From fdeprof@is1.vub.ac.be Thu Dec 15 03:21:52 1994 Received: from rc1 for fdeprof@is1.vub.ac.be by www.ccl.net (8.6.9/930601.1506) id DAA01245; Thu, 15 Dec 1994 03:20:34 -0500 Received: from is1e.vub.ac.be by rc1 (8.6.8.1/3.3.1 (Antoon Pardon)) id JAA09847; Thu, 15 Dec 1994 09:22:59 +0100 Received: from sterfpmc207.vub.ac.be by is1e.vub.ac.be (5.61/BFUCC-920211) id AA13164; Thu, 15 Dec 94 09:20:29 +0100 Date: Thu, 15 Dec 94 09:20:29 +0100 Message-Id: <9412150820.AA13164@is1e.vub.ac.be> X-Sender: fdeprof@is1.vub.ac.be (Unverified) Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" To: chemistry@ccl.net From: fdeprof@is1.vub.ac.be Subject: AM1 in Gaussian Hi all, I am doing semi empirical calculations with the Gaussian 92 program. When I do an AM1 calculation on water, I get the following output RHF-AM1 calculation of energy. MO and density RWFs will be updated. Closed-shell calculation: 4 occupied levels. NNHCO= 0. References: H: (AM1): M.J.S. DEWAR ET AL, J. AM. CHEM. SOC. 107 3902-3909 (1985) O: (AM1): M.J.S. DEWAR ET AL, J. AM. CHEM. SOC. 107 3902-3909 (1985) Ext34=T Pulay=F Camp-King=F BShift= 0.00E+00 It= 1 PL= 1.05E+00 DiagD=T ESCF= 27.432133 Diff=-1.59E+00 RMSDP= 6.67E-01. It= 2 PL= 1.19E-01 DiagD=T ESCF= -19.150981 Diff=-4.66E+00 RMSDP= 4.24E-02. It= 3 PL= 6.35E-02 DiagD=T ESCF= -24.295951 Diff=-5.14E-01 RMSDP= 3.46E-02. It= 4 PL= 6.37E-03 DiagD=F ESCF= -26.378849 Diff=-2.08E-01 RMSDP= 2.71E-03. It= 5 PL= 2.24E-03 DiagD=F ESCF= -25.392639 Diff= 9.86E-02 RMSDP= 7.08E-04. It= 6 PL= 6.75E-04 DiagD=F ESCF= -25.394366 Diff=-1.73E-04 RMSDP= 2.63E-04. It= 7 PL= 3.40E-05 DiagD=F ESCF= -25.394533 Diff=-1.67E-05 RMSDP= 1.58E-05. It= 8 PL= 8.23E-06 DiagD=F ESCF= -25.394482 Diff= 5.10E-06 RMSDP= 4.05E-06. 4-point extrapolation. It= 9 PL= 3.09E-06 DiagD=F ESCF= -25.394482 Diff=-6.29E-09 RMSDP= 2.01E-06. Energy= -0.093324818016 NIter= 10. Can anyone tell me in what units the final energy is given ? Moreover, when I look at the population analysis given by Gaussian, it is different from the one given in MOPAC for the same test system. Can anyone help me with this ? Thanks, Frank De Proft Vrije Universiteit Brussel From ev@dim.jussieu.fr Thu Dec 15 11:23:19 1994 Received: from shiva.jussieu.fr for ev@dim.jussieu.fr by www.ccl.net (8.6.9/930601.1506) id LAA05756; Thu, 15 Dec 1994 11:16:48 -0500 Received: from liliput.dim.jussieu.fr (liliput.dim.jussieu.fr [134.157.90.1]) by shiva.jussieu.fr (8.6.9/jtpda-5.0) with SMTP id RAA06895 for ; Thu, 15 Dec 1994 17:16:43 +0100 Received: by liliput.dim.jussieu.fr (4.1/jn930126) at Thu, 15 Dec 94 17:17:34 FRA From: ev@dim.jussieu.fr (Earl EVLETH p 74208) Message-Id: <9412151717.AA05141@liliput.dim.jussieu.fr> Subject: vector file on Xmol To: CHEMISTRY@ccl.net Date: Thu, 15 Dec 1994 17:17:33 +0000 (MET) X-Mailer: ELM [version 2.4 PL21] Content-Type: text Content-Length: 594 If anyone has an example of the use of the VECTOR file option on the XMOL graphic soft I would appreciate it. I have not been able to extract this information from the XMOL manual is understandable form and the manual does not offer sample input files for such a simple case. The manual states that it can be included in the XYZ file and except to generating atomic charges. Thanks in advance. E. M. Evleth (ev@dim.jussieu.fr) Dynamique des Intereactions Moleculaires. Universite Pierre et Marie Curie 4 Place Jussieu, Tour 22, Paris, France 75240 From anlackey@blue.weeg.uiowa.edu Thu Dec 15 12:21:44 1994 Received: from ns-mx.uiowa.edu for anlackey@blue.weeg.uiowa.edu by www.ccl.net (8.6.9/930601.1506) id LAA06255; Thu, 