From Jennie.Weston@org.chemie.uni-giessen.de Thu Nov 7 05:11:47 1996 Received: from hermes.hrz.uni-giessen.de for Jennie.Weston@org.chemie.uni-giessen.de by www.ccl.net (8.8.2/950822.1) id EAA16494; Thu, 7 Nov 1996 04:17:58 -0500 (EST) Received: from maier.org.chemie.uni-giessen.de by hermes.hrz.uni-giessen.de; Thu, 7 Nov 96 10:17:27 +0100 Received: by maier.org.chemie.uni-giessen.de (AIX 3.2/UCB 5.64/4.03) id AA13739; Thu, 7 Nov 1996 10:04:46 +0100 From: Jennie.Weston@org.chemie.uni-giessen.de (Jennie Weston) Message-Id: <9611070904.AA13739@maier.org.chemie.uni-giessen.de> Subject: Re: CCL:G94 nbo problem THANKS+SOLN To: CHEMISTRY@www.ccl.net Date: Thu, 7 Nov 1996 10:04:45 +0100 (CET) X-Mailer: ELM [version 2.4 PL23] Mime-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Dear Everybody, Thanks for the helpful comments Doug Fox at gaussian had the soln. (Thanks Doug...) Some Unix systems eat the $ symbol(IBM RS600) if it is standing in column 1. Gives really nice errors. Soln. put some white space before the $nbo or $del commands in gaussian input files. > > Jennie, > > check out g94/tests/com/test166.com for a more extensive example. The > basic input is POP=NBODEL which looks for the required NBO input at the > end just as you have it except put the $ in column 2 to make sure Unix > does not consume it. > > > Hello everybody, > > > > I have a little problem with the nbo implementation in gaussian94. > > According to the NBO manual, in order to do matrix element deletions, > > i need to use a non-standard gaussian input stream. Well, i have an > > nbo manual version 3.0, which describes the implementation in gaussian88. > > The code has changed a little since then........ > > I managed to get the manual's example working for a normal nbo analysis, > > but when it enters the link to calculate the matrix deletion, my job > > dies wanting a g94-5262.nbo file. Does any Guru out there know how to > > induce the program to write this file? Or is there a simpler way to do > > this? A working example file would be AWFULLY nice....... > > From hinsen@ibs.ibs.fr Thu Nov 7 05:23:32 1996 Received: from ibs.ibs.fr for hinsen@ibs.ibs.fr by www.ccl.net (8.8.2/950822.1) id FAA16652; Thu, 7 Nov 1996 05:07:37 -0500 (EST) Received: from lmshp2.ibs.fr (lmshp2.ibs.fr [192.134.36.228]) by ibs.ibs.fr (8.6.12/8.6.12) with SMTP id LAA13033; Thu, 7 Nov 1996 11:07:05 +0100 Message-Id: <199611071007.LAA13033@ibs.ibs.fr> Received: by lmshp2.ibs.fr (1.37.109.4/16.2) id AA16542; Thu, 7 Nov 96 11:07:09 +0100 Date: Thu, 7 Nov 96 11:07:09 +0100 From: Konrad Hinsen To: walt@panix.com Cc: echamot@xnet.com, rochus@felix.anorg.chemie.tu-muenchen.de, chemistry@www.ccl.net In-Reply-To: (message from Walter Polkosnik on Wed, 6 Nov 1996 14:33:30 -0500 (EST)) Subject: Re: CCL:MD/MM combination > What I was trying to point out (perhaps in a very roundabout way) is that > defining 'temperature' in this way for an MD situation is a problem (and it > seems like all MD simply uses ideal gas results). This 'temperature' is not > simply related to the real physical temperature. I still don't see the problem, much less where "ideal gas" results are used. Of course defining temperature via the equipartition theorem is something else than using the proper definition, and it makes sense only under certain assumptions (equilibrium, sufficiently large system, etc.) that are perhaps not fulfilled and that many users are not aware of. But then that is true for many other subtle problems related to MD. For example, conventional wisdom says that the time step is small enough if the energy is reasonably well conserved, even if high frequencies are not sufficiently sampled and other conserved quantities (momentum, angular momentum) show a constant drift. I do agree, of course, that such topics should be discussed and analyzed, and that users of MD should be aware of the huge range of assumptions they are implicitly making. -- ------------------------------------------------------------------------------- Konrad Hinsen | E-Mail: hinsen@ibs.ibs.fr Laboratoire de Dynamique Moleculaire | Tel.: +33-76.88.99.28 Institut de Biologie Structurale | Fax: +33-76.88.54.94 41, av. des Martyrs | Deutsch/Esperanto/English/ 38027 Grenoble