptdo. 644 > E-48080 Spain > > Phone: +34 94 6015529/5522 > Fax: +34 94 4648500 > ----------------------------------------- > > > > -= 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 ------------------------------------------------------------ Vetere Valentina e-mail:vetere@drfmc.ceng.cea.fr DRFMC/SCIB/RI2M Tel(office):04-76-88-35-78 CEA_Grenoble ------------------------------------------------------------ From chemistry-request@server.ccl.net Fri Nov 10 09:00:25 2000 Received: from drew.berry.edu (drew.berry.edu [168.31.232.19]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id JAA12152 for ; Fri, 10 Nov 2000 09:00:25 -0500 Received: from fsgw.berry.edu (fsgw.berry.edu [168.31.232.96]) by drew.berry.edu (8.9.3/8.9.3) with SMTP id IAA23082 for ; Fri, 10 Nov 2000 08:59:59 -0500 Received: from [168.31.235.19] ([168.31.235.19]) by fsgw.berry.edu; Fri, 10 Nov 2000 08:59:36 -0500 User-Agent: Microsoft-Outlook-Express-Macintosh-Edition/5.02.2022 Date: Fri, 10 Nov 2000 08:59:42 -0500 Subject: Aromaticity From: Gary Breton To: Message-ID: Mime-version: 1.0 Content-type: text/plain; charset="US-ASCII" Content-transfer-encoding: 7bit Hello all, If one is interested in optimizing the geometry of a molecule that has the POSSIBILITY of exhibiting "aromatic" characteristics (i.e., does the molecule "flatten" to allow good orbital overlap even though at "lower" levels of calculations [e.g. RHF/3-21G] it does not) is it necessary to move to UHF versus RHF calculations (e.g. UHF/6-31G*)? Will 6-31G* properly "find" aromaticity where it may exist? Many thanks! Gary W. Breton Department of Chemistry Berry College PO Box 495016 Mount Berry, GA 30149 From chemistry-request@server.ccl.net Fri Nov 10 11:29:44 2000 Received: from newmail.DKFZ-Heidelberg.DE (newmail.inet.dkfz-heidelberg.de [193.174.53.39]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id LAA12743 for ; Fri, 10 Nov 2000 11:29:42 -0500 Received: from DKFZ-heidelberg.de (vishnu.inet.dkfz-heidelberg.de [193.174.62.115]) by newmail.DKFZ-Heidelberg.DE (8.9.3/8.9.3/DKFZ-8.9.3) with ESMTP id RAA10327 for ; Fri, 10 Nov 2000 17:27:22 +0100 (MET) Message-ID: <3A0C21E2.47BA4434@DKFZ-heidelberg.de> Date: Fri, 10 Nov 2000 17:27:14 +0100 From: Chaitanya Athale Organization: DKFZ-Heidelberg X-Mailer: Mozilla 4.7 [en] (WinNT; I) X-Accept-Language: en MIME-Version: 1.0 To: chem computing Subject: Application Polymer Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Subj.: Polymer Simulations Package Application Polymer Hi Everbody, Has anybody ever used this rather "low end" environment for polymer simulations: Application Polymer by Dr. Sergei Buldyrev, A.Y. Grosberg and A.R. Khokhlov- companion to the book "Giant Molecules"? I wondered if the source code of the program might be available? Cheers, Chaitanya. -- Chaitanya Athale From chemistry-request@server.ccl.net Fri Nov 10 09:08:03 2000 Received: from mail-a.bcc.ac.uk (mail-a.bcc.ac.uk [144.82.100.21]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id JAA12221 for ; Fri, 10 Nov 2000 09:08:01 -0500 Received: from ucl.ac.uk (actually host chlorine.chem.ucl.ac.uk) by mail-a.bcc.ac.uk with SMTP (Mailer) with ESMTP; Fri, 10 Nov 2000 14:07:33 +0000 Sender: mb@ucl.ac.uk Message-ID: <3A0C0E44.8ADCE11C@ucl.ac.uk> Date: Fri, 10 Nov 2000 15:03:32 +0000 From: Michael Brunsteiner Organization: University College London X-Mailer: Mozilla 4.7C-SGI [en] (X11; I; IRIX64 6.5 IP30) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net Subject: Gaussian / WFN-file ... the answer Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit i'd like to thank all the people who sent replies to my question: > I run a small job on a simple molecule with Gaussian98 > (example input script below) ... and i'd like to have Gaussian > to write a WFN-file at the end of the run for further > analysis, however, it seems just to ignore the OUTPUT keyword given. > I can find no wfn-file in the working nor in the scratch > directory and there is no according message in the output ... > > i'd be very grateful if anybody could tell me what i made wrong > > thanks in advance > mic > > > --------------------------------------------- > # HF/6-31G** OPT=VERYTIGHT OUTPUT=WFN > > co optimization > > 0, 1 > C 0.000000 0.000000 -0.636408 > O 0.000000 0.000000 0.477306 > > HF.631++.wfn > --------------------------------------------- special thanks go to Steve Williams who sent the definite answer (see below) > Michael > The undocumented fix for this is to add punch=archive to the route line. I > learned this from Doug Fox, and it has worked for me. The .wfn file > produced works fime in AIMPAC and AIM2000. > Steve =================================================== The Golden Rule of Arts and Sciences: He who has the gold makes the rules. "Why should we subsidize intellectual curiosity?" -Ronald Reagan --------------------------------------------------- Michael Brunsteiner Centre for Theoretical and Computational Chemistry University College London mailto:m.brunsteiner@ucl.ac.uk, http://www.ucl.ac.uk/~uccambr/ --------------------------------------------------- From chemistry-request@server.ccl.net Fri Nov 10 09:21:44 2000 Received: from interlock.amoco.com (texgate.amoco.com [204.149.20.10]) by server.ccl.net (8.8.7/8.8.7) with SMTP id JAA12285 for ; Fri, 10 Nov 2000 09:21:43 -0500 Received: by interlock.amoco.com id IAA10504 (InterLock SMTP Gateway 3.0 for CHEMISTRY@ccl.net); Fri, 10 Nov 2000 08:20:13 -0600 Received: by interlock.amoco.com (Protected-side Proxy Mail Agent-3); Fri, 10 Nov 2000 08:20:13 -0600 Received: by interlock.amoco.com (Protected-side Proxy Mail Agent-2); Fri, 10 Nov 2000 08:20:13 -0600 Received: by interlock.amoco.com (Protected-side Proxy Mail Agent-1); Fri, 10 Nov 2000 08:20:13 -0600 Message-Id: From: "Golab, Joseph T" To: "Ccl (E-mail)" Subject: FW: CoMSEF -- the Computational Molecular Science and Engineering Forum Date: Fri, 10 Nov 2000 08:19:57 -0600 Mime-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2650.21) Content-Type: text/plain; charset="ISO-8859-1" Dear colleagues, Next week's AIChE Annual Meeting in Los Angeles will see the kickoff of CoMSEF, the Computational Molecular Science and Engineering Forum (http://www.comsef.aiche.org/). Its first meeting will be on Wednesday, Nov 15, from 5:15-6:00 pm in the San Gabriel A room at the Westin Bonaventure. I've agreed to serve as the first Chair and am writing to explain what ComSEF is and intends to be. The purpose of this organization is to link the community of people who are working in molecular modeling, both in science and engineering applications. It is different from Divisions in AIChE and other societies in two important ways. First, its members can come from outside the sponsoring society. Second, it is intended both to lead new activities and also to collaboratively join together activities from different areas. Membership requires only your interest in joining. Joe Golab of BP is the Vice Chair for Membership, and he will gladly add you to the membership list (no dues!) if you send address and contact information to GolabJT@BP.com, putting "Re: CoMSEF" in your subject line. In return, we will keep you informed and provide avenues for you to share in the growth of this field. The agenda of next Wednesday's