From rameshg@phar.umich.edu Mon Apr 17 00:00:34 1995 Received: from iris.phar.umich.edu for rameshg@phar.umich.edu by www.ccl.net (8.6.10/930601.1506) id XAA07863; Sun, 16 Apr 1995 23:50:50 -0400 Received: from iris.phar.umich.edu (iris.phar.umich.edu [35.211.128.3]) by iris.phar.umich.edu (8.6.10/8.6.10) with SMTP id XAA06557 for ; Sun, 16 Apr 1995 23:49:50 -0400 Date: Sun, 16 Apr 1995 23:49:49 -0400 (EDT) From: Ramesh Gopalaswamy To: chemistry Subject: mm2 params/summary Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hello All, Last week I had posted a question reg. refs. for mm2 params. I got very helpful suggestions and info from many of you. My sincere thanks for all those people :^) A summary of the responses along with my original posting follows: Could anyone give refs for mm2-parameter updates after 1985? I have been using mm2-85 force field as provided with Cerius2. For some of my molecules I get a warning about undefined torsional params. I'm attaching that message at the end of this mail. My guess is the warning has to do with alpha,beta-unsatd carbonyl system in these molecules. So my question is, any ideas about publications in which these parameters are updated? If not, is it OK to ignore these "undefined params" ? How much would these torsional energies contribute to overall energy. The energies (atleast relative) are important to me as I need to save low energy conformers of these molecules. I really do not want to change force fields at this point :( as I have already made some progress with mm2-85 and plus as these are small organic molecules (steroids) mm2 is most appropriate, right? ****************************************************************************** The warning message from Cerius2 is as follows: Reading force field from: ./Cerius2-Resources/FORCE-FIELD/untested/mm2_85_1.01 Finished reading force field parameter file. WARNING: The following force field atom types have undefined torsions parameters. O_3_L C_3 C_2+ C_3 O_3_L C_3 C_2+ O_2+ Torsion terms are missing. Quitting energy expression setup. All terms with missing parameters may be ignored if the `ignore undefined terms` toggle is turned on. See `Open Force Field/Energy Expression/Setup.` Automatic setup for model ste8 failed ****************************************************************************** Please send your suggestions to me directly. Thanks in advance for your help. Ramesh ............................................................................. From: Lipkowitz I have an appendix in the next volume of Reviews in Computational Chemistry that will help you. The appendix has listed, by force field, references to published molecular mechanics parameters. This volume of Reviews in Computational Chemistry, vol.6, will be available for purchase by your library this June. I can not send you the material directly because of copyright agreement with VCH but I can tell you that this will be in your library soon (assuming your library subscribes to Rev. Comp. Chem.) I hope this helps you in your future modeling work. Kenny ................................................................... From: Jane-Jane Ou I don't know if this paper is right for you, "A Molecular Mechanics (MM2) Study of Furan, Thiophene, and Related Compounds" by Lii&Allinger in Journal of Comuptational Chemistry, Vol.10, No.5, 635-647 (1989). .................................................................. From: "Yuriev, Elizabeth" Hi Ramesh, I found the compilation of references on MM2 parameters by K.Lipkowitz [1] very useful, though it was done in 1992 which is "very