Cedex 1, France | Nederlands/Francais ------------------------------------------------------------------------------- From hutschka@quantix.u-strasbg.fr Thu Nov 7 08:11:48 1996 Received: from quantix.u-strasbg.fr for hutschka@quantix.u-strasbg.fr by www.ccl.net (8.8.2/950822.1) id HAA17269; Thu, 7 Nov 1996 07:48:31 -0500 (EST) From: Received: by quantix.u-strasbg.fr (AIX 3.2/UCB 5.64/4.03) id AA46384; Thu, 7 Nov 1996 13:49:37 +0100 Date: Thu, 7 Nov 1996 13:49:37 +0100 Message-Id: <9611071249.AA46384@quantix.u-strasbg.fr> To: chemistry@www.ccl.net Subject: SUMARY:MP2 density in CHK file. Cc: hutschka@quantix.u-strasbg.fr MIME-Version: 1.0 Content-Type: text/plain; charset=unknown-8bit Content-Transfer-Encoding: 8bit Hello, Here is the sumary about my question to the CCL: THE QUESTION: I am using gaussian92 to fit atomic charges with potential derived methods. To save computer time the electronic density can be read from the checkpoint file to avoid to calculate it several time if you want to use it for different calculations. By default, the HF density is saved in the CHK file. Since I want to use the MP2 density, could somebody tell me if there is a way to save the MP2 density in the CHK file and if so, how to do it ?? More is it possible to save both the HF and the MP2 densities in the same CHK file?? ****************************************************************** THE ANSWERS: ****************************************************************** From Seiji Mori e-mail: smori@utsc3.chem.s.u-tokyo.ac.jp **************************************** By default, even in the MP2 calculations, SCF density was shown in the output file and stored in chkpoint file. To show and store MP2 density to checkpoint file, you need to add the option , "density=MP2" or "density=current", that is OK. > More is it possible to save both the HF and the MP2 densities in the > same CHK file?? Of course, you can split to two jobs (SCF and MP2 density calculations) but I do not know . ******************************************************************* From Jean-Marie Teuler e-mail: teuler@idris.fr In French.. Je vous reponds directement concernant votre question concernant les matrices de densite. En effet, par defaut c'est la matrice de densite HF qui est stockee dans le checkpoint. - Si vous specifiez DENSITY=MP2, ce sera la matrice MP2. - Si vous specifiez DENSITY=ALL, les deux matrices seront stockees et vous pourrez selectionner celle que vous voulez utiliser avec ce meme mot-cle DENSITY. ********************************************************************* From Michael Schimeczek e-mail: schimi@sg1506.chemie.uni-marburg.de ******************************************* first of all, I am using Gaussian94 not 92, so I'm not sure if the results will be the same, but here we go: First, to check if the resulting checkpoint file really contains the desired data, use the program formchk, which resides in the gaussian executable directory. It reads in your checkpoint file and writes a formatted checkpointfile (name.fchk) that you can easily read. Then, use the keyword DENSITY in the route card. The options are: HF, MP2, ALL, CURRENT, and several others for CI etc. Normally, the HF density will be used as default for pop analysis (and also for writing to the checkpoint), but if you specify DENSITY=CURRENT, the density belonging to the method you are using is taken. Gaussian94 then writes both HF and MP2 densities to the chkfile (if you did an MP2 calculation). Hope this helps (and works for G92, too!) ********************************************************************** From Douglas J. Fox e-mail: help@gaussian.com ************************* If you run G92 with MP2 DENSITY=3DCurrent, both the HF and MP2 density are saved. You can then use DENSITY=3D(CHECK,MP2) to recover the MP2 density or DENSITY=3DCHECK to get the HF density. ********************************************************************** Thanks to all for your help. ============================================================================= ¤ François HUTSCHKA Ph.D. Student in Quantum Chemistry ¤ ¤ ¤ ¤ Laboratoire de Chimie Quantique ¤ ¤ UPR 139 du CNRS ¤ ¤ 4, rue Blaise Pascal Phone: (33).03.88.41.60.32 ¤ ¤ 67000 STRASBOURG Fax: (33).03.88.61.20.85 ¤ ¤ FRANCE E-Mail: hutschka@quantix.u-strasbg.fr ¤ ============================================================================= From dsmith@CTCnet.Net Thu Nov 7 10:11:57 1996 Received: from home.CTCnet.Net for dsmith@CTCnet.Net by www.ccl.net (8.8.2/950822.1) id JAA17849; Thu, 7 Nov 1996 09:52:55 -0500 (EST) Received: from fock by home.CTCnet.Net (SMI-8.6/SMI-SVR4) id JAA05550; Thu, 7 Nov 1996 09:00:16 -0500 Date: Thu, 7 Nov 1996 09:00:16 -0500 Message-Id: <199611071400.JAA05550@home.CTCnet.Net> X-Sender: dsmith@pop.dasgroup.com X-Mailer: Windows Eudora Version 1.4.4 Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" To: CHEMISTRY@www.ccl.net From: dsmith@CTCnet.Net (Douglas A. Smith Ph.D.) Subject: need IR frequencies/intensities Dear All: Because we just moved our offices, I do not have access to my usual sources of information, so I would appreciate an answer to the following simple question. Can someone provide me with the EXPERIMENTAL IR frequencies and intensities for nitromethane and nitrobenzene? I am particularly interested in the frequencies related to the nitro group. Doug -- Dr. Douglas A. Smith, President and CEO | voice: (814) 255-7859 The DASGroup, Inc. | fax: (814) 255-3517 1732 Lyter Drive, 2nd Floor | email: dsmith@dasgroup.com Johnstown, PA 15905 | WWW: http://www.dasgroup.com Contract R&D specialists in modeling, simulation, synthesis and risk assessment for chemistry, materials science, and biotechnology. From dsmith@CTCnet.Net Thu Nov 7 10:24:38 1996 Received: from home.CTCnet.Net for dsmith@CTCnet.Net by www.ccl.net (8.8.2/950822.1) id JAA17853; Thu, 7 Nov 1996 09:52:58 -0500 (EST) Received: from fock by home.CTCnet.Net (SMI-8.6/SMI-SVR4) id JAA05545; Thu, 7 Nov 1996 09:00:06 -0500 Date: Thu, 7 Nov 1996 09:00:06 -0500 Message-Id: <199611071400.JAA05545@home.CTCnet.Net> X-Sender: dsmith@pop.dasgroup.com X-Mailer: Windows Eudora Version 1.4.4 Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" To: CHEMISTRY@www.ccl.net From: dsmith@CTCnet.Net (Douglas A. Smith Ph.D.) Subject: We've Moved! The DASGroup, Inc. has moved. Our new address and contact information are given below. Note that our email addresses have not changed. Starting on Monday, 11 November, check out our new web site at: http://www.dasgroup.com. New Address: The DASGroup, Inc. 1732 Lyter Drive 2nd Floor Johnstown, PA 15905 voice: (814) 255-7859 fax: (814) 255-3517 -- Dr. Douglas A. Smith, President and CEO | voice: (814) 255-7859 The DASGroup, Inc. | fax: (814) 255-3517 1732 Lyter Drive, 2nd Floor | email: dsmith@dasgroup.com Johnstown, PA 15905 | WWW: http://www.dasgroup.com Contract R&D specialists in modeling, simulation, synthesis and risk assessment for chemistry, materials science, and biotechnology. From val@nmr1.ioc.ac.ru Thu Nov 7 12:11:52 1996 Received: from nmr1.ioc.ac.ru for val@nmr1.ioc.ac.ru by www.ccl.net (8.8.2/950822.1) id LAA18807; Thu, 7 Nov 1996 11:58:08 -0500 (EST) Received: from [193.233.3.213] (nmr-v.ioc.ac.ru [193.233.3.213]) by nmr1.ioc.ac.ru (8.6.12/8.6.9) with SMTP id UAA23203 for ; Thu, 7 Nov 1996 20:58:28 +0400 Date: Tue, 7 Nov 95 19:58:35 +0300 From: "Ananikov V.P." Message-Id: <82134.val@nmr1.ioc.ac.ru> X-Minuet-Version: Minuet1.0_Beta_17A Reply-To: X-POPMail-Charset: IBM 8-Bit To: chemistry@www.ccl.net Subject: All atom Force Field Dear CCL'ers, I am looking for programs (preferably freeware or shareware) with full periodic table force fields: all atom type version of the YETI force field, Universal Force Field, DREIDING-style scheme and other. I will summarize. Thank you. Sincerely, Valentin. @ Valentin P. Ananikov (Post-Graduate Student) @ @ NMR Laboratory @ @ N.D. Zelinsky Institute of Organic Chemistry @ @ Leninsky Prospect 47 @ @ Moscow 117913 @ @ Russia @ From ryszard@msi.com Thu Nov 7 13:11:52 1996 Received: from bioc1.msi.com for ryszard@msi.com by www.ccl.net (8.8.2/950822.1) id MAA19370; Thu, 7 Nov 1996 12:59:52 -0500 (EST) Received: from aga.msi.com by bioc1.msi.com (5.64/0.0) id AA24159; Thu, 7 Nov 96 09:57:15 -0800 Received: by aga.msi.com (5.65/DEC-OSF/1-29Feb92); id AA08183; Thu, 7 Nov 1996 12:58:08 -0500 Date: Thu, 7 Nov 1996 12:58:08 -0500 (EST) From: Ryszard Czerminski To: Konrad Hinsen Cc: walt@panix.com, echamot@xnet.com, rochus@felix.anorg.chemie.tu-muenchen.de, chemistry@www.ccl.net Subject: Re: CCL:MD/MM combination In-Reply-To: <199611071007.LAA13033@ibs.ibs.fr> Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Few formulas from text book (D. A. McQuarrie "Statistical Thermodynamics") : In microcanonical ensemble ( H(p,q) = E = const) partition function is defined as the volume of phase space accessible at constant energy E $$ \Omega(E) = \int\limits_{H(p,q)=E} dp dq $$ and thermodynamical temperature is defined by $$ {1 \over kT} = {\Bigl( {{\partial \Omega(E)} \over {\partial E}} \Bigr)}_{N,V} $$ (which is just different way of writing 1/T= dS/dE, since S = k ln $\Omega$) so in order to calculate it, it is necessary to be able to calculate partition function $\Omega(E)$ which is formidable challenge for any system a little bit more complicated then ideal gases and harmonic oscillators (not to mention big protein in water with ions, etc...). Interesting question remains how much proper thermodynamic temperature differs from "temperature" calculated from an average kinetic energy using equipartition theorem with all its limitations discussed so far. .................................. Ryszard Czerminski Molecular Simulations Incorporated 8 New England Executive Park Burlington, MA 01803-5297 tel: (617)229-8875 x 217 or 229-9800 fax: (617)229-9899 e-mail: ryszard@msi.com From debay93k@ibmmail.com Thu Nov 7 15:11:54 1996 Received: from ibmmail.COM for debay93k@ibmmail.com by www.ccl.net (8.8.2/950822.1) id PAA20157; Thu, 7 Nov 1996 15:00:59 -0500 (EST) From: Message-Id: <199611072000.PAA20157@www.ccl.net> Received: from ibmmail by ibmmail.COM (IBM VM SMTP V2R3) with BSMTP id 6167; Thu, 07 Nov 96 15:00:42 EST Date: Thu, 07 Nov 1996 12:55:46 EST To: chemistry@www.ccl.net MIME-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Subject: job opportunity at BAYER/Wuppertal Start of Attached Message ========================= Computational Chemist at Bayer In our German Pharmaceutical Research Centre at Wuppertal an opportunity has arisen for a computational chemist to join our Structural Research Group. Our Profile: Bayer is a recognized research-based healthcare company headquartered in Leverkusen/Germany. [For more details please refer to http://www.bayer-ag.de] Your Task: The successful candidate will collaborate in a multidisciplinary team responsible for Structural Analysis (including High Field NMR and X-Ray Analysis) and Molecular Modelling in close cooperation with medicinal chemists and pharmacologists. State-of-the art equipment for computational chemistry is available as well as almost complete access to virtually all TRIPOS and MSI/Biosym software modules. Your Profile: We are currently seeking a PhD research scientist (Computational Chemist) with significant professional expertise in at least one of the following areas: - use and/or development of molecular modelling methods for proteins, protein/small molecule interaction or indirect drug design techniques. - Use of De novo Drug Design and/or Structure Activity Relationship methodology - usage of 2D/3D-Databases and calculated molecular properties in course of drug finding process, high throughput screening analysis and/or structure and property-based design of libraries for automated synthesis. - bio-informatics or biochemistry including homology modelling of proteins Working experience in a pharmaceutical company's molecular modelling group will be an advantage. The successful applicant must have a good working knowledge of chemistry. UNIX experience and C-programming skills are desirable. Demonstrable expertise and experience in available commercial modelling software packages (e.g. the TRIPOS and MSI suite of programs) will be an advantage too. ------------------------------------------------------------------------------- Contact Address: If your background and personal experience fits to this profile, please apply with full CV to: Bayer AG Mr. G. Ritter Personalmarketing Hauptstr. 119 D51368 Leverkusen ------------------------------------------------------------------------------ In urgent cases please contact: Axel Jensen, PhD Pharmaceutical Research Centre PH-RSR D42096 Wuppertal Germany email: DEBAY93K@IBMMAIL.COM