From akn@hcocvx.uni-c.dk Mon Oct 10 05:18:45 1994 Received: from danpost.uni-c.dk for akn@hcocvx.uni-c.dk by www.ccl.net (8.6.9/930601.1506) id FAA27128; Mon, 10 Oct 1994 05:08:47 -0400 Received: from hcocvx.uni-c.dk (hcocvx.uni-c.dk [129.142.6.92]) by danpost.uni-c.dk (8.6.4/8.6) with ESMTP id KAA11292 for ; Mon, 10 Oct 1994 10:08:37 +0100 Received: from localhost by hcocvx.uni-c.dk (8.6.4/10.0.0.3) id KAA06493; Mon, 10 Oct 1994 10:05:26 +0100 From: akn@hcocvx.uni-c.dk (Anita Kildebaek Nielsen) Message-Id: <199410100905.KAA06493@hcocvx.uni-c.dk> Subject: CCL:Question: a N+Ar potential To: CHEMISTRY@ccl.net Date: Mon, 10 Oct 94 10:05:25 MET X-Mailer: ELM [version 2.3 PL11] Dear Netters I would like to do simulaions of N2(g) in an argon cluster, but I have been unsuccessful in finding a (probably Lennard-Jones 6-12) potential between argon-atom and nitrogen-atom. Can anyone help me with references or other informations? Please send it directly to me.I will of course give the results here if anyone should be interested. Thank you for your help in advance. Anita Kildebaek. ************************************* * Anita Kildebaek Nielsen * * Dept. of Chemistry * * Division of Theoretical Chemistry * * Aarhus University * * * * E-mail:akn@hcocvx.uni-c.dk * * S-mail:Langelandsgade 140, * * 8000 Aarhus C * * Denmark * * Phone: +45 89 42 38 33 * ************************************* * "All of science is physics * * or stamp collecting" * * Rutherford * ************************************* From CULMER@uoft02.utoledo.edu Mon Oct 10 09:18:58 1994 Received: from uoft02.utoledo.edu for CULMER@uoft02.utoledo.edu by www.ccl.net (8.6.9/930601.1506) id IAA29353; Mon, 10 Oct 1994 08:57:13 -0400 Received: from UOFT02.UTOLEDO.EDU by UOFT02.UTOLEDO.EDU (PMDF V4.3-7 #5345) id <01HI3T18WF800000HT@UOFT02.UTOLEDO.EDU>; Mon, 10 Oct 1994 08:57:08 EST Date: Mon, 10 Oct 1994 08:57:07 -0500 (EST) From: "Chuck Ulmer, D.A.Smith Group" Subject: AVS on DEC Alpha To: chemistry@ccl.net Message-id: <01HI3T18WF820000HT@UOFT02.UTOLEDO.EDU> X-Envelope-to: chemistry@ccl.net X-VMS-To: IN%"chemistry@ccl.net" X-VMS-Cc: CULMER MIME-version: 1.0 Content-type: TEXT/PLAIN; CHARSET=US-ASCII Content-transfer-encoding: 7BIT Let me first apologize for sending to the list; however, I am not able to send directly to the poster of the original question. Duane Walker writes: > >Hello, > >WE are considering buying a DEC alpha system for our computational chemsitry >group. I need to know if AVS or another similar visualization package is >available for the alpha systems running OSF, if they are available, what the >academic pricing is, and finally how is the performace for generation of >isosurfaces. I am especially interested in avs with the chemistry viewer >added. > > >all information appreciated > >Duane Walker >Mathematical Chemistry Research Unit >University of Saskatchewan >Saskatoon, Saskatchewan, Canada > >walkerd@usask.sask.ca -- Duane: AVS does run on the Alpha with OSF/1. The DASGroup, Inc., has all rights to the development, distribution, and sales of the the AVS Chemistry Viewer and we have done the port to the DEC Alpha under OSF/1. I constantly run the Chem. Viewer on an Alpha with Denali graphics and am amazed at the performance. While I have not seen the Chemistry Viewer running on an Alpha with ZLX graphics, I have been told that responce time is "fantastic". If and when you get an Alpha running AVS, let me know and I can give you a demo copy of the AVS Chemistry Viewer and you can judge for yourself. I have also written several demo scripts which Degital Equipment Corp. has used to show off the graphics at various shows. These scripts demonstrate several Chemistry Viewer features, such as molecular orbital display, electro- static