long ago" :-). (From this compilation ref. for alpha,betta-unsaturated ketones [2].) Also the recent paper by Dr.N.Allinger [3] developes a scheme on how to specify missing parameters in MM2 and MM3. [1].MM2 Parameters. K.Lipkowitz. QCPE Bulletin, 1992, V.12, p.6-11. [2].D.W.Moreland and W.G.Dauben JACS, 1985, V.107, p.2264-2273. [3].Molecular Mechanics Parameters. N.L.Allinger, X.Zhou, J.Bergsma J.Mol.Structure(Theochem)312(1994)69-83 Of course, there are a lot of other publications around on the parametrization of MM2, but IMHO these two are fundamental and a good place to start. Hope this helps. ................................................................. From: David White Ramesh, This file might help: it contains the full set of MM2 parameters (including the MANY which Cerius2 does not contain). The parameters marked with an * are preliminary. I got the file from Dr. Allinger at the University of Georgia. Good luck Dave ******************************************************************** NOTE: I'm not including the file Dave White had sent me, for the sake of saving band width. If anyone's interested, I can mail it to them (Dave said I could). ********************************************************************* From: "Gregory L. Durst - DowElanco R&D" Kenny Lipkowitz published a very useful review of MM2 parameters in "QCPE Bulletin", vol 12, No 1, Feb 1992, pg 6-11. It is a compilation of published papers that contain MM2 parameters. >From Kenny's compilation I found the following: "Enols and B-alkoxy a-B-unsaturated ketones", D.W. Moreland & W.G. Dauben, "JACS", v107, (1985), 2264-2273. Regards, Greg ...................................................................... From: "Felice Chu" Hello, Ramesh, I read your mm2 parameter question on ccl. In my experience the torsional parameters can contribute a significant amount to the overall steric energy and especially to the conformation. Your results are only as good as your parameters. From Allinger's book, I get the impression that he would like the MM energies to be comparable to experimental energies. If that is the way you wish to use your results then missing 2 torsional parameters will change the outcome. Looking at your undefined parameters, my recommendation is to use the new MM3(94). I believe MM3(92) has much better parameters for oxygen (ketones, esters, acids) than MM2. At the recent ACS meeting, there was some discussion about the accuracy of the O-C-C-O parameter. It seems that MM3(94) has fixed that problem. As for references : P. Aped and N. L. Allinger, J. Amer. Chem. Soc., 114, 1 (1992) N. L. Allinger and A. Pathiaseril, J. Comput. Chem., 8, 1225, (1987) J. Tai and N. L. Allinger, J. Amer. Chem. Soc., 110, 2050,(1988) J. C. Tai, J.-H. Lii, and N. L. Allinger, J. Comput. Chem., 10, 635 (1989) N. L. Allinger, R. A. Kok, and M. R. Imam, J. Comput. Chem., 9, 591 (1988) J.-H. Lii and N. L. Allinger, J. Comput. Chem., 17, 186 (1991) J. T. Sprague, J. C. Tai, Y. Yuh, and N. L. Allinger, J. Comput. Chem., 8, 581 (1987) T. Liljefors, J. C. Tai, S. Li, and N. L. Allinger, J. Comput. Chem., 8, 1051 (1987) N. L. Allinger, et al. J. Amer. Chem. Soc., 114, 2880, (1992) There are also several MM3 papers starting in 1989 I would appreciate a summery of your responses. Good luck, Felice Lightstone From rameshg@phar.umich.edu Mon Apr 17 00:15:37 1995 Received: from iris.phar.umich.edu for rameshg@phar.umich.edu by www.ccl.net (8.6.10/930601.1506) id AAA08217; Mon, 17 Apr 1995 00:11:38 -0400 Received: from iris.phar.umich.edu (iris.phar.umich.edu [35.211.128.3]) by iris.phar.umich.edu (8.6.10/8.6.10) with SMTP id AAA07019 for ; Mon, 17 Apr 1995 00:10:39 -0400 Date: Mon, 17 Apr 1995 00:10:38 -0400 (EDT) From: Ramesh Gopalaswamy To: chemistry Subject: mm2 params/summary2 Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII To add to my summaryof responses posted earlier, ......................................................................... From: MARTIN@cmda.abbott.com You probably need MMP2 for such a system. Allinger will send out all parameters he has. Just send a reprint request for MM2 parameters. Yvonne Martin Abbott laboratories ........................................................................... Thanks again for all your help. From CUNDARIT@MSUVX1.MEMPHIS.EDU Mon Apr 17 11:32:02 1995 Received: from msuvx1.memphis.edu for CUNDARIT@MSUVX1.MEMPHIS.EDU by www.ccl.net (8.6.10/930601.1506) id LAA14520; Mon, 17 Apr 1995 11:28:17 -0400 From: Received: from MSUVX1.MEMPHIS.EDU by MSUVX1.MEMPHIS.EDU (PMDF V4.3-8 #7188) id <01HPFXP2YLRK9B06PD@MSUVX1.MEMPHIS.EDU>; Mon, 17 Apr 1995 10:31:50 -0500 (CDT) Date: Mon, 17 Apr 1995 10:31:50 -0500 (CDT) Subject: Kinetic Simulation Software To: chemistry@ccl.net Message-id: <01HPFXP2ZXZM9B06PD@MSUVX1.MEMPHIS.EDU> X-VMS-To: IN%"chemistry@ccl.net" MIME-version: 1.0 Content-type: TEXT/PLAIN; CHARSET=US-ASCII Content-transfer-encoding: 7BIT Hi, A colleague of mine at U Memphis is trying to solve simultaneuous ordinary diff eqs such as you would find in kinetics. Below is his sample description. ############################################################################ I am trying to solve simultaneously the following ODEs: dY/dt = k1.X - k2.Y + K3.X.Y - K4.X.Z + K5.Y.Z + K6.X.W - K7.Y.W + K8.Y^2 - K9.Y.Z dZ/dt = K5.X.Z - K6.Y.Z + K9.Y.Z + K11.Y.Z - K12.Z^2 + K13.Y - K14.Z dW/dt = K7.X.W + K15.Z - K16.W + K17.W.Z + K19.Z.W - K20.W^2. X, Y, Z and W are all functions of t. k1, k2, k3, k4, .......k20 are parameters to be estimated. constraints: k1, k2,.....are all positive and lie between 0 and 100. initial conditions can be assumed to be x(t=0) = 40, y(t=0)=z(t=0)=w(t=0)= 0. sample data set: t x y z w 1 50 5 2 1 2 45 9 1 3 3 60 6 2 5 4 55 6 3 7 5 50 8 3 10 6 40 10 5 15 7 35 8 6 18 ############################################################################ If anyone has any suggestions about software for carrying out such a task we would be most appreciative. Tom Cundari +===+===+===+===+===+===+===+===+===+===+===+===+===+===+===+===+===+===+===+=== Thomas R. Cundari Asst. Professor of Chemistry Computational Inorganic Chemistry Lab University of Memphis Memphis, TN 38152 phone: 901-678-2629 fax: 901-678-3447 e-mail: cundarit@cc.memphis.edu http://www.memst.edu/chemistry/umchem.html +===+===+===+===+===+===+===+===+===+===+===+===+===+===+===+===+===+===+===+=== From polowin@hyper.hyper.com Mon Apr 17 12:45:50 1995 Received: from www.hyper.com for polowin@hyper.hyper.com by www.ccl.net (8.6.10/930601.1506) id MAA16199; Mon, 17 Apr 1995 12:39:35 -0400 Received: from hyper.hyper.com (hyper.hyper.com [204.50.3.217]) by www.hyper.com (8.6.9/8.6.9) with SMTP id MAA11097 for <@www.hyper.com:CHEMISTRY@ccl.net>; Mon, 17 Apr 1995 12:32:36 -0400 Received: by hyper.hyper.com (920330.SGI/920502.SGI) for @www.hyper.com:CHEMISTRY@ccl.net id AA11390; Mon, 17 Apr 95 12:52:01 -0400 Date: Mon, 17 Apr 95 12:52:01 -0400 From: polowin@hyper.hyper.com (Joel Polowin) Message-Id: <9504171652.AA11390@hyper.hyper.com> To: CHEMISTRY@ccl.net Subject: Hypercube Press Releases available: HyperChem 4.5 On April 2, 1995, at the ACS meeting in Anaheim, Hypercube Inc. issued a pair of press releases about