From chemistry-request@server.ccl.net Mon Feb 17 08:40:43 2003 Received: from vspnt017.isiconsulting.it ([213.140.25.217]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h1HDefx01294 for ; Mon, 17 Feb 2003 08:40:42 -0500 Received: by smtp.xelionfinancialstudio.it with Internet Mail Service (5.5.2650.21) id ; Mon, 17 Feb 2003 14:40:33 +0100 Message-ID: <5C1E071BB0B1E4449C53F68EEF7DF47F0D5BB0@vspw2217.getracenter.it> From: Forlani Roberto To: chemistry@ccl.net Subject: 2D beautify Date: Mon, 17 Feb 2003 14:40:33 +0100 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2650.21) Content-Type: text/plain; charset="iso-8859-1" X-IMAPbase: 1045499370 5 Status: O X-Status: X-Keywords: X-UID: 1 Dear CCLers, I wonder if anyone could tell me of any method to "beautify" a 3D multi sdf file into a 2D multi sdf file. I'll summarize. Very best, Roberto From chemistry-request@server.ccl.net Mon Feb 17 08:40:43 2003 Message-ID: <3E42EAB1.20901@web.de> From: Christian Boehme Date: Mon, 17 Feb 2003 14:40:33 +0100 To: chemistry@ccl.net Subject: Viewmol problem / IR data visualization Status: O X-Status: X-Keywords: X-UID: 2 Dear all, I want to use Viewmol for IR data visualization, because it imitates the look of experimental spectra. I compiled version 2.3 from the sourceforge website without problems (the binaries did not work for me). However, each file loading attempt, including the contained examples, results in a "wrong file type error", even if I specify the type on the command line. Does anyone have an idea what's wrong? Alternatively, does anyone know another program which shows Gaussian98 calculated IR spectra in a way resembling an experimental spectrum, preferably under Linux? I think this question has been asked before, but I did not find it in the archives. WebMO is not a good solution for me, because of the webserver requirements. If there is interest I will summarize to the list. Best regards Christian -- Dr. Christian Boehme Dorstener Str. 40 44787 Bochum Germany email: ChristianBoehme@web.de phone: +49-(0)234-3243655 fax: +49-(0)234-3246741 From chemistry-request@server.ccl.net Mon Feb 17 11:18:51 2003 Received: from cuces.unisi.it ([193.205.4.2]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h1HGIpI04789 for ; Mon, 17 Feb 2003 11:18:51 -0500 Received: from CONVERSION-DAEMON.cuces.unisi.it by cuces.unisi.it (PMDF V6.1-1 #30546) id <01KSJW9LBS9S0060W2@cuces.unisi.it> for chemistry@ccl.net; Mon, 17 Feb 2003 17:18:43 +0100 (MET) Received: from pc-val9.unisi.it (pc-val9.chim.unisi.it [172.16.3.109]) by cuces.unisi.it (PMDF V6.1-1 #30546) with ESMTP id <01KSJW9BF4WC0058YY@cuces.unisi.it> for chemistry@ccl.net; Mon, 17 Feb 2003 17:18:33 +0100 (MET) Date: Mon, 17 Feb 2003 17:18:36 +0100 From: Elena Molteni Subject: Gaussian98 "alter" keyword X-Sender: molteni@mailsrv.unisi.it To: chemistry@ccl.net Message-id: <5.2.0.9.0.20030217170305.009ebaa0@mailsrv.unisi.it> MIME-version: 1.0 X-Mailer: QUALCOMM Windows Eudora Version 5.2.0.9 Content-type: text/plain; format=flowed; charset=us-ascii Content-transfer-encoding: 7BIT Status: O X-Status: X-Keywords: X-UID: 3 Dear all, I need to perform a single point energy calculation on a system containing Fe(II) in high spin state (S=2) coordinated to two oxygens of one carboxylate and 4 nitrogens belonging to 4 histidine residues. I had really hard times in obtaining convergence both using DFT, UHF methods. I use Gaussian 98. I tried the followings: reducing the system to the miminum number of atoms (cutting the ligands and saturating valences with hydrogens). My aim was to use this output as a starting checkpoint file for the extensive calculation. Unfortunately the results I obtain even with the small system are hardly believable. The frontier orbitals do not resemble d orbitals very much and the spin density is not concentrated on iron (only 1/4 of it is on Fe). Moreover cutting the histidines is not very beautiful because i loose the aromaticity and this would change electronic environment a lot. I also tried the QC method to allow the big system to converge but the energy continues to jump a lot. I was told that i could take the output of a calculation converged with the wrong unpaired electron population and artificially put the population of the level with the unpaired electron into one level which is basically formed by d orbitals. That is artificially put unpaired electrons onto d orbitals. If I understood well this option is called alter. Does anybody know how to solve this problem and if this is the way i can perform