potential, vibrational frequency animation, setting up Gaussian and Mopac input, and of course, the moleclar editor. Thanks, Chuck -- Charles W. Ulmer, II Senior Scientist Product Manager - The AVS Chemistry Viewer The DASGroup, Inc. 3807 Elmhurst Road Toledo, OH 43613 phone: (419)537-4028 culmer@uoft02.utoledo.edu fax: (419)537-4033 From savary@sc2a.unige.ch Mon Oct 10 10:18:52 1994 Received: from UNI2B.UNIGE.CH for savary@sc2a.unige.ch by www.ccl.net (8.6.9/930601.1506) id KAA00986; Mon, 10 Oct 1994 10:01:54 -0400 Received: from PCC2333F (129.194.51.63) by uni2b.unige.ch (PMDF V4.3-8 #2502) id <01HI462OPPY8003FPG@uni2b.unige.ch>; Mon, 10 Oct 1994 15:01:45 WET-DST Date: Mon, 10 Oct 1994 15:01:44 +0100 From: savary@sc2a.unige.ch (Francois Savary) Subject: simple geometry minimizer X-Sender: savary@sc2a.unige.ch To: CHEMISTRY@ccl.net Message-id: <01HI462P90EA003FPG@uni2b.unige.ch> X-Envelope-to: CHEMISTRY@ccl.net MIME-version: 1.0 X-Mailer: Windows Eudora Version 1.4.3b4 Content-type: text/plain; charset="us-ascii" Content-transfer-encoding: 7BIT Hi dear CCListers, I'm looking for a simple molecular mechanics minimization tool, the simpler the better, if possible with source. (:-) thanks in advance Francois Savary ---------------------------------------------------------------------------- Francois Savary University of Geneva Department of Physical Chemistry CHIFI Weber 30 quai Ernest-Ansermet CH-1211 Geneva 4 Lab : 112 Phone : +4122 702 65 32 Fax : +4122 702 65 18 e-mail : savary@sc2a.unige.ch HTML : http://scsg9.unige.ch/tabmat.html (in french) : http://scsg9.unige.ch/eng/toc.html (in english) ---------------------------------------------------------------------------- From SATYAM@vms.cis.pitt.edu Mon Oct 10 10:19:57 1994 Received: from VAXVM2.CIS.PITT.EDU for SATYAM@vms.cis.pitt.edu by www.ccl.net (8.6.9/930601.1506) id KAA01008; Mon, 10 Oct 1994 10:04:10 -0400 From: Received: from vms.cis.pitt.edu by vms.cis.pitt.edu (PMDF V4.2-14 #4065) id <01HI3UYWLOHCB9SJ9M@vms.cis.pitt.edu>; Mon, 10 Oct 1994 10:04:07 EST Date: Mon, 10 Oct 1994 10:04:07 -0500 (EST) Subject: Help with ... Installing .. MOPAC.93... on SGI with 4.0.5 and 5.2..? To: chemistry@ccl.net Message-id: <01HI3UYWLY4IB9SJ9M@vms.cis.pitt.edu> X-Envelope-to: chemistry@ccl.net X-VMS-To: IN%"chemistry@ccl.net" MIME-version: 1.0 Content-transfer-encoding: 7BIT Dear Netters, The sys. adm. of our group wants to know the changes made to (i) Makefile (s) (ii) Sources of the MOPAC 93 (a Sun version from QCPE) for Installing it on SGI (Indigo/INDY using OS 4.0.5/5.2 ). Some of you have done this..and..this will save lot of time for the Grad. Student..who will be installing it. Please send replies to me. Satyam@vms.cis.pitt.edu Thanks in advance. Regards Satyam ______________________________________________________________________________ Dr. Satyam Priyadarshy Quantum Mechanics enables us to understand 905,Chevron Science Center Electron Transfer in DNA Department of Chemistry which in turn University of Pittsburgh helps us to Pittsburgh, PA 15260, U.S.A understand Fax : 1-412-624 8552 Some Aspects of Complicated LIFE Phone : 1-412-624 1217 (W) 1-412-247 4652 (H) Email : satyam@vms.cis.pitt.edu satyam@babar.chem.pitt.edu ______________________________________________________________________________ From Don_Gregory@msi.com Mon Oct 10 10:21:02 1994 Received: from msi.com for Don_Gregory@msi.com by www.ccl.net (8.6.9/930601.1506) id JAA00565; Mon, 10 Oct 1994 09:40:29 -0400 Received: from qmail-gw.msi.com by msi.com (4.1/SMI-4.1) id AA24397; Mon, 10 Oct 94 09:41:10 EDT Message-Id: <9410101341.AA24397@msi.com> Date: 10 Oct 1994 09:39:53 +0000 From: "Don Gregory" Subject: counterions for N.A. To: "Chemistry osc" Subject: Time:10:51 AM OFFICE