From zhu@marge.phys.uh.edu Tue Mar 7 00:10:22 1995 Received: from marge.phys.uh.edu for zhu@marge.phys.uh.edu by www.ccl.net (8.6.10/930601.1506) id XAA02031; Mon, 6 Mar 1995 23:56:24 -0500 Received: by marge.phys.uh.edu (5.65/DEC-Ultrix/4.3) id AA23256; Mon, 6 Mar 1995 22:56:19 -0600 From: zhu@marge.phys.uh.edu (Wie Zhu) Message-Id: <9503070456.AA23256@marge.phys.uh.edu> Subject: support-letter: sample To: chemistry@ccl.net Date: Mon, 6 Mar 95 22:56:19 CST X-Mailer: ELM [version 2.3 PL11] Dear CCLers, Could some one kindly send me a copy of sample-support-letter? Thx in advance. Wie Zhu From cmartin@rainbow.uchicago.edu Tue Mar 7 03:10:16 1995 Received: from midway.uchicago.edu for cmartin@rainbow.uchicago.edu by www.ccl.net (8.6.10/930601.1506) id CAA03617; Tue, 7 Mar 1995 02:30:21 -0500 Received: from rainbow.uchicago.edu (rainbow.uchicago.edu [128.135.136.33]) by midway.uchicago.edu (8.6.10/8.6.4) with SMTP id BAA12696 for <@midway.uchicago.edu:chemistry@ccl.net>; Tue, 7 Mar 1995 01:30:20 -0600 Received: by rainbow.uchicago.edu (931110.SGI/930416.SGI) for @midway.uchicago.edu:chemistry@ccl.net id AA03772; Tue, 7 Mar 95 01:29:57 -0600 From: cmartin@rainbow.uchicago.edu (Charles Martin) Message-Id: <9503070729.AA03772@rainbow.uchicago.edu> Subject: Convergence of CASSCF calculations To: chemistry@ccl.net Date: Tue, 7 Mar 1995 01:29:56 -0600 (CST) X-Mailer: ELM [version 2.4 PL24] Mime-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Content-Length: 1746 Netters, Recently one of the grad students in our group has been using Gaussian CASSCF calculations to describe the excited state potential energy surface of a long chain polyene: C=C-C=C-C=C-C=C-C=NH2(+) (the polyene is twisted and has no symmetry) He has been unable, however, to converge the CASSCF(2nd root) calculations at some of the twisted geometries. Of course, there could be a near degeneracy which is causing the problem, but I am also suspecting that CASSCF orbitals which Gaussian uses may be inappropriate, and that instead the virtual orbitals for the CASSCF active space calculation should be some Unitary Transformation of the HF orbitals which Gaussian uses (like Improved Virtual Orbitals). First, I am wondering if anyone else has had similar experiences and could offer some insight or suggestions. Second, I would like to know if anyone has a proogram which will perform such Unitary Transformations with Gaussian, or will I have to write my own or use a different package. Third, just out of curiosity, do any other packages perform such feats with ease? For instance, I have programs which will do this using the COLUMBUS suite of codes, but the COLUMBUS codes and my adjoining codes are pretty low compared to Gaussian. On the other hand, COLUMBUS is pretty easy to interface to, although I do not know alot about the internal components of the other packages available. Perhaps we could open up a discussion about this. For instance, are there mail lists for users and programmers of specific packages (GAMESS, COLUMBUS, GAUSSIAN, etc.) With Best Regards Charles Martin Theoretical Biophysics The Beckman Institute The University of Illinois at Urbana-Champaign (cmartin@ks.uiuc.edu) From c00ayi00@nchc.gov.tw Tue Mar 7 04:10:16 1995 Received: from nchc.gov.tw for c00ayi00@nchc.gov.tw by www.ccl.net (8.6.10/930601.1506) id DAA04251; Tue, 7 Mar 1995 03:49:02 -0500 Message-Id: <199503070849.DAA04251@www.ccl.net> Received: by nchc.gov.tw (th3.8s.nchc.gov) from cronus.nchc.gov.tw id AA18858; Tue, 7 Mar 95 16:42:20 CST Received: by cronus.nchc.gov.tw (station v4.0) from elc052.nchc id AA20045; Tue, 7 Mar 95 16:46:24 CST From: c00ayi00@nchc.gov.tw (Yi-Chun Tsai) Subject: DGEOM95 To: chemistry@ccl.net Date: Tue, 7 Mar 1995 16:46:56 +0800 (CST) Cc: c00ayi00@nchc.gov.tw (Yi-Chun Tsai) X-Mailer: ELM [version 2.4 PL24] Mime-Version: 1.0 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 8bit Content-Length: 992 Hi,Netters, As the Jeff Blaney mentioned, > > I have been working with steroid conformational analysis in connection > > with receptor modeling. I have generated several (typically 100) structu res > > (conformers) for each steroid using DGEOM program. Now I need to pick ou t > > those conformers that are unique. (DGEOM generated structures might conv erge > > to same minimum upon minimization). Any ideas on how to do that using > > commercial modeling software or other shareware programs? > > > The new release of DGEOM (DGEOM95) contains an option to filter > conformations based on RMS deviation. There is also a new version of > COMPARE (supplied with DGEOM95) which uses Jarvis-Patrick clustering > to cluster conformers based on RMS deviation. You can use either > approach to generate a unique set of conformers to an arbitrary cutoff > based on RMS. > > > Jeff Blaney > Chiron > Where I can get DGEOM95 the program? Thanks in advance. Yi-Chun Tsai From GAO_YING-DUO_NONLILLY@Lilly.com Tue Mar 7 09:10:24 1995 Received: from Lilly.com for GAO_YING-DUO_NONLILLY@Lilly.com by www.ccl.net (8.6.10/930601.1506) id IAA06799; Tue, 7 Mar 1995 08:37:19 -0500 From: Received: from DECNET-MAIL (RXX2505@MCVAX0) by INET.D48.LILLY.COM (PMDF V4.3-10 #6224) id <01HNUJCQXLM80000A9@INET.D48.LILLY.COM>; Tue, 07 Mar 1995 08:36:44 -0500 (EST) Date: Tue, 07 Mar 1995 08:36:44 -0500 (EST) Subject: modeling on A beta Amyloid To: CHEMISTRY@ccl.net Message-id: <01HNUJCQY4WI0000A9@INET.D48.LILLY.COM> X-VMS-To: IN::"CHEMISTRY@ccl.net" MIME-version: 1.0 Content-transfer-encoding: 7BIT Dear Netters, I'm thinking about starting