my calculation? thanks a lot Elena Molteni e-mail:molteni@unisi.it From chemistry-request@server.ccl.net Mon Feb 17 11:19:10 2003 Received: from cuces.unisi.it ([193.205.4.2]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h1HGJ9I04813 for ; Mon, 17 Feb 2003 11:19:10 -0500 Received: from CONVERSION-DAEMON.cuces.unisi.it by cuces.unisi.it (PMDF V6.1-1 #30546) id <01KSJW9LBS9S0060W2@cuces.unisi.it> for chemistry@ccl.net; Mon, 17 Feb 2003 17:19:00 +0100 (MET) Received: from pc-val9.unisi.it (pc-val9.chim.unisi.it [172.16.3.109]) by cuces.unisi.it (PMDF V6.1-1 #30546) with ESMTP id <01KSJW9BF4WC0058YY@cuces.unisi.it> for chemistry@ccl.net; Mon, 17 Feb 2003 17:18:36 +0100 (MET) Date: Mon, 17 Feb 2003 17:19:33 +0100 From: Elena Molteni Subject: Gaussian98 "alter" keyword X-Sender: molteni@mailsrv.unisi.it To: chemistry@ccl.net Message-id: <5.2.0.9.0.20030217171929.009ecb30@mailsrv.unisi.it> MIME-version: 1.0 X-Mailer: QUALCOMM Windows Eudora Version 5.2.0.9 Content-type: text/plain; format=flowed; charset=us-ascii Content-transfer-encoding: 7BIT Status: O X-Status: X-Keywords: X-UID: 4 Dear all, I need to perform a single point energy calculation on a system containing Fe(II) in high spin state (S=2) coordinated to two oxygens of one carboxylate and 4 nitrogens belonging to 4 histidine residues. I had really hard times in obtaining convergence both using DFT, UHF methods. I use Gaussian 98. I tried the followings: reducing the system to the miminum number of atoms (cutting the ligands and saturating valences with hydrogens). My aim was to use this output as a starting checkpoint file for the extensive calculation. Unfortunately the results I obtain even with the small system are hardly believable. The frontier orbitals do not resemble d orbitals very much and the spin density is not concentrated on iron (only 1/4 of it is on Fe). Moreover cutting the histidines is not very beautiful because i loose the aromaticity and this would change electronic environment a lot. I also tried the QC method to allow the big system to converge but the energy continues to jump a lot. I was told that i could take the output of a calculation converged with the wrong unpaired electron population and artificially put the population of the level with the unpaired electron into one level which is basically formed by d orbitals. That is artificially put unpaired electrons onto d orbitals. If I understood well this option is called alter. Does anybody know how to solve this problem and if this is the way i can perform my calculation? thanks a lot Elena Molteni e-mail:molteni@unisi.it From chemistry-request@server.ccl.net Mon Feb 17 10:45:01 2003 Received: from antivirus1.its.rochester.edu ([128.151.57.50]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h1HFj1x04013 for ; Mon, 17 Feb 2003 10:45:01 -0500 Received: from antivirus1.its.rochester.edu (localhost [127.0.0.1]) by antivirus1.its.rochester.edu (8.12.4/8.12.4) with ESMTP id h1HFj0Ca000578 for ; Mon, 17 Feb 2003 10:45:00 -0500 (EST) Received: from mail.rochester.edu (mail1.ats.rochester.edu [128.151.224.31]) by antivirus1.its.rochester.edu (8.12.4/8.12.4) with SMTP id h1HFj0kR000575 for ; Mon, 17 Feb 2003 10:45:00 -0500 (EST) Received: from frenkel.chem.rochester.edu (frenkel.chem.rochester.edu [128.151.195.84]) by mail.rochester.edu (8.12.4/8.12.1) with ESMTP id h1HFixGk014700 for ; Mon, 17 Feb 2003 10:44:59 -0500 (EST) Content-Type: text/plain; charset="us-ascii" From: wei Reply-To: weiz@mail.rochester.edu Organization: university of rochester To: chemistry@ccl.net Subject: what is ramachandran space? Date: Mon, 17 Feb 2003 10:43:23 -0500 User-Agent: KMail/1.4.1 MIME-Version: 1.0 Message-Id: <200302171043.23624.weiz@mail.rochester.edu> Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id h1HFj1x04014 Status: O X-Status: X-Keywords: X-UID: 5 Dear All: Could anybody explain to what is "ramachandran space"? I will appreciate it. Best Regards Wei Zhuang University of Rochester From chemistry-request@server.ccl.net Mon Feb 17 11:33:59 2003 Received: from bgl1mr1-a-fixed ([61.1.128.45]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h1HGXtI05428 for ; Mon, 17 Feb 2003 11:33:58 -0500 Received: from conversion-daemon.bgl1mr1-a-fixed.sancharnet.in by bgl1mr1-a-fixed.sancharnet.in (iPlanet Messaging Server 5.2 HotFix 0.9 (built Jul 29 2002)) id <0HAG00F01OH1VJ@bgl1mr1-a-fixed.sancharnet.in> for chemistry@ccl.net; Mon, 17 Feb 2003 22:03:54 +0530 (IST) Received: from a3y3x0 ([61.1.39.176]) by bgl1mr1-a-fixed.sancharnet.in (iPlanet