MEMO counterions for N.A. Date:10/9/94 To accompany Drs. Monaco and Loomis' note on their mac program for generating ions around nucleic acids: " We have written a Mac application, CounterIon 1.0, which will place counterions around a DNA helix (from a pdb file format). This may be useful to users of CHARMm ..." We, too, have heard this request from a number of users; note the spirited discussion on this BBS a number of weeks ago about empirical and theoretical investigations into the "appropriate" number of counter ions around nucleic acids. For working with CHARMm, I recently created a CHARMm RTF file for DNA which places a sodium ion near the phosphate oxygens. As an example as to how easily this could be done, we have provided this RTF file on our anon. ftp server (server.msi.com: archives/quanta/dna_na.rtf.Z and dnaions.txt.Z) This RTF can be used both with QUANTA/CHARMm, and with CHARMm standalone. This file not meant as a reference on the positioning, nor the number of recommended counter ions around nucleic acid, but rather a template as to how one may include them should one wish. Don Gregory Mgr.Appl.Science, MSI From akn@hcocvx.uni-c.dk Mon Oct 10 10:21:46 1994 Received: from danpost.uni-c.dk for akn@hcocvx.uni-c.dk by www.ccl.net (8.6.9/930601.1506) id FAA27128; Mon, 10 Oct 1994 05:08:47 -0400 Received: from hcocvx.uni-c.dk (hcocvx.uni-c.dk [129.142.6.92]) by danpost.uni-c.dk (8.6.4/8.6) with ESMTP id KAA11292 for ; Mon, 10 Oct 1994 10:08:37 +0100 Received: from localhost by hcocvx.uni-c.dk (8.6.4/10.0.0.3) id KAA06493; Mon, 10 Oct 1994 10:05:26 +0100 From: akn@hcocvx.uni-c.dk (Anita Kildebaek Nielsen) Message-Id: <199410100905.KAA06493@hcocvx.uni-c.dk> Subject: CCL:Question: a N+Ar potential To: CHEMISTRY@ccl.net Date: Mon, 10 Oct 94 10:05:25 MET X-Mailer: ELM [version 2.3 PL11] Dear Netters I would like to do simulaions of N2(g) in an argon cluster, but I have been unsuccessful in finding a (probably Lennard-Jones 6-12) potential between argon-atom and nitrogen-atom. Can anyone help me with references or other informations? Please send it directly to me.I will of course give the results here if anyone should be interested. Thank you for your help in advance. Anita Kildebaek. ************************************* * Anita Kildebaek Nielsen * * Dept. of Chemistry * * Division of Theoretical Chemistry * * Aarhus University * * * * E-mail:akn@hcocvx.uni-c.dk * * S-mail:Langelandsgade 140, * * 8000 Aarhus C * * Denmark * * Phone: +45 89 42 38 33 * ************************************* * "All of science is physics * * or stamp collecting" * * Rutherford * ************************************* From psubram@texaco.com Mon Oct 10 14:18:51 1994 Received: from texaco.com for psubram@texaco.com by www.ccl.net (8.6.9/930601.1506) id NAA04991; Mon, 10 Oct 1994 13:53:54 -0400 Received: by texaco.com (4.1/SMI-4.1) id AA26601; Mon, 10 Oct 94 12:53:41 CDT Date: Mon, 10 Oct 94 12:53:41 CDT From: psubram@texaco.com (Palavo Subramanian) Message-Id: <9410101753.AA26601@texaco.com> To: chemistry@ccl.net Subject: Summary Interaction Hi, Sometime back I had posted a query regarding using MOPAC to calculate interaction energy of octane, I have summarised all the responses that I recd. Thank you all for the responses The general consensus seems to be to use MM rather than semi-empirical procedures. -------------------------------------------------------------------- A quick tip: One of the main (long-range) interactions between alkanes is London dispersion forces. As these are an effect of electron correlation, you will not be able to account for these using a semi-empiric calculation (eg, MOPAC). If you want a result, use a molecular mechanics method. MM2 and MM3 are parameterized to reproduce alkane