our forthcoming *HyperChem Release 4.5 for Windows* and *HyperChem Release 4.5 for SGI* software. Jan Labanowski was kind enough to place the press releases in the CCL archives for people to access by ftp, WWW, or gopher (port 73): gopher://www.ccl.net:73/00/info/software-packages/Hypercube-ab-initio gopher://www.ccl.net:73/00/info/software-packages/Hypercube-sgi or via e-mail by sending a message: select chemistry get info/software-packages/Hypercube* to MAILSERV@ccl.net The first press release describes the new features that have been added to Release 4.5 of HyperChem for Windows -- primarily ab initio functionality -- while the second describes in somewhat greater detail the abilities of the SGI package. (The improvements from the last SGI version, Release 2, to the new Release 4.5 are considerable.) Regards, Joel ------------ Joel Polowin, Ph.D. Manager, Scientific Support Email to: polowin@hyper.com Hypercube Inc, 7-419 Phillip St, Waterloo, Ont, Canada N2L 3X2 (519)725-4040 Info requests to: info@hyper.com Support questions to: support@hyper.com Email group: Send "subscribe hyperchem" to hyperchem-request@hyper.com WWW: http://www.hyper.com/ From Thorsten.Kluener@RUBA.RZ.ruhr-uni-bochum.de Mon Apr 17 13:00:51 1995 Received: from rubb.rz.ruhr-uni-bochum.de for Thorsten.Kluener@RUBA.RZ.ruhr-uni-bochum.de by www.ccl.net (8.6.10/930601.1506) id MAA16061; Mon, 17 Apr 1995 12:33:59 -0400 From: Received: from ruba.rz.ruhr-uni-bochum.de (ruba_el.rz.ruhr-uni-bochum.de [134.147.192.2]) by rubb.rz.ruhr-uni-bochum.de (8.5/8.5) with SMTP id SAA18566; Mon, 17 Apr 1995 18:33:17 +0200 Received: from DE*D400*RUHR-UNI-BOCHUM by RUBA.RZ.RUHR-UNI-BOCHUM.DE via QTFS with X.400; Mon, 17 Apr 1995 18:31:47 +0200 X400-Received: by /PRMD=RUHR-UNI-BOCHUM/ADMD=D400/C=DE/ ; Relayed ; Mon, 17 Apr 1995 18:31:45 +0200 X400-Received: by mta MTARUBA ; Relayed ; Mon, 17 Apr 1995 18:31:46 +0200 Date: Mon, 17 Apr 1995 18:31:45 +0200 Message-Id: <950417183011202-MTARUBA*Thorsten.Kluener@RUBA.RZ.ruhr-uni-bochum.de> P1-Message-ID: DE*D400*RUHR-UNI-BOCHUM; 950417183011202-MTARUBA UA-Content-ID: 950417183011202- Subject: SGI INDY and PCNFSD Problems ?! Autoforwarded: FALSE To: Chemistry@ccl.net Dipl.-Chem. Thorsten Kluener Ruhr-Universitaet Bochum Fakultaet fuer Chemie Lehrstuhl fuer Physikalische Chemie 1 Universitaetsstr. 150 D-44780 Bochum Telefon (0234) 700-4219 Telefax (0234) 7094-182 Email: Thorsten.Kluener@ ruba.rz.ruhr-uni-bochum.de Hello everybody ! I have a special problem which is not directly connected to computational chemistry but maybe someone has an idea: I am responsible for a network including 20 personal computers and four INDY-Workstations of Silicon Graphics. The File- and Printserver of our net runs PCNFSD is NIS Server (IRIX5.3) and shows very often system crashes (KERNEL FAULTS, SGV, Read addrres errors, bus errors). The hardware has been checked and is o.k. Most crashes occur when there is network activity of the PC's on a UNIX disk. Does anybody know if there are any known bugs or incompatibilities between IRIX 5.3 and PCNFSD. Any help or idea is welcome. Thank you very much Thorsten From ars@ari.net Mon Apr 17 13:30:45 1995 Received: from mtolympus.ari.net for ars@ari.net by www.ccl.net (8.6.10/930601.1506) id NAA17196; Mon, 17 Apr 1995 13:27:44 -0400 Received: from arsoftware.ari.net (arsoftware.ari.net [198.69.192.82]) by mtolympus.ari.net (8.6.5/8.6.5) with SMTP id NAA20543 for ; Mon, 17 Apr 1995 13:19:16 -0400 Date: Mon, 17 Apr 1995 13:19:16 -0400 Message-Id: <199504171719.NAA20543@mtolympus.ari.net> X-Sender: ars@mtolympus.ari.net (Unverified) X-Mailer: Windows Eudora Version 1.4.4 Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" To: CHEMISTRY@ccl.net From: ars@ari.net (ARSoftware Corporation) Subject: Re: CCL:Kinetic Simulation Software >To: >From: ars@ari.net (ARSoftware Corporation) >Subject: Re: CCL:Kinetic Simulation Software > >>Hi, >> >> A colleague of mine at U Memphis is trying to solve simultaneuous >>ordinary diff eqs such as you would find in kinetics. >> >>Below is his sample description. >> >>############################################################################ >>I am trying to solve simultaneously the following ODEs: >> >> >> dY/dt = k1.X - k2.Y + K3.X.Y - K4.X.Z + K5.Y.Z + K6.X.W - K7.Y.W + K8.Y^2 - >> K9.Y.Z >> >> dZ/dt = K5.X.Z - K6.Y.Z + K9.Y.Z + K11.Y.Z - K12.Z^2 + K13.Y - K14.Z >> >> dW/dt = K7.X.W + K15.Z - K16.W + K17.W.Z + K19.Z.W - K20.W^2. >> >> >> X, Y, Z and W are all functions of t. >> k1, k2, k3, k4, .......k20 are parameters to be estimated. >> constraints: k1, k2,.....are all positive and lie between 0 and 100. >> >> initial conditions can be assumed to be x(t=0) = 40, y(t=0)=z(t=0)=w(t=0)= 0. >> >>sample data set: >> >> t x y z w >> 1 50 5 2 1 >> 2 45 9 1 3 >> 3 60 6 2 5 >> 4 55 6 3 7 >> 5 50 8 3 10 >> 6 40 10 5 15 >> 7 35 8 6 18 >>############################################################################ >> >>If anyone has any suggestions about software for carrying out such a task >>we would be most appreciative. >> >>Tom Cundari > Kinetics for Windows is a PC based software which will write your differential equations and solve them. It has an easy to use graphical user interface and gives you a plot of concentration vs. time. The user can add up to 100 reversible reactions, with their starting concentrations and the rate contstants, and the program does the rest. Contact ARSoftware (ars@ari.net). Leave an address or fax number if you'd like more information. > >Sincerely, > >Sat Want S. Khalsa >Marketing Manager >ARSoftware > ===================================================== ARSoftware Corporation 8201 Corporate Drive Landover, MD 20785 Phone: (301) 459-3773 FAX: (301) 459-3776 e-mail: ars@ari.net From raman@bioc01.uthscsa.edu Mon Apr 17 13:45:52 1995 Received: from thorin.uthscsa.edu for raman@bioc01.uthscsa.edu by www.ccl.net (8.6.10/930601.1506) id NAA17410; Mon, 17 Apr 1995 13:42:46 -0400 Received: from bioc01.uthscsa.edu by thorin.uthscsa.edu with SMTP; Mon, 17 Apr 1995 12:46:32 -0500 (CDT) Received: by bioc01.uthscsa.edu (4.1/SMI-4.1) id AA02252; Mon, 17 Apr 95 12:42:46 CDT From: raman@bioc01.uthscsa.edu (C.S.RAMAN) Message-Id: <9504171742.AA02252@bioc01.uthscsa.edu> Subject: Re: CCL:Kinetic Simulation Software To: CUNDARIT@MSUVX1.MEMPHIS.EDU Date: Mon, 17 Apr 1995 12:42:45 -0500 (CDT) Cc: chemistry@ccl.net In-Reply-To: <01HPFXP2ZXZM9B06PD@MSUVX1.MEMPHIS.EDU> from "CUNDARIT@MSUVX1.MEMPHIS.EDU" at Apr 17, 95 10:31:50 am X-Mailer: ELM [version 2.4 PL3] Content-Type: text Content-Length: 2358 Tom: > A colleague of mine at U Memphis is trying to solve simultaneuous > ordinary diff eqs such as you would find in kinetics. > My recommendation would be to go with KINSIM and FITSIM suite of programs developed by Carl Frieden and associates. It is very powerful and I like it a lot with respect to ease of use and flexibility in kinetic modelling. Versions for Mac, PC and the SGI are available free of charge from wuarchive.wustl.edu (via anon. FTP of course). I am including the reference of a recent review which discusses the capabilities of these programs at length: FRIEDEN C. NUMERICAL INTEGRATION OF RATE EQUATIONS BY COMPUTER - AN UPDATE. TRENDS IN BIOCHEMICAL SCIENCES, 1994 APR, V19 N4:181-182. Software Review. This ftp site is very busy until the evening hours and I would strongly recommend that you try ftp after 1900 hrs. Cheers -raman -- _/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/ _/ _/ _/ C.S.RAMAN _/ _/ Department of Biochemistry _/ _/ University of Texas Health Science Center _/ _/ 7703 Floyd Curl Drive _/ _/ San Antonio, TX 78284-7760 _/ _/ USA _/ _/ _/ _/ Tel: (210) 567-6623 _/ _/ Fax: (210) 567-6595 _/ _/ E-mail: raman@bioc01.uthscsa.edu _/ _/ _/ _/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/ _/ _/ _/ How can it be that mathematics, a product of human thought _/ _/ independent of experience, is so admirably adapted to the _/ _/ objects of reality? -Albert Einstein _/ _/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/ From omni@ufba.br Mon Apr 17 14:00:47 1995 Received: from canudos.ufba.br for omni@ufba.br by www.ccl.net (8.6.10/930601.1506) id NAA17589; Mon, 17 Apr 1995 13:47:37 -0400 Received: by canudos.ufba.br (AIX 3.2/UCB 5.64/4.03) id AA13036; Mon, 17 Apr 1995 14:38:17 -0300 Date: Mon, 17 Apr 1995 14:38:16 -0300 (GRNLNDST) From: Oswaldo Rodrigues Leite Filho To: CUNDARIT@MSUVX1.MEMPHIS.EDU Cc: chemistry@ccl.net Subject: Re: CCL:Kinetic Simulation Software In-Reply-To: <01HPFXP2ZXZM9B06PD@MSUVX1.MEMPHIS.EDU> Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Try http://gams.nist.gov/ There are a lot of math soft there. Oswaldo Leite On Mon, 17 Apr 1995 CUNDARIT@MSUVX1.MEMPHIS.EDU wrote: > Hi, > > A colleague of mine at U Memphis is trying to solve simultaneuous > ordinary diff eqs such as you would find in kinetics. > > Below is his sample description. > > ############################################################################ > I am trying to solve simultaneously the following ODEs: > > > dY/dt = k1.X - k2.Y + K3.X.Y - K4.X.Z + K5.Y.Z + K6.X.W - K7.Y.W + K8.Y^2 - > K9.Y.Z > > dZ/dt = K5.X.Z - K6.Y.Z + K9.Y.Z + K11.Y.Z - K12.Z^2 + K13.Y - K14.Z > > dW/dt = K7.X.W + K15.Z - K16.W + K17.W.Z + K19.Z.W - K20.W^2. > > > X, Y, Z and W are all functions of t. > k1, k2, k3, k4, .......k20 are parameters to be estimated. > constraints: k1, k2,.....are all positive and lie between 0 and 100. > > initial conditions can be assumed to be x(t=0) = 40, y(t=0)=z(t=0)=w(t=0)= 0. > > sample data set: > > t x y z w > 1 50 5 2 1 > 2 45 9 1 3 > 3 60 6 2 5 > 4 55 6 3 7 > 5 50 8 3 10 > 6 40 10 5 15 > 7 35 8 6 18 > ############################################################################ > > If anyone has any suggestions about software for carrying out such a task > we would be most appreciative. > > Tom Cundari > > +===+===+===+===+===+===+===+===+===+===+===+===+===+===+===+===+===+===+===+=== > Thomas R. Cundari > Asst. Professor of Chemistry > Computational Inorganic Chemistry Lab > University of Memphis > Memphis, TN 38152 > phone: 901-678-2629 > fax: 901-678-3447 > e-mail: cundarit@cc.memphis.edu > http://www.memst.edu/chemistry/umchem.html > +===+===+===+===+===+===+===+===+===+===+===+===+===+===+===+===+===+===+===+=== > > -------This is added Automatically by the Software-------- > -- Original Sender Envelope Address: CUNDARIT@MSUVX1.MEMPHIS.EDU > -- Original Sender From: Address: CUNDARIT@MSUVX1.MEMPHIS.