modeling on A beta Amyloid Peptide, but can't find articles related to this subject. Any references, suggestions and hint would be helpful. I'll summarize the responses to the net. Ying-Duo Gao ydg@lilly.com 317-277-3439 (office) 317-277-1125 (FAX) From: GAO YING-DUO NONLILLY (MCVAX0::RXX2505) To: VMS MAIL ADDRESSEE (IN::"CHEMISTRY@ccl.net") From rvgloss@criba.edu.ar Tue Mar 7 10:10:23 1995 Received: from sic4.cnea.edu.ar for rvgloss@criba.edu.ar by www.ccl.net (8.6.10/930601.1506) id JAA07556; Tue, 7 Mar 1995 09:26:10 -0500 Received: from criba.edu.ar by sic4.cnea.edu.ar with smtp (Smail3.1.28.1 #1) id m0rm0CI-00040SC; Tue, 7 Mar 95 11:25 GMT-3:00 Received: by criba.edu.ar (4.1/SMI-4.1) id AA27618; Tue, 7 Mar 95 11:28:43 WST Date: Tue, 7 Mar 95 11:28:43 WST From: rvgloss@criba.edu.ar (Daniel Glossman) Message-Id: <9503071528.AA27618@criba.edu.ar> To: chemistry@ccl.net Subject: Gaussian z-matrix Dear netters: I am trying to dos some calculations with Gaussian 92. Is there anybody out there who can tell me an elegant way of writing the Gaussian z-matrix for pyrrol with C2v symmetry? Thanks in advance Daniel Glossman Programama QUINOR - UNLP Republica Argentina E-mail: rvgloss@arcriba.edu.ar From D.A.Buttar@bath.ac.uk Tue Mar 7 10:15:10 1995 Received: from goggins.bath.ac.uk for D.A.Buttar@bath.ac.uk by www.ccl.net (8.6.10/930601.1506) id JAA07669; Tue, 7 Mar 1995 09:33:22 -0500 Received: from bath.ac.uk (actually ss1.bath.ac.uk) by goggins.bath.ac.uk with SMTP (PP); Tue, 7 Mar 1995 14:31:44 +0100 Date: Tue, 7 Mar 95 14:32:36 GMT From: David Buttar To: CHEMISTRY@ccl.net Subject: AM1 parameters Organization: University of Bath Message-ID: <9503071432.aa13503@ss1.bath.ac.uk> Has anyone performed any modifications to the zinc parameterisation in AM1, especially with relation to zinc nitrogen parameters. I would be interested in hearing of any work that had been done. Thanks, David ************************************************************************* * David Buttar Tel.(0225) 826 826 ext.5137 * * (Research Fellow) * * Chemistry Dept. E-mail chsdab@uk.ac.bath.midge * * University of Bath * * Claverton Down * * Bath * * U.K. * * * ************************************************************************* From nauss@ucmod2.che.uc.EDU Tue Mar 7 10:22:19 1995 Received: from ROLL.SAN.UC.EDU for nauss@ucmod2.che.uc.EDU by www.ccl.net (8.6.10/930601.1506) id JAA07180; Tue, 7 Mar 1995 09:14:47 -0500 Received: from ucmod2.che.uc.edu by UCBEH.SAN.UC.EDU (PMDF V4.3-10 #7238) id <01HNUL11I3HC01DGMS@UCBEH.SAN.UC.EDU>; Tue, 07 Mar 1995 09:13:30 -0500 (EST) Received: by ucmod2.che.uc.edu (920330.SGI/920502.SGI.AUTO) for @uc.edu:CHEMISTRY@ccl.net id AA04743; Tue, 7 Mar 95 09:16:31 -0500 Date: Tue, 07 Mar 1995 09:16:31 -0500 From: nauss@ucmod2.che.uc.EDU (Jeffrey L. Nauss) Subject: Re: CCL:CCL support To: CHEMISTRY@ccl.net Cc: Marla Babcock Reply-to: nauss@ucmod2.che.uc.EDU Message-id: <9503071416.AA04743@ucmod2.che.uc.edu> Content-transfer-encoding: 7BIT >From: Marla Babcock >Can someone please repost the information necessary to send support to >Jan and the CCL. How much time is there left for support letters to get >through? Use Mosaic or some other WWW browser to get the information from http://www.ccl.net/chemistry.html. The information can be found under "Proposal for list future development." If anyone would like a copy of my letter, look on my home page at http://ucmodl.che.uc.edu/~nauss/homepage.html. The link is at the top of the page. Jeff Nauss **************************************************************************** * UU UU Jeffrey L. Nauss, PhD * * UU UU Director, Molecular Modeling Services * * UU UU Department of Chemistry * * UU UU CCCCCCC University of Cincinnati * * UU UU CCCCCCCC Cincinnati, OH 45221-0172 * * UUUU CC * * CC Telephone: 513-556-0148 Fax: 513-556-9239 * * CC * * CCCCCCCC e-mail: nauss@ucmod2.che.uc.edu * * CCCCCCC http://ucmodl.che.uc.edu/~nauss/homepage.html * **************************************************************************** From TILBROOK@chem.surrey.ac.uk Tue Mar 7 10:29:43 1995 Received: from mail-server.surrey.ac.uk for TILBROOK@chem.surrey.ac.uk by www.ccl.net (8.6.10/930601.1506) id JAA08083; Tue, 7 Mar 1995 09:57:38 -0500 Received: from central.surrey.ac.uk by mail-server.surrey.ac.uk with SMTP (PP); Tue, 7 Mar 1995 14:57:00 +0000 Received: from chemcharon.chem.surrey.ac.uk by central.surrey.ac.uk with SMTP (1.37.109.8/16.2) id AA27454; Tue, 7 Mar 1995 14:56:26 GMT Received: From CHEMISTRY-1/WORKQUEUE by chemcharon.chem.surrey.ac.uk via Charon-4.0-VROOM with IPX id 100.950307145648.736; 07 Mar 95 14:59:04 +500 Message-Id: To: CHEMISTRY@ccl.net From: David Organization: Chemistry Department, Uni of Surrey Date: Tue, 7 Mar 1995 14:56:42 GMT Subject: Modelling IR Vibrational Modes. Priority: normal X-Mailer: WinPMail v1.0 (R1) Dear CCL Sometime ago I posted a question regarding the simulation of IR vibrational modes. Asking for the pro's and con's of various methods. I now have access to both semi-empirical methods (MOPAC) and molecular mechanics (in the form of Cerius2 by MSI). What I would be very interested to hear from anyone invloved in similar work. I have a number of questions to pose you. 1.If you are doing MD work what kind of time scale and duration do you have to run on to get reasonable results? I am presently using a time slice of 0.0001 ps and doing of the order of 100 000 iterations to provide a trajectory file to pass onto the VAC code. 2. What kind of scaling do you find is necessary to