From SATYAM@vms.cis.pitt.edu Mon Nov 27 11:38:23 1995 Received: from myriad.cis.pitt.edu for SATYAM@vms.cis.pitt.edu by www.ccl.net (8.6.10/950822.1) id LAA02658; Mon, 27 Nov 1995 11:32:57 -0500 From: Received: from vms.cis.pitt.edu by vms.cis.pitt.edu (PMDF V4.3-10 #10002) id <01HY4WF0ACQOAAUFS1@vms.cis.pitt.edu>; Mon, 27 Nov 1995 11:32:48 -0400 (EDT) Date: Mon, 27 Nov 1995 11:32:47 -0400 (EDT) Subject: Writing Huge Z-matrix ? To: chemistry@www.ccl.net Message-id: <01HY4WF0B5O2AAUFS1@vms.cis.pitt.edu> X-Envelope-to: chemistry@www.ccl.net X-VMS-To: IN%"chemistry@www.ccl.net" MIME-version: 1.0 Content-type: TEXT/PLAIN; CHARSET=US-ASCII Content-transfer-encoding: 7BIT Dear Netters, I am interested in knowing if anyone has written program(s) to write Z-matrix for LARGE MOLECULE..using Z-matrix of SMALL FRAGMENT(s)..which may /may not be same..e.g. A simple one.. P-NITROANILINE = NO2 + BENZENE + NH2 + DUMMY ATOMS But the interest is in very large molecules .. THANKS satyam@vms.cis.pitt.edu Satyam (satyam@vms.cis.pitt.edu) From jhwang@bphp.sci.ccny.cuny.edu Mon Nov 27 11:53:27 1995 Received: from bphp.sci.ccny.cuny.edu for jhwang@bphp.sci.ccny.cuny.edu by www.ccl.net (8.6.10/950822.1) id LAA03060; Mon, 27 Nov 1995 11:53:16 -0500 Message-Id: <199511271653.LAA03060@www.ccl.net> Received: by bphp.sci.ccny.cuny.edu (1.38.193.4/16.2) id AA03407; Mon, 27 Nov 1995 11:52:14 -0500 Date: Mon, 27 Nov 1995 11:52:14 -0500 From: jianghua wang To: chemistry@www.ccl.net Subject: force field transformation Dear Colleagues: I am looking for a program which can transform cartsian force constants to internal force constants. Thanks, Joshua Wang ************************************************************ *Joshua Wang *Phone: 212-650-5502 * *Physics Department *Fax: 212-650-5503 * *CCNY *Email: * *New York, NY 10031 * jhwang@scisun.sci.ccny.cuny.edu * ************************************************************ From toukie@zui.unizh.ch Mon Nov 27 12:07:54 1995 Received: from rzusuntk.unizh.ch for toukie@zui.unizh.ch by www.ccl.net (8.6.10/950822.1) id LAA02912; Mon, 27 Nov 1995 11:46:13 -0500 Received: by rzusuntk.unizh.ch (4.1/SMI-4.1.9) id AA17155; Mon, 27 Nov 95 17:46:08 +0100 X-Nupop-Charset: Swiss Date: Mon, 27 Nov 1995 18:46:37 +0100 (MET) From: "Hr Dr. S. Shapiro" Sender: toukie@zui.unizh.ch Reply-To: toukie@zui.unizh.ch Message-Id: <67597.toukie@zui.unizh.ch> To: chemistry@www.ccl.net Subject: Queuing .bat file for GMMX Dear Colleagues; Has anyone out there ever written a functional .bat file for queuing runs for the programme GMMX? GMMX is a sort-of DOS implementation of the conformational searching subroutine of MacroModel, and is sold by Serena Software of Bloomington, Indiana. The file that I wrote. named "qgmmx.bat", appears at the end of this letter, but does not work without periodic inter- vention on my part. I would liike to have a .bat file which just lets me queue the compounds for which I wish to do a conformational search and does them automatically so that I can go off and do other things meanwhile. It should be assumed that I have already prepared the relevent .inp files using the "gmmxinp" command for compounds a, b, c, etc. (see "qgmmy.bat", be- low). I would appreciate hearing from anyone who has successfully written such a .bat file. Thanks in advance to all responders. Sincerely, S. Shapiro ZH, CH toukie@zui.unizh.ch . . . QGMMX.BAT (non-functional) @echo off