15 Dec 1994 11:34:40 -0500 Received: from blue.weeg.uiowa.edu by ns-mx.uiowa.edu (8.6.8.2/19940322) on Thu, 15 Dec 1994 10:34:39 -0600 id KAA08166 with ESMTP Received: by blue.weeg.uiowa.edu (8.6.9/940408) on Thu, 15 Dec 1994 10:34:27 -0600 id KAA223392 Date: Thu, 15 Dec 1994 10:34:26 -0600 (CST) From: "A. Lackey" Subject: subscription To: CHEMISTRY@ccl.net cc: anlackey@blue.weeg.uiowa.edu Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII I would like to know how to get on this mailing list. I am a graduate student of biochemistry at the university of iowa. My main interest is in NMR applications to molecular modeling of carbohydrates. From pavan@daffy.bnpi.com Thu Dec 15 13:21:45 1994 Received: from beavis.bnpi.com for pavan@daffy.bnpi.com by www.ccl.net (8.6.9/930601.1506) id MAA07518; Thu, 15 Dec 1994 12:25:27 -0500 From: Received: from daffy.bnpi.com by beavis.bnpi.com (AIX 3.2/UCB 5.64/4.03) id AA17752; Thu, 15 Dec 1994 11:24:51 -0600 Received: by daffy.bnpi.com (AIX 3.2/UCB 5.64/4.03) id AA13702; Thu, 15 Dec 1994 11:24:50 -0600 Date: Thu, 15 Dec 1994 11:24:50 -0600 Message-Id: <9412151724.AA13702@daffy.bnpi.com> To: CHEMISTRY@ccl.net Subject: Public Domain Source for EHT and FMO programs Hello Everyone, Does any one know the public domain source for Extended Huckel and Frontier Molecular Orbital Method (FMO) programs? Please reply to pavan@bnpi.com Thanks in advance pavan From doherty@msc.edu Thu Dec 15 13:27:02 1994 Received: from noc.msc.edu for doherty@msc.edu by www.ccl.net (8.6.9/930601.1506) id NAA08333; Thu, 15 Dec 1994 13:04:23 -0500 Received: from uh.msc.edu by noc.msc.edu (5.65/MSC/v3.0.1(920324)) id AA00545; Thu, 15 Dec 94 12:04:22 -0600 From: doherty@msc.edu (David C. Doherty) Received: (doherty@localhost) by uh.msc.edu (8.6.8.1/8.6.6) id MAA19815; Thu, 15 Dec 1994 12:04:21 -0600 Message-Id: <199412151804.MAA19815@uh.msc.edu> Subject: Re: CCL:vector file on Xmol To: ev@dim.jussieu.fr (Earl EVLETH p 74208) Date: Thu, 15 Dec 1994 12:04:19 -0600 (CST) Cc: CHEMISTRY@ccl.net, xmol@msc.edu In-Reply-To: <9412151717.AA05141@liliput.dim.jussieu.fr> from "Earl EVLETH p 74208" at Dec 15, 94 05:17:33 pm X-Mailer: ELM [version 2.4 PL22] Mime-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Content-Length: 1847 >If anyone has an example of the use of the VECTOR >file option on the XMOL graphic soft I would appreciate >it. I have not been able to extract this >information from the XMOL manual is understandable form >and the manual does not offer sample input files for >such a simple case. The manual states that it can be >included in the XYZ file and except to generating atomic >charges. > Quoted from the XYZ file specification man page: Each line of text describing a single atom must contain at least four fields of information, separated by whitespace: the atom's type (a short string of alphanumeric characters), and its x-, y-, and z-positions. Optionally, extra fields may be used to specify a charge for the atom, and/or a vec- tor associated with the atom. If an input line contains five or eight fields, the fifth field is interpreted as the atom's charge; otherwise, a charge of zero is assumed. If an input line contains seven or eight fields, the last three fields are interpreted as the components of a vector. These components should be specified in angstroms. You mean that's not clear? ;) -- Here are some examples (where Vx,Vy,Vz are the x,y, and z components of some vector): - hydrogen atom with x,y,z defined (charge zero is implied): H 1.0 1.0 1.0 [4 fields] - hydrogen atom with x,y,z,charge