give good values for vibrational frequencies? The results I have obtained using UFF with the cross terms implemented by MSI seem to be okay but for the most part are off by a factor of approximately 0.9 (although some C-H bands seem to be quite close to the experimental values without scaling). In the vibrational visualisation module for MOPAC under Cerius2 v1.6 uses and standard scaling for all frequencies calculated by the FORCE option under MOPAC of 0.893 (quite similar to the discrepancy observed with the UFF calculations) 3. Can anybody tell me why this 'magic number' 0.9? Is there any theoretical basis for it's use or is it simply a fudge factor that seems to work? Any help you can give me with these questions or any comments you wish to make about the subject of IR simulation in general will be gratefully received and summarised to the list in due course. Thanks in advance and Kindest Regards David Tilbrook ********************************************************** David Tilbrook * Tel: 44 1483 300 800 x 9591 Polymer Group, * x 2617 Chemistry Department, * University of Surrey, * Fax: 44 1483 259 514 Guildford, Surrey, GU2 5XH * U.K. * ********************************************************** From Jonathan.Connor@mailhost.mcc.ac.uk Tue Mar 7 10:37:30 1995 Received: from nessie.mcc.ac.uk for Jonathan.Connor@mailhost.mcc.ac.uk by www.ccl.net (8.6.10/930601.1506) id JAA08023; Tue, 7 Mar 1995 09:54:53 -0500 Message-Id: <199503071454.JAA08023@www.ccl.net> Received: from mailhost.mcc.ac.uk by mailhost.mcc.ac.uk id <05848-0@mailhost.mcc.ac.uk>; Tue, 7 Mar 1995 14:53:18 +0000 Subject: Wednesday at Kings To: chemistry@ccl.net Date: Tue, 7 Mar 1995 14:52:04 +0000 (GMT) X-Mailer: ELM [version 2.4 PL21] MIME-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Content-Length: 2570 From: Jonathan Connor Sender: Jonathan.Connor@mailhost.mcc.ac.uk Forwarded message: Delivery-Date: Mon, 6 Mar 1995 18:45:38 +0000 Message-Id: <21053.9503061840@tcibm2> From: peterk@tc.mols.susx.ac.uk Subject: Wednesday at Kings --- revised programme To: J.N.L.Connor@manchester.ac.uk (Jonathan Connor), udca700@bay.cc.kcl.ac.uk (M. A. ROBB), Richard.Hall@man.ac.uk, aml@theor.ch.cam.ac.uk, F.Gogtas@bris.ac.uk Date: Mon, 6 Mar 1995 18:40:52 +0000 (GMT) Content-Type: text Content-Length: 1642 Royal Society of Chemistry Theoretical Chemistry Group Spring Meeting --- March 8th 1995 King's College, London ------------------------------------------------------------------------ Programme: 1330 Chairman's Introduction, J. N. L. Connor (University of Manchester) 1340 A Density Functional Model of Solvation, Richard Hall (University of Manchester). 1405 Theoretical Study of non-conjugated enone rearrangements, Sarah Wilsey (King's College, London). 1430 The Calculation of Magnetisabilities and Nuclear Shielding Tensors with Density Functional Theory, Aaron M. Lee (University of Cambridge). 1455 Theoretical Study of ground and excited state isomerization and Fragmenation reactions of Ketene, Naoko Yamamoto (King's College, London). 1520 Tea 1600 Assessment of the Langevin dipoles solvation model for Hartree Fock wavefunctions, N. O. J. Malcolm (University of Manchester). 1625 Time-Dependent Quantum Dynamics of Reactive Scattering: Li + HF -> LiF + H, Fahrettin Gogtas (University of Bristol). 1650 Spin-Correlation effects in Radiation Chemistry, Charlotte Bolton (King's College, London). 1715 Close ------------------------------------------------------------------------ ------------------------------------------------------------------------ -- Dr. Peter J. Knowles | P.J.Knowles@Sussex.ac.uk School of Chemistry and Molecular Sciences, | University of Sussex, | Phone: +44-1273-678624 Falmer, Brighton, BN1 9QJ, UK. | Fax: +44-1273-677196 -- ****************************************************************************** Professor J.N.L. Connor, Phone(direct line): 061-275-4693 (national) Department of Chemistry, :+44-61-275-4693 (international) University of Manchester, Manchester M13 9PL, Phone(secretary): 061-275-4686 or 4600 England. Fax: 061-275-4734 or 4598 ****************************************************************************** From gabriel@jg1.bchem.temple.edu Tue Mar 7 11:10:30 1995 Received: from jg1.bchem.temple.edu for gabriel@jg1.bchem.temple.edu by www.ccl.net (8.6.10/930601.1506) id KAA08773; Tue, 7 Mar 1995 10:30:07 -0500 Received: by jg1.bchem.temple.edu (931110.SGI/911001.SGI) for CHEMISTRY@ccl.net id AA21545; Tue, 7 Mar 95 06:41:58 -0800 Date: Tue, 7 Mar 95 06:41:58 -0800 From: gabriel@jg1.bchem.temple.edu (Dr. Jerome L. Gabriel) Message-Id: <9503071441.AA21545@jg1.bchem.temple.edu> To: CHEMISTRY@ccl.net Subject: Xservers for WindowsDear CCLers I would like to be able to display graphics from my SGI workstation at home on my PC. My internet access provider will provide a slp account which runs winsoc. I would appreciate hearing from anyone who has experience with Xservers for Windows which are compatible with winsoc. Please respond directly to me and I will summarize for the net. Thank you for your help. Jerome L. Gabriel Department of Biochemistry , 406 MRB 1-215-707-1517 Temple University Medical School 1-215-707-7536(FAX) 3420 N. Broad Street gabriel@jg1.bchem.temple.edu Philadelphia, PA 19140 From gabriel@jg1.bchem.temple.edu Tue Mar 7 11:30:01 1995 Received: from jg1.bchem.temple.edu for gabriel@jg1.bchem.temple.edu by www.ccl.net (8.6.10/930601.1506) id KAA08795; Tue, 7 Mar 1995 10:31:40 -0500 Received: by jg1.bchem.temple.edu (931110.SGI/911001.SGI) for