break=on cls gmmx a gmmx a1 gmmx b gmmx b1 gmmx c gmmx c1 .. .. .. .. From huang@mazda.wavefun.com Mon Nov 27 12:08:25 1995 Received: from volvo.wavefun.com for huang@mazda.wavefun.com by www.ccl.net (8.6.10/950822.1) id MAA03264; Mon, 27 Nov 1995 12:01:57 -0500 Received: by volvo.wavefun.com (931110.SGI/930416.SGI) for hiroshi@U.Arizona.EDU id AA16057; Mon, 27 Nov 95 08:58:15 -0800 Received: from mazda.wavefun.com(198.147.95.6) by volvo.wavefun.com via smap (V1.3) id sma016053; Mon Nov 27 08:58:01 1995 Received: by mazda.wavefun.com (931110.SGI/930416.SGI) for @volvo.wavefun.com:CHEMISTRY@www.ccl.net id AA16679; Mon, 27 Nov 95 08:57:26 -0800 From: "Wayne Huang" Message-Id: <9511270857.ZM16677@mazda.wavefun.com> Date: Mon, 27 Nov 1995 08:57:26 -0800 In-Reply-To: Hiroshi Ogura "CCL:Spartan: a multiplicity problem with a porphyrin" (Nov 23, 9:15pm) References: Reply-To: huang@wavefun.com X-Mailer: Z-Mail (3.1.0 22feb94 MediaMail) To: Hiroshi Ogura , CompChem List Subject: Re: CCL:Spartan: a multiplicity problem with a porphyrin Content-Type: text/plain; charset=us-ascii Mime-Version: 1.0 On Nov 23, 9:23pm, Hiroshi Ogura wrote: > Subject: CCL:Spartan: Fe parameters for semiempirical calculations? > I would like to attempt semiempircal calculations (AM1 or PM1) of iron > porphyrin complexes with Spartan. Unfortunately, our computer does not > have the parameters for iron. Could anybody please tell me if the > parameters are available somewhere? Thanks. > Spartan PM3(tm) module has Fe parameters which is available from Wavefunction ftp site: ftp://ftp.wavefun.com/pub/PARAMS/params.PM3D Drop a note to support@wavefun.com if you have any Spartan-related question. --Wayne -- +---------------------------------------------------------------------+ | Wayne Huang, Ph.D. | 18401 Von Karman, Suite 370 | | Computational Chemist | Irvine, California 92715 | | Wavefunction, Inc. | (714)955-2120 Fax: (714)955-2118 | | huang@wavefun.com | World Wide Web: http://wavefun.com | +---------------------------------------------------------------------+ From topper@cooper.edu Mon Nov 27 12:23:25 1995 Received: from magnum.cooper.edu for topper@cooper.edu by www.ccl.net (8.6.10/950822.1) id MAA03518; Mon, 27 Nov 1995 12:21:12 -0500 Received: from zeus.cooper.edu by magnum.cooper.edu with SMTP id AA07286 (5.65c/IDA-1.4.4 for ); Mon, 27 Nov 1995 12:23:50 -0500 Received: by zeus.cooper.edu id AA26924 (5.67b/IDA-1.5); Mon, 27 Nov 1995 12:16:55 -0500 From: TOPPER ROBERT Message-Id: <199511271716.AA26924@zeus.cooper.edu> Subject: Re: CCL:Molecular Mechanics To: cletner@remcure.bmb.wright.edu (Charles Letner) Date: Mon, 27 Nov 1995 12:16:55 -0500 (EST) Cc: CHEMISTRY@www.ccl.net In-Reply-To: from "Charles Letner" at Nov 24, 95 01:39:49 pm X-Mailer: ELM [version 2.4 PL24alpha3] Mime-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Content-Length: 1737 > > On Wed, 22 Nov 1995, Robert K. Szilagyi wrote: > > > My 0.02$ to this question is that molecular mechanical results MUST NOT > > be compared with each other if the molecules are different. It has no chemical > > and physical meaning at all! The MM model is constructed with different > > equations due to the different parameters. Hi, Some interesting approaches to this problem have been suggested by DeTar: for example, see J.Org.Chem. 56, 1463 (1991) and accompanying articles. Also see DeTar, Ninzet and Darba, J.Org.Chem. 50, 2826 (1985); ibid., 