heats of sublimation, so interactions between octanes should be OK (at least in MM3). If you want to get a non-MM, non-experimental result (why would you?), you have to go to fairly large ab initio methods with electron correlation. Per-Ola Norrby * Per-Ola Norrby * The Royal Danish School of Pharmacy, Dept. of Med. Chem. * Universitetsparken 2, DK 2100 Copenhagen, Denmark * tel. +45-35376777-506, +45-35370850 fax +45-35372209 * Internet: peon@medchem.dfh.dk *************************************************************************** I've found that you can only get quasi-decent interaction energies using MOPAC for materials that have strong H-bonding interactions, like base pairs in DNA. For weaker interactions, you won't get much of anywhere, which is the case for octane. There's a program called AMYR that lets you calculate the interactions between 2 *rigid* molecules that WILL give you results for weaker interactions, but won't compute any structural changes. For the full treatment, you'd be better off using a properly parametrised force field & molecular dynamics. I assume texaco has some sort of library service? A search ought to reveal some references. I had a file with references to AMYR somewhere, but can't seem to locate it right now, sorry... Good luck, Irene Newhouse ************************************************************************** I would have thought that you would want to calculate the interaction of the octane molecules using a MD package as opposed to Mopac. Simply duplicate the basic molecule and turn it loose in a periodic box. Knowing the energy of an individual molecule and determining the energy of the liquid you would come up with an interaction energy. Because the geometry of two interacting molecules is highly variable, it seems it would be extremely tedious to do using a semi-empirical technique. You can do MD using semi-empirical techniques in Hyperchem but to handle more than a couple of molecules would be very time consuming. Ross Underhill ************************************************************************* With regard to using MNDO for calculating the intereaction energy of octane or any weakly intereaction system, it is possible in a computational sense, i.e. one will get a number, but the results are of no particularly value (not publishable in a well reviewed journal). Why? Semiempirical methods present in MOPAC were not developed for weak interaction calcutions. The interaction energies would be weak in such a case (less than 1-2 kcal),which is far smaller than the standard deviation errors of the method. Even in ab initio theory, where basis set composition, basis set superposition error, and correlation can be taken into account the interaction energy between two alkanes would be a formidable calculation. One method which has been used in computing crystallization enthalpies is Allinger's molecular mechanics programs, espcially those which take into account dispersion terms. Since there are no strong dipole dipole intereactions, the interaction energy in alkcanes is dominated by dispersion forces, and the van der Waals type interaction potentials used in some modeling schemes will take into account this. Good luck Earl Evleth *********************************************************************** There's no big problem DOING the type of calculation you are attempting: > I am interested in calculating interaction energies between 2 > octane molecules. I would like to use MOPAC. Could someone let me know > as to how I should go about setting the calculation etc. ( I am > assuming that this can be done using MOPAC!). It would be another matter, however, to get MEANINGFUL results. If an interaction energy for a specific geometry is adequate (a