chemistry@ccl.net id AA21525; Tue, 7 Mar 95 06:40:30 -0800 Date: Tue, 7 Mar 95 06:40:30 -0800 From: gabriel@jg1.bchem.temple.edu (Dr. Jerome L. Gabriel) Message-Id: <9503071440.AA21525@jg1.bchem.temple.edu> To: chemistry@ccl.net Subject: Xservers for Windows Dear CCLers I would like to be able to display graphics from my SGI workstation at home on my PC. My internet access provider will provide a slp account which runs winsoc. I would appreciate hearing from anyone who has experience with Xservers for Windows which are compatible with winsoc. Please respond directly to me and I will summarize for the net. Thank you for your help. Jerome L. Gabriel Department of Biochemistry , 406 MRB 1-215-707-1517 Temple University Medical School 1-215-707-7536(FAX) 3420 N. Broad Street gabriel@jg1.bchem.temple.edu Philadelphia, PA 19140 From john@cv1.chem.purdue.edu Tue Mar 7 13:10:35 1995 Received: from mentor.cc.purdue.edu for john@cv1.chem.purdue.edu by www.ccl.net (8.6.10/930601.1506) id MAA11799; Tue, 7 Mar 1995 12:55:26 -0500 Received: from cv1.chem.purdue.edu by mentor.cc.purdue.edu (5.61/Purdue_CC) id AA09594; Tue, 7 Mar 95 12:55:25 -0500 Received: by cv1.chem.purdue.edu (931110.SGI.ANONFTP/931108.SGI.ANONFTP) for @mentor.cc.purdue.edu:chemistry@ccl.net id AA26072; Tue, 7 Mar 95 13:03:13 -0500 Date: Tue, 7 Mar 95 13:03:13 -0500 From: john@cv1.chem.purdue.edu (John J. Nash) Message-Id: <9503071803.AA26072@cv1.chem.purdue.edu> To: chemistry@ccl.net, Z-matrix@cv1.chem.purdue.edu Subject: Pyrrole Dear Daniel, I whipped out a z-matrix for you: x h,1,1.0 x,2,1.0,1,90.0 n,2,r1,3,90.0,1,180.0 c,4,r2,2,a1,3,-90.0 c,4,r2,2,a1,3,90.0 c,5,r3,4,a2,2,180.0 c,6,r3,4,a2,2,180.0 h,5,r4,4,a3,2,0.0 h,6,r4,4,a3,2,0.0 h,7,r5,5,a4,4,180.0 h,8,r5,6,a4,4,180.0 I will let you supply the various geometric parameters (i.e., r1, r2, a1,...). I think this should come out perfectly as C2v. Good luck! Sincerely, John J. Nash Purdue University john@cv1.chem.purdue.edu From john@cv1.chem.purdue.edu Tue Mar 7 13:16:21 1995 Received: from mentor.cc.purdue.edu for john@cv1.chem.purdue.edu by www.ccl.net (8.6.10/930601.1506) id MAA11812; Tue, 7 Mar 1995 12:56:14 -0500 Received: from cv1.chem.purdue.edu by mentor.cc.purdue.edu (5.61/Purdue_CC) id AA09614; Tue, 7 Mar 95 12:56:13 -0500 Received: by cv1.chem.purdue.edu (931110.SGI.ANONFTP/931108.SGI.ANONFTP) for @mentor.cc.purdue.edu:chemistry@ccl.net id AA26082; Tue, 7 Mar 95 13:04:01 -0500 Date: Tue, 7 Mar 95 13:04:01 -0500 From: john@cv1.chem.purdue.edu (John J. Nash) Message-Id: <9503071804.AA26082@cv1.chem.purdue.edu> To: chemistry@ccl.net Subject: Pyrrole Dear Daniel, I whipped out a z-matrix for you: x h,1,1.0 x,2,1.0,1,90.0 n,2,r1,3,90.0,1,180.0 c,4,r2,2,a1,3,-90.0 c,4,r2,2,a1,3,90.0 c,5,r3,4,a2,2,180.0 c,6,r3,4,a2,2,180.0 h,5,r4,4,a3,2,0.0 h,6,r4,4,a3,2,0.0 h,7,r5,5,a4,4,180.0 h,8,r5,6,a4,4,180.0 I will let you supply the various geometric parameters (i.e., r1, r2, a1,...). I think this should come out perfectly as C2v. Good luck! Sincerely, John J. Nash Purdue University john@cv1.chem.purdue.edu From elewars@alchemy.chem.utoronto.ca Tue Mar 7 16:12:33 1995 Received: from alchemy.chem.utoronto.ca for elewars@alchemy.chem.utoronto.ca by www.ccl.net (8.6.10/930601.1506) id QAA15996; Tue, 7 Mar 1995 16:02:53 -0500 Received: (from elewars@localhost) by alchemy.chem.utoronto.ca (8.6.10/8.6.10) id QAA07340 for chemistry@ccl.net; Tue, 7 Mar 1995 16:02:45 -0500 Date: Tue, 7 Mar 1995 16:02:45 -0500 From: "E. Lewars" Message-Id: <199503072102.QAA07340@alchemy.chem.utoronto.ca> To: chemistry@ccl.net Subject: PYRROLE Z-MATRIX Daniel Glossman asked about a Z-matrix for pyrrole. Here's one. The internal coord's of atoms in cyclic systems shouldn't be defined sequentially, because of the ratcheting effect (Tim Clark, *A Handbook of Computational Chemistry*). Labelling distances X2N1..., angles A432..., and dihedrals D4321.... will make Z-matrices easier to interpret, till the happy day when they are extinct. The input param's are from a MM opt with the Sybil forcefield, using Spartan for visualization. =========== # am1 PYRROLE, C2V 0 1 N1 X2 N1 X2N1 C3 X2 C3X2 N1 90. C4 C3 C4C3 X2 A432 N1 0. C5 X2 C3X2 N1 90. C3 180. C6 C5 C4C3 X2 A432 N1 0. H7 C6 H7C6 C5 A765 X2 180. H8 C5 H8C5 C6 A856 X2 180. H9 C3 H8C5 C4 A856 X2 180. H10 C4 H7C6 C3 A765 X2 180. H11 X2 H11X2 C3 90. C4 0. X2N1 1.9970 C3X2 0.7345 C4C3 1.3351 H7C6 1.090 H8C5 1.089 z A432 105.5 /\ A765 125.8 H9 | H8 A856 127.5 \ | / H11X2 3.029 \ | / C3------X2-----C5 / | \ H10--- C4 / | \C6 ---H7 | | x < ----------------------N1 /| / | / H11 y From rameshg@umich.edu Tue Mar 7 18:10:32 1995 Received: from seawolf.rs.itd.umich.edu for rameshg@umich.edu by www.ccl.net (8.6.10/930601.1506) id RAA17730; Tue, 7 Mar 1995 17:36:23 -0500 Received: by seawolf.rs.itd.umich.edu (8.6.9/2.2) id RAA07298; Tue, 7 Mar 1995 17:35:59 -0500 Date: Tue, 7 Mar 1995 17:35:57 -0500 (EST) From: Ramesh Gopalaswamy X-Sender: rameshg@seawolf.rs.itd.umich.edu To: c00ayi00@nchc.gov.tw cc: chemistry@ccl.net Subject: Re: CCL:DGEOM95 Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII On Tue, 7 Mar 1995, Yi-Chun Tsai wrote: > > > Hi,Netters, > > As the Jeff Blaney mentioned, > > > The new release of DGEOM (DGEOM95) contains an option to filter > > conformations based on RMS deviation. There is also a new version of > > COMPARE (supplied with DGEOM95) which uses Jarvis-Patrick clustering > > to cluster conformers based on RMS deviation. You can use either > > approach to generate a unique set of conformers to an arbitrary