meeting is: (1) Describe the Formation Committee's vision of CoMSEF (2) Introduce the initial officers and acknowledge the other members of the Formation Committee: Past Chair - Tim Anderson Chair - Phil Westmoreland 1st Vice Chair - Grant Heffelfinger 2nd Vice Chair - Peter T. Cummings Secretary-Treasurer - Carol Hall Vice Chair for Communications - Thanos Panagiotopoulos Vice Chair for Membership - Joe Golab Liaison Director (1 yr) - Paulette Clancy [MRS, ...] Liaison Director (1 yr) - Matthew Neurock [20, ...] Liaison Director (2 yr) - Pablo Debenedetti [1a, ...] Liaison Director (2 yr) - Sanat Kumar [8, ...] (3) Describe the organization structure (4) Describe the scheduled 2001 Reno Topical Conference [Phil Westmoreland and Grant Heffelfinger] (5) Solicit programming input for 2002 Indianapolis [Peter Cummings] We have come to this point thanks to the CoMSEF Formation Committee, led by Tim Anderson. This group has put together the consensus and the documents needed to achieve official status within AIChE. It and the Forum involve people from different parts of AIChE and outside it, including programming groups and areas in AIChE Group 1, 2, 4, 8, 9, 10, 15, and 20. As participants in such groups, we have vested interests in complementing and augmenting their strengths, recognizing at the same time that no existing group encompasses the range of techniques and applications in molecularly based modeling. For example, 1a (Thermo and Transport) and 20 (Catalysis and Reaction Engineering) have many common interests in the field but many different ones, too, plus interests beyond molecular modeling. Likewise, molecular modeling is increasingly a complement to experiments. This confederated and intentionally synergistic approach is quite new for AIChE or most other societies. We want to draw people together to make the Forum a successful medium for making effective use of these theories and methods. We hope you share this commitment. Phil Westmoreland and Tim Anderson -- Phillip R. Westmoreland, Professor and Graduate Program Director Department of Chemical Engineering, University of Massachusetts Amherst 157A Goessmann, Box 33110; 686 N Pleasant; Amherst MA 01003-3110 413-545-1750 (6159 sect'y), FAX 413-545-1647; Lexington 781-259-8207 http://www.ecs.umass.edu/che/westmoreland.html From chemistry-request@server.ccl.net Fri Nov 10 09:49:58 2000 Received: from gatekeeper.itqb.unl.pt (qmailr@gatekeeper.itqb.unl.pt [193.136.177.1]) by server.ccl.net (8.8.7/8.8.7) with SMTP id JAA12397 for ; Fri, 10 Nov 2000 09:49:56 -0500 Received: (qmail 7475 invoked from network); 10 Nov 2000 14:49:39 -0000 Received: from mistral.itqb.unl.pt (herrmann@193.136.176.14) by gatekeeper.itqb.unl.pt with SMTP; 10 Nov 2000 14:49:39 -0000 Received: from localhost (herrmann@localhost) by mistral.itqb.unl.pt (8.9.3/8.9.3) with ESMTP id OAA16479; Fri, 10 Nov 2000 14:49:39 GMT Date: Fri, 10 Nov 2000 14:49:39 +0000 (WET) From: Rudolf Herrmann To: Luis Gracia cc: CCL list Subject: Re: CCL:latex style for protein alignments In-Reply-To: <3A0ACA9C.DA361D84@alumni.unav.es> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hello, you may try the texshade-package. You will find it on every ctan-server. for example at www.dante.de macros/latex/contrib/supported/texshade/texshade.dtx Hope this helps, R.Herrmann On Thu, 9 Nov 2000, Luis Gracia wrote: > Hi, > > does anybody know about a latex style that manage protein alignments > properly? > > Thanks in advance. > > Luis Gracia Valen > Unidad de Modelizacion Molecular > Dpto. Q. Organica y Farmaceutica > Universidad de Navarra > C/ Irunlarrea 1, Pamplona 31080, Espana > Tel: +34 948 425600 ext 6292 o 6359 > lgracia2@alumni.unav.es > http://www.unav.es/organica/luis/ > -- Dr. Rudolf Herrmann Instituto de Tecnologia Quimica e Biologica (ITQB) Av. da Republica, EAN, Apt. 127 P-2781-901 Oeiras e-mail: herrmann@itqb.unl.pt From chemistry-request@server.ccl.net Fri Nov 10 10:49:00 2000 Received: from mailhost.msi.com (fire.msi.com [146.202.0.242]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id KAA12625 for ; Fri, 10 Nov 2000 10:48:59 -0500 Received: (from daemon@localhost) by mailhost.msi.com (980427.SGI.8.8.8/970903.SGI.AUTOCF) id HAA15943; Fri, 10 Nov 2000 07:48:43 -0800 (PST) Received: from osman-pc.msi.com(146.202.7.202) by mailhost.msi.com via smap (V2.0) id xmac15930; Fri, 10 Nov 00 07:48:28 -0800 Message-Id: <5.0.0.25.0.20001110074234.029cb1c0@146.202.6.217> X-Sender: osman@146.202.6.217 X-Mailer: QUALCOMM Windows Eudora Version 5.0 Date: Fri, 10 Nov 2000 07:44:10 -0600 To: sohail qamar , chemistry@ccl.net From: "Osman F. Guner" Subject: Re: CCL:hi friends! Cc: chemistry@ccl.net In-Reply-To: <20001110070707.46959.qmail@web9608.mail.yahoo.com> Mime-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1"; format=flowed Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id KAA12626 Maybridge is free and is a subset of ACD; NCI also has free databases. These are available as SDFile format that you will have to build into a DOCK database. At 01:07 AM 11/10/00, sohail qamar wrote: >hi ccl friends! again...... > I am in search of a database (compounds).I will use >DOCK for screening purpose.Any reliable(free) database >other then AVAILABLE CHEMICALS DIRECTORY. > Any suggestion would be greatly appreciated.... > with the best of luck for u good future plans. >sohail >university sains malaysia. > >__________________________________________________ >Do You Yahoo!? >Thousands of Stores. Millions of Products. All in one Place. >http://shopping.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 --- Osman F. Güner, Ph.D. Director, Lead Identification & Optimization Molecular Simulations Inc. (858) 799-5341 osman@msi.com http://www.msi.com From chemistry-request@server.ccl.net Fri Nov 10 16:38:33 2000 Received: from rmx306-mta.mail.com (rmx306-mta.mail.com [165.251.48.168]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id QAA14779 for ; Fri, 10 Nov 2000 16:38:33 -0500 Received: from web569-mc (web569-mc.mail.com [165.251.48.92]) by rmx306-mta.mail.com (8.9.3/8.9.3) with SMTP id QAA16993 for ; Fri, 10 Nov 2000 16:38:32 -0500 (EST) Message-ID: <384297301.973892312880.JavaMail.root@web569-mc> Date: Fri, 10 Nov 2000 16:38:32 -0500 (EST) From: nicolas saettel To: chemistry@ccl.net Subject: Cosmo calculation + ALPHA + TSNUM Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: mail.com X-Originating-IP: 129.74.38.67 Hi all, I am trying to run a COSMO calculation with Gaussian98 using SCRF=(CPCM,Read,solvent=water) and additional 'Read' instructions after the coordinates. Those are: RADII=PAULING ALPHA=1.21 TSNUM=70 for example. However, gaussian always ignores the second instruction after RADII=PAULING (in the above case, TSNUM is kept the defaults 60, if I switch ALPHA and TSNUM; ALPHA is the default 1.2...) I try hundreds of different combinations, which do not seem to work. Do any of you have any clue or experienced the same problems? Any help will be greatly appreciated... Nicolas Saettel Nicolas SAETTEL University of Notre Dame Department of Chemistry and Biochemistry NOTRE DAME,IN 46556 tel: +1 (219) 631-4007 ______________________________________________ FREE Personalized Email at Mail.com Sign up at http://www.mail.com/?sr=signup