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 jle@toyota.wavefun.com Mon Apr 17 17:45:47 1995 Received: from volvo.wavefun.com for jle@toyota.wavefun.com by www.ccl.net (8.6.10/930601.1506) id RAA22888; Mon, 17 Apr 1995 17:33:38 -0400 Received: by volvo.wavefun.com (931110.SGI/930416.SGI) for chemistry@ccl.net id AA07230; Mon, 17 Apr 95 14:33:59 -0700 Received: from toyota.wavefun.com(198.147.95.4) by volvo via smap (V1.3) id sma007228; Mon Apr 17 14:33:31 1995 Received: by toyota.wavefun.com (931110.SGI/930416.SGI) for @volvo.wavefun.com:chemistry@ccl.net id AA23791; Mon, 17 Apr 95 14:33:14 -0700 From: "Joe Leonard" Message-Id: <9504171433.ZM23789@toyota.wavefun.com> Date: Mon, 17 Apr 1995 14:33:13 -0700 Reply-To: jle@wavefun.com X-Mailer: Z-Mail (3.1.0 22feb94 MediaMail) To: chemistry@ccl.net Subject: 6th row STO-NG* basis sets Content-Type: text/plain; charset=us-ascii Mime-Version: 1.0 Folks, I am interested in learning whether anybody has STO-NG* basis sets for the 6th row elements (Cs-Rn)... I have checked in a couple of places, but cannot find anything above Xe. Pointers or citations or the basis sets themselves appreciated! Joe -- ------------------------------------------------------------------------ Joe Leonard Wavefunction Inc. 18401 Von Karman, Suite 370 Irvine, CA 92715 I am a professional... 714-955-2120 do not attempt this at home. 714-955-2118 fax jle@wavefun.com From sunger@crl.com Mon Apr 17 18:45:49 1995 Received: from mail.crl.com for sunger@crl.com by www.ccl.net (8.6.10/930601.1506) id SAA23813; Mon, 17 Apr 1995 18:44:13 -0400 Received: from crl6.crl.com by mail.crl.com with SMTP id AA22430 (5.65c/IDA-1.5 for ); Mon, 17 Apr 1995 15:43:35 -0700 Received: by crl6.crl.com id AA25054 (5.65c/IDA-1.5); Mon, 17 Apr 1995 15:42:31 -0700 Date: Mon, 17 Apr 1995 15:42:30 -0700 (PDT) From: Stefan Unger To: "Jeffrey L. Nauss" Cc: CHEMISTRY@ccl.net Subject: Re: CCL:Searching for sequences In-Reply-To: <9504121351.AA22866@ucmod2.che.uc.edu> Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Protein Expert (for MAC and PowerMAC) will do this. You create a folder with whatever PDB files you want and it will then create a database of sequence, contact distance and phi/psi angles. You can then construct searches with up to five "positions". Each position can be an ambiguous sequence (e.g. "lipophilic"), or specific amino acid, distance or angle relationship. The hits are shown visually and data can also be output to, say, Excel. I am the distributor. Please contact me directly if you would like further information. BioSoftware Marketing 4151 Middlefield Rd., Ste 109 Palo Alto, Ca 94303-4743 415-858-0522 fx: 415-858-0521 On Wed, 12 Apr 1995, Jeffrey L. Nauss wrote: > > I want to search the PDB for structures that have the tripeptide > sequence Asn-X-Glu where X is any amino acid. The purpose of the > search is to identify possible structural motifs for the sequence > within proteins. Thus far, I have not found how to do this using the > Brookhaven search engines on the WWW. Does any one have a way to > perform this search? > > Alternatively, I could search sequence databases such as SWISS-Prot > and then cross-reference the hits with the PDB. However, I have yet > to find a way to perform the search using wildcards. > > Any suggestions? > > Thanks in advance... > 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://www.che.uc.edu/~nauss * > **************************************************************************** > > > -------This is added Automatically by the Software-------- > -- Original Sender Envelope Address: nauss@ucmod2.che.uc.EDU > -- Original Sender From: Address: nauss@ucmod2.che.uc.