cutoff > > based on RMS. > > > > > > Jeff Blaney > > Chiron > > > > Where I can get DGEOM95 the program? Thanks in advance. > > Yi-Chun Tsai > > DGEOM 95 is available with QCPE (Quantum Chemistry Program Exchange) at the Chemistry Dept. of Indiana University, Bloomington IN. I do not have their address with me on hand (I'm sure you probably received other responses with full details). QCPE info can be accessed on the Web. Ramesh G (rameshg@umich.edu). From landman@hal.physics.wayne.edu Tue Mar 7 19:10:29 1995 Received: from CMS.CC.WAYNE.EDU for landman@hal.physics.wayne.edu by www.ccl.net (8.6.10/930601.1506) id SAA18337; Tue, 7 Mar 1995 18:17:16 -0500 Received: from hal.physics.wayne.edu by CMS.CC.WAYNE.EDU (IBM VM SMTP V2R2) with TCP; Tue, 07 Mar 95 18:17:24 EST Received: from hal (hal.physics.wayne.edu) by hal.physics.wayne.edu (4.1/SMI-4.1) id AA06740; Tue, 7 Mar 95 18:17:10 EST Date: Tue, 7 Mar 1995 18:17:10 -0500 (EST) From: Joe Landman Subject: Re: CCL:Xservers for WindowsDear CCLers To: "Dr. Jerome L. Gabriel" Cc: CHEMISTRY@ccl.net In-Reply-To: <9503071441.AA21545@jg1.bchem.temple.edu> Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Jerome: I use OS/2 Warp + TCPIP for OS/2 v 2.0 + PMX x server. I can run all my x apps at home over the modem. I warn you that this is painful except for xapps that dont transfer much information. Joe On Tue, 7 Mar 1995, Dr. Jerome L. Gabriel wrote: > > I would like to be able to display graphics from my SGI workstation at home > on my PC. My internet access provider will provide a slp account which > runs winsoc. I would appreciate hearing from anyone who has experience > with Xservers for Windows which are compatible with winsoc. Please respond > directly to me and I will summarize for the net. > > Thank you for your help. > > > Jerome L. Gabriel Department of Biochemistry , 406 MRB > 1-215-707-1517 Temple University Medical School > 1-215-707-7536(FAX) 3420 N. Broad Street > gabriel@jg1.bchem.temple.edu Philadelphia, PA 19140 > > > -------This is added Automatically by the Software-------- > -- Original Sender Envelope Address: gabriel@jg1.bchem.temple.edu > -- Original Sender From: Address: gabriel@jg1.bchem.temple.edu > CHEMISTRY@ccl.net -- everyone | CHEMISTRY-REQUEST@ccl.net -- coordinator > MAILSERV@ccl.net: HELP CHEMISTRY | Gopher: www.ccl.net 73 > Anon. ftp www.ccl.net | CHEMISTRY-SEARCH@ccl.net -- archive search > http://www.ccl.net/chemistry.html | for info send: HELP SEARCH to MAILSERV > > From TILBROOK@chem.surrey.ac.uk Tue Mar 7 19:24:41 1995 Received: from mail-server.surrey.ac.uk for TILBROOK@chem.surrey.ac.uk by www.ccl.net (8.6.10/930601.1506) id SAA18791; Tue, 7 Mar 1995 18:55:34 -0500 Received: from central.surrey.ac.uk by mail-server.surrey.ac.uk with SMTP (PP); Tue, 7 Mar 1995 23:46:08 +0000 Received: from chemcharon.chem.surrey.ac.uk by central.surrey.ac.uk with SMTP (1.37.109.8/16.2) id AA25120; Tue, 7 Mar 1995 23:45:48 GMT Received: From CHEMISTRY-1/WORKQUEUE by chemcharon.chem.surrey.ac.uk via Charon-4.0-VROOM with IPX id 100.950307234601.256; 07 Mar 95 23:48:36 +500 Message-Id: To: CHEMISTRY@ccl.net From: Dave Organization: Chemistry Department, Uni of Surrey Date: 7 Mar 95 23:45:51 GMT Subject: Frequency Scaling (Summ) and Thanks! Priority: normal X-Mailer: Pegasus Mail v2.3 (R5). Dear CCL To start off with many thanks to everyone who replied so promptly to the question about vibrational scaling. The original question is enclosed followed by the various responses that I recieved. ORIGINAL MESSAGE ---------------- Dear CCL Sometime ago I posted a question regarding the simulation of IR vibrational modes. Asking for the pro's and con's of various methods. I now have access to both semi-empirical methods (MOPAC) and molecular mechanics (in the form of Cerius2 by MSI). What I would be very interested to hear from anyone invloved in similar work. I have a number of questions to pose you. 1.If you are doing MD work what kind of time scale and duration do you have to run on to get reasonable results? I am presently using a time slice of 0.0001 ps and doing of the order of 100 000 iterations to provide a trajectory file to pass onto the VAC code. 2. What kind of scaling do you find is necessary to give good values for vibrational frequencies? The results I have obtained using UFF with the cross terms implemented by MSI seem to be okay but for the most part are off by a factor of approximately 0.9 (although some C-H bands seem to be quite close to the experimental values without scaling). In the vibrational visualisation module for MOPAC under Cerius2 v1.6 uses and standard scaling for all frequencies calculated by the FORCE option under MOPAC of 0.893 (quite similar to the discrepancy observed with the UFF calculations) 3. Can anybody tell me why this 'magic number' 0.9? Is there any theoretical basis for it's use or is it simply a fudge factor that seems to work? Any help you can give me with these questions or any comments you wish to make about the subject of IR simulation in general will be gratefully received and summarised to the list in due course. Thanks in advance and Kindest Regards David Tilbrook ********************************************************** David Tilbrook * Tel: 44 1483 300 800 x 9591 Polymer Group, * x 2617 Chemistry Department, * University of Surrey, * Fax: 44 1483 259 514 Guildford, Surrey, GU2 5XH * U.K. * ********************************************************** RESPONSES ========== From: Anthony P Scott Received: (aps501@localhost) by huxley.anu.edu.au (8.6.10/8.6.10) id JAA28130; Wed, 8 Mar 1995 09:25:23 +1000 Date: Wed, 8 Mar 1995 09:25:23 +1000 Message-Id: <199503072325.JAA28130@huxley.anu.edu.au> To: TILBROOK@chem.surrey.ac.uk Subject: frequency scaling. Cc: aps501@anugpo.anu.edu.au Hi, I can't say where the mopac frequency scaling factor of 0.893 came from but it looks awfully close to the HF/6-31g* scale factor derived by us. I suspect that a comprehensive study similar to our one has not been carried out for the semi-empirical methods. The scale factor is of course designed to correct fot he harmonic frequencies calculated being compared to anharmonic frequencies found by experiment. See our paper: Isr. J. Chem. 33, 1993 p345 Hope this helps. Kind regards, Anthony P. Scott Research Officer Computational Chemistry Group Research School of Chemistry Australian National University Canberra, ACT, Australia ========================================================================== From: John Sichel Sender: John Sichel Reply-To: John Sichel Subject: Re: CCL:Modelling IR Vibrational Modes. To: David In-Reply-To: Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; CHARSET=US-ASCII On Tue, 7 Mar 1995, David wrote: > 3. Can anybody tell me why this 'magic number' 0.9? Is there any > theoretical basis for it's use or is it simply a fudge factor that > seems to work? This question was asked by Peter Gedeck about two months ago. I attach a copy of his summary dated 10 Jan 1995 which I saved in my files. There may be more in the CCL archives at about the same date. John Sichel, Universite de Moncton, Moncton, NB, Canada Date: Tue, 10 Jan 1995 13:42:20 +0100 (NFT) From: Peter Gedeck To: CHEMISTRY@ccl.net Cc: Peter Freunscht , czernek@chemi.muni.cz, jabs@cis.biochemtech.uni-halle.de Subject: CCL:Summary - Scaling of vibrational frequencies I received a lot of responses for the following question: >this time I would like to ask, why vibrational frequencies are usually >scaled by a factor (0.89-0.9)? > >As far as I know, this is independent of the calculational method used >(ab-initio or semiempirical). So, is it a deficiency of the theoretical >approach or is it just a question of the accuracy of the calculation? Thanks a lot to all who replied, Peter Gedeck ============================================================ Summary - Scaling of vibrational frequencies: ------------------------------------------------------------ Suggested literature: o J. A. Pople, R. Krishnan, H. B. Schlegel, D. DeFrees, J. S. Binkley, M. J. Frisch, R. F. Whiteside, R. F. Hout and W. J. Hehre, Int. J. Quantum Chem., Quantum Chem. Symposium, 15 (1981) 269. o MP2 scaling D. J. DeFrees, J Comp Chem 82 (1985) 333. o B.H. Besler, et.al., J. Chem. Phys. 89(1) (1988) 360. o Possible sources of error in empirical scaling... C. L. Janssen and H. F. Schaefer, J Chem Phys 95 (1991) 5128. o J.F. Stanton, et.al., J. Chem. Phys. 94(1) (1991) 404. o M. Flock and M. Ramek, Int J. Quantum Chem., Quantum Chem. Symposium 27 (1993) 331-341. o There is also a recent (ca. 1993) paper by Pople et al in Israel J Chem on scaling MP2 freqs. o A. P. Scott et.al. Israel J. Chem. 33 (1993) 345. o Ab Initio Molecular Orbital Theory - by Hehre, Radom, Schleyer and Pople. (Wiley, New York, 1986) Possible reasons for the deficiency of simple HF-calculations: Vibrational frequencies are usually calculated from the normal mode frequencies using a harmonic osciallator model - Zero point energy - Anharmonicity in the vibrational potential energy surface - Basis sets are too small - neglect of electron correlation - the Hartree-Fock potential is too steep and therefore frequencies too high. ============================================================ Following are all responses (edited): ------------------------------------------------------------ From: Dave Young The answer is that all of these frequencies are being computed with a harmonic oscilator approximation. For high frequency modes, the difference between the harmonic oscilator prediction and the exact or Morse potential like behavior is about 10% . If you try to look at very low frequency modes, below a few hundred wave numbers, you will see that the frequencies calculated are off by a large amount. ------------------------------------------------------------ From: "David W. Ewing (216) 397-4241" There are three sources of error in the calculation of vibrational frequencies via ab initio methods: calculated frequencies are usually harmonic, basis sets are too samll, and electron correlation is neglected or inadequately treated. For discussions of the last two factors, see B.H. Besler, et.al., J. Chem. Phys. 89(1), 360 (1988). J.F. Stanton, et.al., J. Chem. Phys. 94(1), 404 (1991). ------------------------------------------------------------ From: Anthony P Scott The scaling of calculated harmonic vibrational frequencies to match the experimentally determined (anharmonic) vibrational frequencies is designed to allow for the harmonic approximation that is used in the theoretically determined values. Our paper, Israel J. Chem. 1993, 33, 345 is a good place to start when exploring this. ------------------------------------------------------------ From: Doug Fox The vibrational frequencies predicted by ab initio and semi empirical methods are almost all harmonic approximations and limited in some respect by the dissociation behaviour of the underlying method. The first approximation tends to produce values higher than experimental due to the lack of anharmonic corrections. The improper