geometry from an X- ray Crystal Structure, for instance) then you could just input the geometry with two octanes and calculate the enthalpy and subtract the enthalpy of a single octane. (If you need free energies, you will need to do a FORCE calculation to include the entropy, but an XRD geometry will not be suitable: you will have to optimize the geometry within the semi-empirical method. Otherwise, you will end up with negative eigenvalues and the frequency calculations will be meaningless.) If you are trying to study the interaction energy in the bulk liquid, there are two problems. 1) You will need to consider the many possible conformations and orientations of the two octanes relative to each other. You could generate a set of representative starting geometries to sample the real distribution, then optimize each, calculate the energies, and calculate a weighted average (assuming a Boltzman distribution). This would not be a pleasant task to do manually with Mopac, although I have done this sort of thing. Even then, you will not be sure how accurately your sample represents the true distribution (especially if you missed the most stable configuration which would be the major contributor to the energy). A Monte Carlo, or Molecular Dynamics type code which uses AM1 or PM3 energy calculations would do a more proper job of sampling, but I don't know of a commercial product to recommend. 2) In my experience, I have not found Mopac (or any of the semi-empirical Hamiltonians) to represent long range interactions (ie. intermolecular) very accurately: it is difficult to even find stable geometries for molecule pairs. For your type problem, I would expect Molecular Mechanics to provide better answers. MM is what is typically used in the commercial Molecular Dynamics and Monte Carlo codes, anyway, and hydrocarbons should be handled particularly well. I hope this helps. EC --W-h-o---W-h-o---W-h-o---W-h-o--|--W-h-e-r-e---W-h-e-r-e---W-h-e-r-e-- | Ernie Chamot | Amoco Chemical Company Senior Research Chemist | PO Box 3011 Computational Chemistry Project | Naperville, Illinois, 60566 echamot@amoco.com | Voice (708)961-0752, Fax 420-4678 ---C-o-r-p-o-r-a-t-e---R-e-q-u-i-r-e-d---D-i-s-c-l-a-i-m-e-r--- Should any of my views expressed in this EMail message resemble the official views and/or an endorsement by my corporation, I would be astonished and gratified at Amoco's sudden enlightenment. ************************************************************************* Unfortunately I stripped off the header info. while saving and some of the respondents email info. is missing. My apologies for that. Once again thank you all for taking the time. P.S.Subramanian psubram@texaco.com From berry@ccl.net Mon Oct 10 16:25:39 1994 Received: for berry@ccl.net by www.ccl.net (8.6.9/930601.1506) id QAA07327; Mon, 10 Oct 1994 16:02:22 -0400 Date: Mon, 10 Oct 1994 16:02:22 -0400 From: "Robby A. Berry" Message-Id: <199410102002.QAA07327@www.ccl.net> To: tchemistry@ccl.net Subject: Test message Cc: berry@ccl.net Just getting a baseline reading. If anybody besides Jan or myself can read this, please notify me (berry@ccl.net) immediately. Thanks! Rob From bak@isadora.albany.edu Mon Oct 10 16:25:53 1994 Received: from UACSC2.ALBANY.EDU for bak@isadora.albany.edu by www.ccl.net (8.6.9/930601.1506) id QAA07552; Mon, 10 Oct 1994 16:15:13 -0400 Received: from isadora.albany.edu by UACSC2.ALBANY.EDU (IBM VM SMTP V2R2) with TCP; Mon, 10 Oct 94 16:12:25 EDT Received: by isadora.albany.edu (931110.SGI/920502.SGI) for @uacsc2.albany.edu:chemistry@ccl.net id AA11897; Mon, 10 Oct 94 16:14:48 -0400 From: bak@isadora.albany.edu (Brian A. Kell) Message-Id: <9410102014.AA11897@isadora.albany.edu> Subject: Re: counterions for N.A. To: chemistry@ccl.net Date: Mon, 10 Oct 94 16:14:47 EDT In-Reply-To: <9410101341.AA24397@msi.com>; from "Don Gregory" at Oct 10, 94 9:39 am X-Mailer: ELM [version 2.3 PL11] At the risk of sounding like a "me too"... Last December, a BCL macro for InsightII was posted on the DIBUG (Discover and Insight -- Biosym Users' Group) mailing list, which also places specified counterions around DNA molecules. It is available in the DIBUG archives. Or, I can send it directly to interested parties. brian ------------------------------------------------------------------ Brian Kell bak@biosym.com Scientific Support Manager, Eastern Region Tel. (518) 482-1436 Biosym Technologies, Inc. Fax. (518) 482-5433 ------------------------------------------------------------------ From bak@isadora.albany.edu Mon Oct 10 19:18:54 1994 Received: from UACSC2.ALBANY.EDU for bak@isadora.albany.edu by www.ccl.net (8.6.9/930601.1506) id TAA09748; Mon, 10 Oct 1994 19:03:21 -0400 Received: from isadora.albany.edu by UACSC2.ALBANY.EDU (IBM VM SMTP V2R2) with TCP; Mon, 10 Oct 94 18:59:13 EDT Received: by isadora.albany.edu (931110.SGI/920502.SGI) for @uacsc2.albany.edu:chemistry@ccl.net id AA13498; Mon, 10 Oct 94 19:00:50 -0400 From: bak@isadora.albany.edu (Brian A. Kell) Message-Id: <9410102300.AA13498@isadora.albany.edu> Subject: How to subscribe to DIBUG To: chemistry@ccl.net Date: Mon, 10 Oct 94 19:00:50 EDT X-Mailer: ELM [version 2.3 PL11] After recieving a number of requests, I realized that not everyone may be aware of how to subscribe to DIBUG. DIBUG (Discover and Insight, the Biosym User's Group) is a mailing list maintained by the users of Biosym software. It is not controlled by Biosym; however, some Biosym employees subscribe to it. For information, or to subscribe, please send your requests to: dibug-request@comp.bioz.unibas.ch brian ------------------------------------------------------------------ Brian Kell bak@biosym.com Scientific Support Manager, Eastern Region Tel. (518) 482-1436 Biosym Technologies, Inc. Fax. (518) 482-5433 ------------------------------------------------------------------ From chamankh@duke.usask.ca Mon Oct 10 20:18:55 1994 Received: from skycat.usask.ca for chamankh@duke.usask.ca by www.ccl.net (8.6.9/930601.1506) id TAA10034; Mon, 10 Oct 1994 19:32:50 -0400 Received: from duke.usask.ca by SKYCAT.USask.CA (PMDF V4.3-11 #5952) id <01HI4BB8D7N48Y5SFN@SKYCAT.USask.CA>; Mon, 10 Oct 1994 17:32:11 -0600 (CST) Received: by duke.usask.ca; (5.65/1.1.8.2/03May94-0555AM) id AA22886; Mon, 10 Oct 1994 17:32:00 -0600 Date: Mon, 10 Oct 1994 17:31:59 -0600 (CST) From: Mahmood Chamankhah Subject: Theoretical Log P values Sender: Mahmood Chamankhah To: Chemistry@ccl.net Reply-to: Mahmood Chamankhah Message-id: X-Envelope-to: Chemistry@ccl.net MIME-version: 1.0 Content-type: TEXT/PLAIN; CHARSET=US-ASCII Content-transfer-encoding: 7BIT Hi everybody; I've seen a couple of questions about how to calculate Log P values. 2 Questions: 1) Has the Reckker's method of calculating log P values been integrated in a software? 2) Recently we tried to calculate Log P values for a series of compounds which are substituted phenyl ring conjugated to a double bond using Reckker's f values (f values are tabulated in Reckker's book, hopefully those who are interested have seen the book). We would like to know if there are substituents in ortho, meta and para positions of this system, would it affect the calculated lipophilicity of the whole molecule or not, because there is no direct explanation in the book regarding such effects and how to include it. I appreciate any comments about the above problem specially from those who are using log P values (calculated or observed) routinely in their QSAR analysis. Yours all M.Chamankhah Canada