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 JDA03546@niftyserve.or.jp Mon Apr 17 19:45:52 1995 Received: from inetnif.niftyserve.or.jp for JDA03546@niftyserve.or.jp by www.ccl.net (8.6.10/930601.1506) id TAA24300; Mon, 17 Apr 1995 19:31:01 -0400 Received: by inetnif.niftyserve.or.jp (8.6.9+2.4W/3.3W8-950117-Mail-Gateway) id IAA03831; Tue, 18 Apr 1995 08:31:08 +0900 Message-Id: <199504172331.IAA03831@inetnif.niftyserve.or.jp> Date: Tue, 18 Apr 1995 08:29:00 +0900 From: =?ISO-2022-JP?B?GyRCQG5FZyEhSXAbKEI=?= Subject: [Summary]:IR intensity To: chemistry@ccl.net MIME-Version: 1.0 Content-Type: text/plain; charset=iso-2022-jp On Date: Thu, 06 Apr 1995 08:28:00 +0900, I posted the question about the IR intensity calculation. Some kind souls have sent me the comments. Here I thank them very much. The summary follows the original question. --- >>Dear CCL'ers >> >>We are trying to determine the orientation of the adsorbed molecules on >>the surface by IR using polarized light. It seems to be possible to calculate >>the intensity from each component of dipole moment derivetives, but are >>there any programs that can do this automatically or rather easy way? >>We have gaussian. >> >>Thanks in advance. --- Date: Wed, 5 Apr 1995 21:53:00 -0400 (EDT) From: Cheol Choi You can easily get the dipole moment derivatives from gaussian program. If you do frequency calculation, you will find a lot of numbers at the end of output files. After the kerword "DipolDeriv", you will have dipole derivative w.r.t cartesian coordinate. However, if you want to calculate IR intensity using it, you need also transformation matrix to normal coordinates. Best wishs Cheol-Ho, Georgetown Univ. --- Date: 6 Apr 95 09:20:20 GMT From: Dave I may have misunderstood your problem but the following would seem to pose a problem... How do you propose to carry out a Gaussian calculation for such a complexed system. I thought that such ab initio approaches were usually only applicable to small isolated systems. A better appraoch might be to try and model the adsorbed system using a MM force field which has been optimised for the prediction of vibrational frequencies and dipole moments. I believe MM3 and CFF91 do this quite well. In my work I trying to do reliable vibrational simulation using a velocity autocorrelation on MD data. We are doing this using the dynamics module under Cerius2 (by MSI). The parameter sets still need tweaking a bit though. In Cerius2 you can split the VAC and power spectrum into its anisotropic components I am not sure if this is what you want. Perhaps you should contact MSI to find out exactly what the significance of these axially resolved power spectra are. 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. * ********************************************************** --- Date: Thu, 6 Apr 1995 10:59:50 +0200 (SAST) From: Magan Govender - PG Dear Sir, As far as I am aware most programs perform a complete normal coordinate analysis requiring the dipole moment derivatives, which are summed and multiplied by a constant to give the intensities, bearing in mind the signs for each component. Some of the programs are Vibra by Dr.Steele, NCA, SPECTRO. I have the email addresses of the authors, if required I shall be pleased to forward them to you. Greetings from South Africa Magan ______________________________________________________________________ M.G. Govender Centre for Theoretical and Computational Chemistry Dept of Chemistry University of Natal King George V Avenue Durban South Africa --- It seems to me that your idea is OK to first order; however, in order to get the IR adsorption lineshapes and the relative intensities correct, I think you'll need to consider the substrate-adsorbate interactions. What kind of surface are the molecules adsorbed onto? Eric R Bittner Univ. of Texas at Austin