Messaging Server 5.2 HotFix 0.9 (built Jul 29 2002)) with ESMTPA id <0HAG00J6AOOFFK@bgl1mr1-a-fixed.sancharnet.in> for chemistry@ccl.net; Mon, 17 Feb 2003 22:03:54 +0530 (IST) Date: Mon, 17 Feb 2003 21:57:14 +0530 From: "Dr. N. V. Sastry" Subject: Request for the values of Free Energy of Hydration for alkane diols To: chemistry@ccl.net Message-id: MIME-version: 1.0 X-MIMEOLE: Produced By Microsoft MimeOLE V5.50.4133.2400 X-Mailer: Microsoft Outlook IMO, Build 9.0.2416 (9.0.2910.0) Content-type: text/plain; charset=iso-8859-1 Content-transfer-encoding: 7BIT Importance: Normal X-Priority: 3 (Normal) X-MSMail-priority: Normal Dear Colleque Researcher, I shall highly appreciate if you share the values of free energy of hydration for various salkane diols such as 1,2-ethane diol, 1,2-propane diol, 12, 1,2, 1,4, 2,3-butane diols or even higher diols etc. I shall also appreciate to know the references for the same. I badly need them for the interpretation of my results from exploration of hydrophobic hydration from ab initio calculations. With regards Sincerely Dr. N. V. Sastry Department of Chemistry Sardar Patel University Vallabh Vidyanagr - 388120 Gujarat, India nvssatry_ad1@sancharnet.in From chemistry-request@server.ccl.net Mon Feb 17 16:44:35 2003 Received: from ultra.chem.ucsb.edu ([128.111.114.119]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h1HLiZI09800 for ; Mon, 17 Feb 2003 16:44:35 -0500 Received: from localhost (bushnell@localhost) by ultra.chem.ucsb.edu (8.12.3/8.12.3) with ESMTP id h1HLiOR1019099; Mon, 17 Feb 2003 13:44:25 -0800 (PST) Date: Mon, 17 Feb 2003 13:44:24 -0800 (PST) From: John Bushnell To: Elena Molteni cc: chemistry@ccl.net Subject: Re: CCL:Gaussian98 "alter" keyword In-Reply-To: <5.2.0.9.0.20030217171929.009ecb30@mailsrv.unisi.it> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-Virus-Scanned: by amavisd-milter (http://amavis.org/) In some cases, the initial guess is very bad. I would suggest looking at the initial guess and trying to fix that up first. Do a "guess=only" run and see where Gaussian is putting the electrons. Using "pop=nbo" can help to see what the overall populations are, visuallizing the orbitals may help (I use Molekel for this, in which case you need "gfprint" and either "pop=regular" or "pop=full" in the input file). Then, yes, try another run with "guess=alter" and the proper input to switch populated orbitals. Probably also use "scf=vshift". There are all kinds of tricks you might try including: Run an rohf calculation first. Change the molecule's charge to simplify the valence space. Converge to a different spin state first? Use scf=QC (which I guess you tried). Yes, this can be frustrating, but once you get a well converged SCF you can usually get things going... Good luck - John On Mon, 17 Feb 2003, Elena Molteni wrote: > Dear all, > I need to perform a single point energy calculation on a system containing > Fe(II) in high spin state (S=2) coordinated to two oxygens of > one carboxylate and 4 nitrogens belonging to 4 histidine residues. > I had really hard times in obtaining convergence both using DFT, UHF > methods. I use Gaussian 98. > I tried the followings: > reducing the system to the miminum number of atoms (cutting the ligands and > saturating valences with hydrogens). > My aim was to use this output as a starting checkpoint file for the > extensive calculation. > Unfortunately the results I obtain even with the small system are hardly > believable. The frontier orbitals do not resemble d orbitals very much and > the spin density is not concentrated on iron (only 1/4 of it is on Fe). > Moreover cutting the histidines is not very beautiful because i loose the > aromaticity and this would change electronic environment a lot. > I also tried the QC method to allow the big system to converge but the > energy continues to jump a lot. > I was told that i could take the output of a calculation converged with the > wrong unpaired electron population and artificially put the population of > the level with the unpaired electron into one level which is basically > formed by d orbitals. > That is artificially put unpaired electrons onto d orbitals. > If I understood well this option is called alter. > Does anybody know how to solve this problem and if this is the way i can > perform my calculation? > > thanks a lot > Elena Molteni > e-mail:molteni@unisi.it From chemistry-request@server.ccl.net Mon Feb 17 11:50:07 2003 Received: from gh1.sims.nrc.ca ([132.246.100.4]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h1HGo7I05737 