5298 (1985); ibid., 5304 (1985). Basically, in DeTar's approach a series of isodesmic comparisons is made to define the "formal steric enthalpy," which is then used to obtain heats of formation. The method, which is quite general, can even be used in conjunction with ab initio methods and contains no adjustable parameters, which is nice. I hope this helps - rqt ************************************************************************ Robert Q. Topper email: topper@cooper.edu Department of Chemistry phone: (212) 353-4378 The Cooper Union FAX: (212) 353-4341 51 Astor Place subway: take the 6 to Astor Place New York, NY 10003 USA or the N/R to 8th St/NYU http://www.cooper.edu/engineering/chemechem/depts_info/topper.html ************************************************************************ The Cooper Union for the Advancement of Science and Art, founded in 1859, is a private institution of higher learning where all students receive full-tuition scholarships. ************************************************************************ From topper@cooper.edu Mon Nov 27 12:38:24 1995 Received: from magnum.cooper.edu for topper@cooper.edu by www.ccl.net (8.6.10/950822.1) id MAA03602; Mon, 27 Nov 1995 12:27:03 -0500 Received: from zeus.cooper.edu by magnum.cooper.edu with SMTP id AA07488 (5.65c/IDA-1.4.4 for ); Mon, 27 Nov 1995 12:29:40 -0500 Received: by zeus.cooper.edu id AA27311 (5.67b/IDA-1.5); Mon, 27 Nov 1995 12:22:50 -0500 From: TOPPER ROBERT Message-Id: <199511271722.AA27311@zeus.cooper.edu> Subject: Re: CCL:statistical error in simulations To: rafapa@obelix.cica.es (Rafael Rodriguez Pappalardo) Date: Mon, 27 Nov 1995 12:22:50 -0500 (EST) Cc: chemistry@www.ccl.net, topper@cooper.edu In-Reply-To: <199511241731.SAA00598@obelix.cica.es> from "Rafael Rodriguez Pappalardo" at Nov 24, 95 06:31:29 pm X-Mailer: ELM [version 2.4 PL24alpha3] Mime-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Content-Length: 1332 > just a question, > I'm looking for references about calculation of errors in quantities > like RDF, running integration numbers,... obtained by means of MD/MC > simulations. Can anyone help me? > > Best regards, > > Rafael I found the following references helpful: Straatsma, Berendsen and Stam, Mol. Phys. 57(1), 89 (1986); Allen and Tildesley, Computer Simulation of Liquids. You might also like to have a look at a paper of mine: Topper and Truhlar, J. Chem. Phys. 97, 3647 (1992). I hope this helps - best, rqt ************************************************************************ Robert Q. Topper email: topper@cooper.edu Department of Chemistry phone: (212) 353-4378 The Cooper Union FAX: (212) 353-4341 51 Astor Place subway: take the 6 to Astor Place New York, NY 10003 USA or the N/R to 8th St/NYU http://www.cooper.edu/engineering/chemechem/depts_info/topper.html ************************************************************************ The Cooper Union for the Advancement of Science and Art, founded in 1859, is a private institution of higher learning where all students receive full-tuition scholarships. ************************************************************************ From epw@ppco.com Mon Nov 27 14:53:26 1995 Received: from charon.ppco.com for epw@ppco.com by www.ccl.net (8.6.10/950822.1) id OAA06039; Mon, 27 Nov 1995 14:49:42 -0500 Received: from ppco.com by charon.ppco.com with SMTP id AA14284 (InterLock SMTP Gateway 3.0 for ); Mon, 27 Nov 1995 