defined: H 1.0 1.0 1.0 0.1 [5 fields] - hydrogen atom with x,y,z,charge,Vx,Vy,Vz defined: H 1.0 1.0 1.0 0.1 0.5 0.5 0.5 [8 fields] - hydrogen atom with x,y,z,Vx,Vy,Vz defined (charge zero is implied): H 1.0 1.0 1.0 0.5 0.5 0.5 [7 fields] Hope that this helps. If not, send mail to xmol@msc.edu and we'll try to provide a more concrete example. Dave Doherty -- David C. Doherty Minnesota Supercomputer Center doherty@msc.edu From choic@gusun.acc.georgetown.edu Thu Dec 15 14:21:59 1994 Received: from gusun.acc.georgetown.edu for choic@gusun.acc.georgetown.edu by www.ccl.net (8.6.9/930601.1506) id NAA08584; Thu, 15 Dec 1994 13:22:45 -0500 Received: by gusun.acc.georgetown.edu (4.1/1a-eef) id AA25849; Thu, 15 Dec 94 13:23:11 EST Date: Thu, 15 Dec 1994 13:23:09 -0500 (EST) From: Cheol Choi Subject: Help! GAMESS To: CHEMISTRY@ccl.net Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi! everyone. I'm looking for GAMESS source file. Does anyone know about this? And does GAMESS calculate the RAMAN intensity? Thank you all, Cheol Ho Choi, ADD : choic@gusun.acc.georgetown.edu From bhardy@convex.ox.ac.uk Thu Dec 15 14:26:42 1994 Received: from oxmail.ox.ac.uk for bhardy@convex.ox.ac.uk by www.ccl.net (8.6.9/930601.1506) id NAA08557; Thu, 15 Dec 1994 13:21:30 -0500 Received: from convex.ox.ac.uk by oxmail.ox.ac.uk with SMTP (PP) id <13561-0@oxmail.ox.ac.uk>; Thu, 15 Dec 1994 18:20:52 +0000 From: Barry Hardy Date: Thu, 15 Dec 94 18:02:58 GMT Message-Id: <7587.9412151802@convex.ox.ac.uk> PP-warning: Illegal Received field on preceding line PP-warning: Illegal Via field on preceding line To: chemistry@ccl.net Subject: Modeling/NMR; Glycosciences A. Lackey wrote: > I would like to know how to get on this mailing list. I am a graduate > student of biochemistry at the university of iowa. My main interest is > in NMR applications to molecular modeling of carbohydrates. Specific answer is: send your mail request to CHEMISTRY-REQUEST@ccl.net not to CHEMISTRY@ccl.net Comment: I also use computational chemistry/NMR to study carbohydrates and I think you will find the osc list a worthwhile subscription. Additionally, I would like to draw attention below to a recent newsgroup that Iain Wilson and I have very recently launched in the 'glycosciences' which will include modeling/structural areas, particularly biology-related problems. Also, an NMR group was formed under the bionet hierarchy earlier in the year; it has been relatively quiet. Being primarily a structure/modeling kind of person, I am interested in seeing this kind of information gathered for the group and am soliciting volunteers to contribute to this project. The work could include development of a glycostructural FAQ, gathering of location-site addresses, access procedures for structural information and databases, writing of structural Web pages with links to Glyco- related URLs, and possibly the eventual construction of our own databases. Structural information can include sequences, models, crystal structures, spectra, or parameters. Barry J. Hardy http://alcyone.pcl.ox.ac.uk/people/barry.html Electronic Newsgroup for the Glycosciences The GLYCOSCI/bionet.glycosci electronic newsgroup is ready, having been passed by 165 yes votes to 1 no vote. The GLYCOSCI newsgroup can be accessed using USENET software - if such is available through your local computing service. If bionet.glycosci does not appear in the list of available newsgroups at your site, ask your news system administrator to enable the group at your site. Through your newsreading softeware you may have a 'subscribe' function