dissociation behaviour also tends toward high estimates because most SCF based methods tend not to dissociate and single configuration representations tend to be worse away >from equilibrium. The remarkable result of the above facts is that for a wide range of molecules studied at the HF level a scaling of 0.89 or about about 12% brings the frequencies into good agreement with experiment. Much better than attempting to correct the problem with high order correlation treatments. A different scaling should be used for MP2 or higher order corrected methods but as you noted often this is not done. There is a good bit of discussion of the results in "Ab Initio Molecular Orbital Theory" by Hehre, Radom, Schleyer and Pople. There are some recent papers which are revisiting this issue. Aue and co-workers have told me they have one in press using MP2 results. ------------------------------------------------------------ From: "E. Lewars" The general belief seems to be that it's because the calculations (which use the eigenvalues of a force constant matrix) assume the vibrations are harmonic. However, it has been claimed that "this straightfoward looking consideration is wrong..."; see M. Flock and M. Ramek, Int J. Quantum Chem., Quantum Chem. Symposium 27, 331-341 (1993). Some other refs to vib freq scaling are Possible sources of error in empirical scaling... C. L. Janssen and H. F. Schaefer, J Chem Phys 1991 95 5128. MP2 scaling D. J. DeFrees, J Comp Chem 1985 82 333. There is also a recent (ca. 1993) paper by Pople et al in Israel J Chem on scaling MP2 freqs. ------------------------------------------------------------ From: Per-Ola Norrby It's a little of both. If you look at earlier postings to this list, you can see that the correction factors are different for different levels of theory, so low level calculations are certainly slightly deficient in the description of the energy hypersurface. However, vibrational frequencies are usually calculated from the Hessian with no consideration of higher derivatives. This gives an harmonic approximation, resulting in a slightly to "hard" system and too high calculated frequencies. Naturally, having one scaling factor for all frequencies at one level of theory is an oversimplification, but I don't know of anyone who tried anything more complicated. If you do, it might not be "ab initio" anymore... ------------------------------------------------------------ From: Csonka Gabor The IR scaling factor IS method dependent. The 0.9 is for HF. For MP2 you should use different scaling. For DFT or CCSD(T) you usually get the correct harmonic frequencies within an error bar, so no scaling is necessary. The scaling is mainly for the zero point energy, and it may give wrong results for individual freqs. I refer to Hehre et al.: ad Initio MO Theory book (Wiley, 1986) and the work P. Pulay and G. Fogarasy ------------------------------------------------------------ From: Adel El-Azhary The ab initio frequencies calculated at the Hartree Fock level are usually overestimated by about 10-20%. This is due to the incompletness of the basis set used, neglect of anharmonicity and neglect of the electron correlation. Frequencies calculated at the MP2 level of theory are overestimated by about 5-10%. This is due to inclusion of the electron correlation at the second level but higher excitations in the wave funcation are also neglected. You can look at the JPC, 1987, there is a paper by R. Amos about furan, pyrrole and thiophene. These is also a paper accepted for publication very recently by Petr Bour in the JPC where frequencies were calculated at the HF, MP2 and MP2 anharmonic also. This is in addition to the other references mentioned in the e-mail you received through the CCL. ------------------------------------------------------------ From: Janet Del Bene <@vm.gmd.de:FR042008@YSUB.BITNET> Ab initio calculations of vibrational frequencies at the Hartree-Fock level are too high compared to experimental frequencies. The scaling (0.89) is an empirical adjustment that brings the computed frequencies into better agreement with the experimental. That computed Hartree-Fock frequencies are too high is a result of two factors: 1) the computed frequencies are based on a parabolic potential and are harmonic, whereas the experimental frequencies are anharmonic; 2) the Hartree-Fock potential is too steep and as a result, frequencies are too high. ------------------------------------------------------------ From: @uunet.uu.net:aefrisch@m10.UUCP (AEleen Frisch) The reference for the HF frequency scale factor is: J. A. Pople, R. Krishnan, H. B. Schlegel, D. DeFrees, J. S. Binkley, M. J. Frisch, R. F. Whiteside, R. F. Hout and W. J. Hehre, Int. J. Quantum Chem., Quantum Chem. Symposium, 15, 269 (1981). Scaling is done to account for well-known, systematic errors in Hartree-Fock frequencies due to its neglect of electron correlation. ------------------------------------------------------------ From: Kui Zhang The fellowing paper and book will answer your question: J.A. Pople et al, Ab Initio Molecular Orbital Theory (Wiley, New York, 1986). H.F. Schaefer III et al, J. Chem. Phys. 95, 5128 (1991). ------------------------------------------------------------ From: Eric Bittner The scaling looks like a fudge factor to compensate for zero point energy and anharmonicity in the vibrational potential energy surface. In most structure calculations, the vbrational frequencies are just the normal mode frequencies...i.e harmonic classical