13:49:14 -0600 Received: from epwpc.ppco.com by ppco.com (/ ppco.1.0) id AA07911; Mon, 27 Nov 1995 13:49:00 -0600 Message-Id: <9511271949.AA07911@ppco.com> X-Sender: epw@charon.ppco.com X-Mailer: Windows Eudora Light Version 1.5.2 Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Mon, 27 Nov 1995 13:44:28 +0000 To: Rafael Rodriguez Pappalardo , chemistry@www.ccl.net From: "Dr. Eric P. Wallis" Subject: Re: CCL:statistical error in simulations At 06:31 PM 11/24/95 +0100, you wrote: >Hello everybody! > >just a question, >I'm looking for references about calculation of errors in quantities >like RDF, running integration numbers,... obtained by means of MD/MC >simulations. Can anyone help me? > I break up the trajectory into 5 smaller trajectories and calculate the RDF's and number of first solvation shell neighbors for each of the smaller trajectories. Using these 5 subsets, you can calculate the deviation or error. This method is similar to the standard way of calculating the error in the averages obtained from and MD or MC simulation. Hope this helps Best regards, Eric ******************************************************************* * Eric P. Wallis, Ph.D * * Computational Chemistry Office (918)-661-7956 * * Phillips Petroleum Company FAX: (918) 662-1097 * * 331A PL PRC email: epw@ppco.com * * Bartlesville, OK 74004 Home email: ewallis@galstar.com * ******************************************************************* From hiroshi@U.Arizona.EDU Mon Nov 27 16:53:28 1995 Received: from bonaire.ccit.arizona.edu for hiroshi@U.Arizona.EDU by www.ccl.net (8.6.10/950822.1) id QAA08683; Mon, 27 Nov 1995 16:46:20 -0500 Received: (from hiroshi@localhost) by bonaire.ccit.arizona.edu (8.6.12/8.6.12) id OAA28562; Mon, 27 Nov 1995 14:50:19 -0700 Date: Mon, 27 Nov 1995 14:50:19 -0700 (MST) From: Hiroshi Ogura X-Sender: hiroshi@bonaire.ccit.arizona.edu To: CompChem List Subject: Fe atom typing for MM2 in Spartan Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Is iron typed in the MM2 implementation for Spartan? Allinger did assign 50 to the metals in general, but it seems as though the assignment is not being made in the software. I obtained the MM2 parameters for iron porphyrins from Munro et al., J.Am.Chem.Soc., 1992, 114, 7218. I wrote them into my parameter file, and then I attempted to do a calculation on iron octamethyl tetraphenyl porphyrin. The software gave me an error message: it said that the iron was untyped. It seems that Spartan did not recognize the type-50 atoms in the parameter file. Have any of you attempted a MM2 calculation on a metal complex, using Spartan? If so, did you have a problem with the metal atom typing? Were you able to get around the problem? Thanks in advance. p.s. Thanks to all of you who gave me informations on the PM3 parameters for iron! As for the multiplicity problem, I have followed the people's suggestions and checked the charge of the molecule and the number of electrons. They looked fine, and therefore I'm still stuck with the problem. This afternoon, I'm going to show the problem to a friend who is very familiar with Spartan. I'm hoping that we'd be able to find the solution then. -- Hiroshi Ogura | One man, he drinks up his whiskey; hiroshi@u.arizona.edu | Another, he drinks up his wine. Dept. Chem., Univ. Az. | And they'll drink till their eyes are red with hate Tucson, AZ 85721 | For those of a different kind. -- Richard Thompson