for ; Mon, 17 Feb 2003 11:50:07 -0500 Received: from localhost (ps@localhost) by gh1.sims.nrc.ca (8.8.8/8.8.8) with ESMTP id LAA17967 for ; Mon, 17 Feb 2003 11:50:10 -0500 (EST) Date: Mon, 17 Feb 2003 11:50:10 -0500 From: Serguei Patchkovskii Reply-To: Serguei.Patchkovskii@nrc.ca To: chemistry@ccl.net Subject: deMon2002 demo version Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear CCL members, On behalf of the members of the deMon developers community, it is my pleasure to offer a binary demo version of the most recent version of deMon2002 for general download. The demo is found at the following URL: http://www.deMon-software.com/public_html/demo.html What deMon can do? * Perform density functional theory (DFT) calculations on large molecules, and within a reasonable time. * Perform geometry optimization and frequncy analysis * Perform molecular dynamics calculations, on Born-Oppenheimer potential energy surface * Calculate NMR parameters (shielding tensors, NICS, electric field gradients ...) * Interface to popular visualization software (MOLDEN, MOLEKEL) for the analysis of the results. The provided demo version is a fully functional program. It does not contain a time limit, and does not require activation. However, the demo version is limited in the following ways: * The number of atoms is limited to 12 * The number of basis functions is limited to 100 * The number of fit funtions is limited to 100 * Only S, P, and D basis functions are supported * The number of molecular dynamics steps is limited to 100 * Experimental MAG program is not included (NMR chemical shifts are still available, with the MASTER-CS code) On behalf of the deMon developers community, Serguei --- Dr. Serguei Patchkovskii Tel: +1-(613)-990-0945 Fax: +1-(613)-947-2838 E-mail: Serguei.Patchkovskii@nrc.ca Coordinator of Modelling Software Theory and Computation Group Steacie Institute for Molecular Sciences National Research Council Canada Room 2011, 100 Sussex Drive Ottawa, Ontario K1A 0R6 Canada From chemistry-request@server.ccl.net Mon Feb 17 11:41:48 2003 Received: from cclh41.chm.tu-dresden.de ([141.30.198.41]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h1HGfmI05616 for ; Mon, 17 Feb 2003 11:41:48 -0500 Received: from cclh41 (localhost [127.0.0.1]) by cclh41.chm.tu-dresden.de (8.11.3/8.11.3/SuSE Linux 8.11.1-0.5) with SMTP id h1HGfll27999 for ; Mon, 17 Feb 2003 17:41:47 +0100 Content-Type: text/plain; charset="iso-8859-1" From: Matthias Mann Reply-To: Matthias.Mann@chemie.tu-dresden.de Organization: TU Dresden To: chemistry@ccl.net Subject: Re: CCL:Viewmol problem / IR data visualization Date: Mon, 17 Feb 2003 17:41:47 +0100 X-Mailer: KMail [version 1.2] References: <3E42EAB1.20901@web.de> In-Reply-To: <3E42EAB1.20901@web.de> MIME-Version: 1.0 Message-Id: <03021717414700.27973@cclh41> Content-Transfer-Encoding: 8bit Hi Christian, in my case the same problem was due to an different language environment. I compiled Viewmol 2.3 under SuSE Linux 8.0 (english environment) and it doesn't run under the complete same installation with german environment. Changing the system language solved the problem. Generally, the program seems to be very sensitive to installation changes, e.g. the path to the executables and convert scripts. So I had the same error also in case of changing the installation path, although I adjusted the VIEWMOLPATH variable. You should try to compile, install and use the program on the same system with default path structure. Matthias On Monday 17 February 2003 17:13, you wrote: > Dear all, > > I want to use Viewmol for IR data visualization, because it imitates the > look of experimental spectra. I compiled version 2.3 from the > sourceforge website without problems (the binaries did not work for me). > However, each file loading attempt, including the contained examples, > results in a "wrong file type error", even if I specify the type on the > command line. Does anyone have an idea what's wrong? > > Alternatively, does anyone know another program which shows Gaussian98 > calculated IR spectra in a way resembling an experimental spectrum, > preferably under Linux? I think this question has been asked before, but > I did not find it in the archives. WebMO is not a good solution for me, > because of the webserver requirements. > > If there is interest I will summarize to the list. Best regards > > Christian -- Dr. Matthias Mann Fachrichtung Chemie, TU Dresden, D-01062 Dresden Tel./Fax: +49 (351) 463-34286 Email: Matthias.Mann@chemie.tu-dresden.de