motion. ------------------------------------------------------------ From: Patrick Bultinck Well, you can't really call it a deficiency in the calculation, but there is a deficiency in the model used for the vibrations... it's the harmonic approximation. This way you get frequencies that are too big, and that's why we use a 0.89 scaling factor. Intensities are even worse, they use the double harmonic approximations... I think about every book on advanced QC will give some insight (Daudel e.g., Pople et al. "Ab Initio MO theory...) ------------------------------------------------------------ From: Earl EVLETH p 74208 The scaling factor 0.89 came from HF 6-31G* level calculations. Larger basis sets might change that scaling and MP2 level calculations at the 6-31G* will change it into the 0.95 or 0.96 range. However, Pulay showed years ago when he did his modeling of various structures, scaling factor depends on the type of vibration one is dealing with, i.e. bond stretching, bond bending, and torsional modes. He scaled force constants, not the final vibrational frequencies. Therefore, the 0.89 magic number is just a convenient, practically off-the-top-of-one's-head factor useable for HF 6-31G* calculations. The computed low energy torsional modes are largely fiction and scaling or not scaling them is a technical detail. As for nearly pure bending and stretching (little coupling) these might be pretty good. Some people find that good old semiempirical calculations gives good unscaled results! ------------------------------------------------------------ Peter Gedeck Inst. f. Physikalische Chemie I Egerlandstrasse 3 91058 Erlangen Germany Tel: ++9131 - 85 7335 Fax: ++9131 - 85 8307 E-Mail: gedeck@pctc.chemie.uni-erlangen.de WWW: http://pctc.chemie.uni-erlangen.de/~gedeck/gedeck.html =========================================================================== From: bittner@czar.cm.utexas.edu (Eric Bittner) Subject: Re: CCL:Modelling IR Vibrational Modes. > 1.If you are doing MD work what kind of time scale and duration do > you have to run on to get reasonable results? If you're really interested in simulating IR spectra, you really should solve the problem via quantum mechanics by either diagonalizing the vibrational hamiltonian for a given potential surface or via wavepacket propagation. Both are very expensive for more than a few degrees of freedom. For MD work, the normal mode spectral should be pretty close to the exact vibrational spectra for covalent and ionic bonds. Wilson, Decius, and Cross (Molecular Vibrations) discusses how to include anharmonic effects, etc... > > 2. What kind of scaling do you find is necessary to give good values > for vibrational frequencies? > > 3. Can anybody tell me why this 'magic number' 0.9? Is there any > theoretical basis for it's use or is it simply a fudge factor that > seems to work? No deep theoretical basis, the scaling is basically a fudge factor to account for zero point motion, anharmonicity, etc... Regards, Eric Bittner ============================================================================= From: "Clifford LeMaster" Organization: Boise State University Experimental frequencies need to be corrected for anharmonicity. This correction is typically 10-12% hence the 0.9 factor to "lower" the theoretical values. I believe that you may expect Hartree-Fock level vibrational calculations to normally be within ~5% of the corrected experimental values. These values may be on the high side but the inclusion of electron correlation should help to lower them. by shortening the bond lengths. ========================================================================================= Again many thanks to those who responded Regards David Tilbrook From steve@carbo.chem.binghamton.edu Tue Mar 7 21:10:28 1995 Received: from carbo.chem.binghamton.edu for steve@carbo.chem.binghamton.edu by www.ccl.net (8.6.10/930601.1506) id UAA20327; Tue, 7 Mar 1995 20:53:00 -0500 Received: by carbo.chem.binghamton.edu (931110.SGI/931108.SGI.ANONFTP) for chemistry@ccl.net id AA08859; Tue, 7 Mar 95 20:42:37 -0500 Date: Tue, 7 Mar 1995 20:36:41 -0500 (EST) From: Steven Schafer Subject: Re: Drug Design? To: chemistry@ccl.net Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII I recently posted a question: Does anyone know if there are any drugs that have been designed with computer techniques and are now legally availible in the marketplace? ... I received many response, including a few that said my question was a F.A.Q. question. In the interest of conserving bandwidth, since it is a fairly large file, I will be sending the summary to people who have asked me to send it to them. If you have not mailed me and would like me to send it to you just drop me a line. I will be sending the summary within the next few days. Steven E. Schafer S.U.N.Y. Binghamton Chemistry Department http://chemiris.chem.binghamton.edu:8080 Binghamton, New York USA From mmccar@postman.essex.ac.uk Tue Mar 7 10:02:51 1995 Received: from postman.essex.ac.uk for mmccar@postman.essex.ac.uk by www.ccl.net (8.6.10/930601.1506) id KAA08132; Tue, 7 Mar 1995 10:00:18 -0500 Received: from postman.essex.ac.uk by postman.essex.ac.uk with SMTP (PP) id <04660-0@postman.essex.ac.uk>; Tue, 7 Mar 1995 14:59:50 +0000 From: Mccarron M Date: Tue, 7 Mar 95 14:59:48 GMT Message-Id: <20272.9503071459@solb1.essex.ac.uk> To: chemistry Subject: CHARMM Status: R Has anybody out there got any explanatory free enrgy component analysis scripts e.g. BLOCK COMP .... thanks in advance mmccar@essex.ac.uk