which loads newsgroups into a default list. Alternatively, you can subscribe via electronic mail by sending the relevant command to one of the BIOSCI sites as follows: If you are located in Europe, Africa or Central Asia send the command (in the body of your mail message - leave the subject line blank) SUB bionet-news.bionet.glycosci to MXT@dl.ac.uk If you are located in the Americas or the Pacific Rim send the command (in the body of your mail message) subscribe glycosci to biosci-server@net.bio.net With e-mail subscriptions, you will receive an introductory document advising you on where to contact in the event of problems, how to post and reply to messages, cancel your subscription or look at the archives. You can post to the group either through USENET software or by mailing glycosci@daresbury.ac.uk (if you are located in Europe, Africa or Central Asia) or glycosci@net.bio.net (if you are located in the Americas or the Pacific Rim). Do not post a message to both sites - otherwise everyone on the list will receive two copies of your message. The charter and archives of the group can be accessed by FTP (file transfer protocol), gopher or WWW (world wide web) at net.bio.net. If you wish to access the charter or archives by WWW, the URL is gopher://gopher.bio.net:70/11/GLYCOSCI. Iain B. H. Wilson Dyson Perrins Laboratory University of Oxford South Parks Road, Oxford, OX1 3QY e-mail: iwilson@molbiol.ox.ac.uk (As from January 1995 at Institut fuer Chemie der Universitaet fuer Bodenkultur, Gregor-Mendel-Strasse 33, A-1180 Wien, Austria) Barry J. Hardy Computer-Aided Molecular Design Group Physical Chemistry Laboratory University of Oxford South Parks Road, Oxford, OX1 3QZ e-mail: bhardy@convex.ox.ac.uk From underhil@hp.rmc.ca Thu Dec 15 15:21:50 1994 Received: from sv2.rmc.ca for underhil@hp.rmc.ca by www.ccl.net (8.6.9/930601.1506) id OAA10417; Thu, 15 Dec 1994 14:53:46 -0500 Received: from underhill.rmc.ca by sv2.rmc.ca with SMTP id AA18655 (5.67b/IDA-1.5 for ); Thu, 15 Dec 1994 14:53:24 -0500 Date: Thu, 15 Dec 1994 14:53:24 -0500 Message-Id: <199412151953.AA18655@sv2.rmc.ca> X-Sender: underhil@137.94.5.141 X-Mailer: Windows Eudora Version 1.4.3 Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" To: chemistry@ccl.net From: underhil@hp.rmc.ca (Ross Underhill) Subject: equilibrium and MD of liquids I'm engaged in trying to obtain the solubility of some large molecules in different solvents to understand the effect of solvent shape and size. The approach I'm trying to use is to bring a large periodic box of solvent molecules containing a single solute molecule into equilibrium and obtain the energy of the system suing MD. As a start I am trying to bring just a large periodic box of solvent into equilibrium. Suffice it to say I've found some interesting effects. In particular it would seem that it is very easy to get hung up in local miminima. I seem to get get convergence to a global minimum much faster if I compress the model into a smaller volume than desired, do a little relaxation and then increase the volume to the final value for the full MD run. Is anyone aware of any other tricks one can do to increase the speed of convergence to equilibrium, or more important avoid falling into a local minimum. I would appreciate any pointers or references I could get. Thanks in advance Dr. Ross Underhill Royal Military College of Canada Kingston, Ontario (613) 541-6000 X6175 From walterse@mis.fuhscms.edu Thu Dec 15 15:29:35 1994 Received: from mis.fuhscms.edu for walterse@mis.fuhscms.edu by www.ccl.net (8.6.9/930601.1506) id OAA10085; Thu, 15 Dec 1994 14:30:48 -0500 Message-Id: <199412151930.OAA10085@www.ccl.net> Subject: Summary: heats of fusion To: chemistry@ccl.net Date: Thu, 15 Dec 1994 13:30:47 -0600 (CST) From: "Dr. D.Eric Walters" X-Mailer: ELM [version 2.4 PL23] MIME-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 8bit Content-Length: 2374 Here is a summary of replies to my question about calculating heats of fusion. Thanks to those who replied! Message 1/3 From Lawrence R. Dodd Dec 7, 94 01:32:59 pm -0500 Date: Wed, 7 Dec 94 13:32:59 -0500 To: walterse@mis.fuhscms.edu Subject: Re: CCL:calculating heat of fusion? X-Attribution: lrd Reply-To: dodd@roebling.poly.edu ::: "DEW" == D Eric Walters writes: DEW> Are there methods for calculating heat of fusion (crystal DEW> melting) for different crystal forms of small organic DEW> compounds? Perhaps you meant `melting' and you probably already know this, but the heat of fusion (aka heat of melting) and heat of crystallization differ by the heat of solution. Often one is approximated by the other but they are different thermodynamically. ----------------------------- Eric-The heat of fusion would be a difficult problem because you would have to have a good model of the liquid state structure. The heat of sublimation(crystal to vapor transformation) is easier to compute. We've discussed this in JACS 1994,116,455-470(see p. 458 in particular). Basically what you do is to compute the interaction energy between an aribitrary molecule in the packed crystal structure and all the other molecules using an appropriate atom-atom potential forcefield. We have code written for this using the MM2 forcefield or the CFF91 forcefield. The code requires packing the structure using CHEMX/CHEMLIB modeling package. If you have these, I can send you the rest. *************** Jerry Perlstein Center for Photoinduced Charge Transfer Department of Chemistry University of Rochester Rochester,NY 14627-0216 -------------------------- A method for the calculation of entropies and enthalpies of fusion is described in J. S. Chickos, et.al., J. Org. Chem. 1991, 56, 927-938. Peter W. Rose, Computational Chemistry Agouron Pharmaceuticals, Inc. email: rose@agouron.com ------------------------- * D. Eric Walters, Ph.D., Associate Professor, Biological Chemistry * Finch University of Health Sciences/The Chicago Medical School * 3333 Green Bay Road, North Chicago, IL 60064 * ph 708-578-3000, x-498;fax 708-578-3240; email: walterse@mis.fuhscms.edu * "A man would do nothing if he waited until he could do it so well that * no one would find fault with what he had done." --Cardinal Newman From gcarde02@fiu.edu Thu Dec 15 20:21:48 1994 Received: from rottweiler.fiu.edu for gcarde02@fiu.edu by www.ccl.net (8.6.9/930601.1506) id UAA14230; Thu, 15 Dec 1994 20:10:15 -0500 Received: from solix.fiu.edu by rottweiler.fiu.edu; (5.65/1.1.8.2/26Aug94-0438PM) id AA22534; Thu, 15 Dec 1994 20:11:34 -0500 Date: Thu, 15 Dec 1994 20:11:34 -0500 From: gabriel a cardenas Message-Id: <9412160111.AA22534@rottweiler.fiu.edu> To: chemistry@ccl.net Subject: calculation of mol. films I am doing research using atomic force and scanning tunneling microscopy and would like to know is there a way to predict the orientation that molecule will form as a monolayer on top of a surface when the greatest intermolecular interactions are hydrogen bonding. I am putting guanine on highly oriented pyrolytic graphite and would like to try to predict the superstructure that will occur in solution on the surface as a monolayer. Thank in advance.