From JSMCM@jazz.ucc.uno.edu Tue Oct 8 00:53:52 1996 Received: from jazz.ucc.uno.edu for JSMCM@jazz.ucc.uno.edu by www.ccl.net (8.8.0/950822.1) id AAA03368; Tue, 8 Oct 1996 00:24:30 -0400 (EDT) Received: from jazz.ucc.uno.edu by jazz.ucc.uno.edu (PMDF V5.0-4 #11893) id <01IADNIODUQ8901BVN@jazz.ucc.uno.edu> for chemistry@www.ccl.net; Mon, 07 Oct 1996 23:19:57 -0600 (CST) Date: Mon, 07 Oct 1996 23:19:57 -0600 (CST) From: "Dr. Jorge Seminario" Subject: ACS Symposium on DFT (San Francisco) To: chemistry@www.ccl.net Message-id: <01IADNIOENO2901BVN@jazz.ucc.uno.edu> X-VMS-To: IN%"chemistry@www.ccl.net" X-VMS-Cc: JSMCM MIME-version: 1.0 Content-type: TEXT/PLAIN; CHARSET=US-ASCII Content-transfer-encoding: 7BIT ACS SYMPOSIUM ON DFT - SAN FRANCISCO Dear CCL Colleague: Since the deadline for abstracts is around the corner, I would like to suggest interested persons to send their abstracts as soon as possible to my address below. It is a great pleasure to know the overwhelming acceptation of invited and contributed papers, see preliminary list below. I am looking forward to see you in San Francisco next year. With my best regards, Jorge Seminario -------------------------------------------------------------- CALL FOR PAPERS 213th National American Chemical Society Meeting Computers in Chemistry Division Symposium on Recent Developments in Density Functional Theory: From First Principles to Molecular Dynamics April 13-17, 1997 San Francisco, California Topics of Interest Include Basic and Advanced Theory Computational Techniques Applications to Chemistry, Physics, and Engineering Interested persons please send a tentative title to: Jorge M. Seminario Department of Chemistry University of New Orleans New Orleans, LA 70148 e-mail: jsmcm@uno.edu Tel: 504-280-7216 Fax: 504-280-6860 Abstracts due by October 15, 1996 Speakers who already accepted the invitation are Alonso J. (Spain) Andzelm J. (USA) Baerends E. (Netherlands) Balbuena P. (USA) Broclawic E.(Poland) Burke K. (USA) Casida M. (Canada) Castro M. (Mexico) Catlow R. (UK) Chermette H. (France) Cioslowski J. (USA) Delley B. (Switzerland) Dunlap B. (USA) Frisch M. (USA) Gill P. (UK) Geerlings P. (Belgium) Gill P. (UK) Gonis A. (USA) Gross E. (Germany) Johnson B. (USA) Jursic B. (USA) Labanowski J. (USA) Levy M. (USA) Lowdin P.(USA, Sweden) Ludena E. (Venezuela) Malkin V. (Slovakia) Nesbet R. (USA) Norskov J. (Denmark) Pacchioni G. (Italy) Percus J. (USA) Perdew J. (USA) Peterson L. (Sweden) Politzer P. (USA) Roesch N. (Germany) Russo N. (Italy) Sahni V. (USA) Salahub D. (Canada) Sanders F. (USA) Savin A. (France) Seminario J. (USA) St-Amant A. (Canada) Tomasi J. (Italy) Umrigar C. (USA) Van Santen R. (Netherlands) Vela A. (Mexico) From val@nmr1.ioc.ac.ru Tue Oct 8 03:59:16 1996 Received: from nmr1.ioc.ac.ru for val@nmr1.ioc.ac.ru by www.ccl.net (8.8.0/950822.1) id DAA04899; Tue, 8 Oct 1996 03:47:15 -0400 (EDT) Received: from [193.233.3.193] (nmr2.ioc.ac.ru [193.233.3.193]) by nmr1.ioc.ac.ru (8.6.12/8.6.9) with SMTP id LAA10506 for ; Tue, 8 Oct 1996 11:49:19 +0400 Date: Tue, 8 Oct 96 11:48:59 +0300 From: "Ananikov V.P." Message-Id: <55393.val@nmr1.ioc.ac.ru> X-Minuet-Version: Minuet1.0_Beta_17A Reply-To: X-POPMail-Charset: IBM 8-Bit To: chemistry@www.ccl.net Subject: SUMMARY: MOL to HPGL conversion Dear CCL's, Some days ago I posted the following question: >Dear CCl's, > >I want to write my own converter from MOL to HPGL format which >can work as a pipe. >and I need your help: >Does anyone can help me to find a full description of MOL format? >Does anyone know where can I find the sources of such programs (for >any platforms, DOS, WINDOWS, UNIX, etc.)? > >Please write direct to me, I will summarize. >thank you. > >sincerely, >Ananikov V. > I received a few answers concerning mol file description. There are two documents available in which mol format is fully described: 1) Arthur Dalby et al., J. Chem. Inf. Comput. Sci, 1992, 32, 244-255 2) and a new document is now available online that describes MDL file formats(includes the recent extensions and changes) at: http://www.mdli.com/prod/fileformats.html I thank to all responders! regards, Ananikov V. From qibvigap@lg.ehu.es Tue Oct 8 04:53:56 1996 Received: from lgsx01.lg.ehu.es for qibvigap@lg.ehu.es by www.ccl.net (8.8.0/950822.1) id EAA05014; Tue, 8 Oct 1996 04:08:44 -0400 (EDT) Received: from lgdx02.lg.ehu.es by lgsx01.lg.ehu.es (4.1/4.7 ) id AA29940; Tue, 8 Oct 96 10:07:42 +0100 Received: by lgdx02.lg.ehu.es (5.65/4.7) id AA13183; Tue, 8 Oct 1996 10:15:55 +0100 Date: Tue, 8 Oct 1996 10:15:55 +0100 (WET DST) From: Pablo Vitoria Garcia X-Sender: qibvigap@lgdx02 To: ccl Subject: Information about G94 basis for transition metals coordination compounds Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear colleagues, I've been using G94 and GAMESS for a while now, and I'm more or less familiar with their methods, but only for organic molecules. Now I need to do some energy calculations on diethylentriamine complexes of Co(III), Ni(II) and several other metals, and I am quite lost, due to SCF convergence problems. Could anybody give mesom einformation about the 'best' methods and basis for these kind of chemical compounds? Or point me to some literature about it? I've read the books by Tim Clark and Hehre, but since they are quite 'old' they deal mostly with small organic molecules. Thanks a lot Pablo -------------------------------------------------------------------------------- Pablo Vitoria Garcia Departamento de Quimica Inorganica, Facultad de Ciencias Universidad del Pais Vasco (UPV/EHU) Apartado 644, E-48080 Bilbao SPAIN e-mail: qibvigap@lgdx02.lg.ehu.es Phone: +34 4 4647700 Ext. 2450 -------------------------------------------------------------------------------- From qibvigap@lg.ehu.es Tue Oct 8 05:53:58 1996 Received: from lgsx01.lg.ehu.es for qibvigap@lg.ehu.es by www.ccl.net (8.8.0/950822.1) id FAA05406; Tue, 8 Oct 1996 05:30:28 -0400 (EDT) Received: from lgdx02.lg.ehu.es by lgsx01.lg.ehu.es (4.1/4.7 ) id AA01342; Tue, 8 Oct 96 11:29:55 +0100 Received: by lgdx02.lg.ehu.es (5.65/4.7) id AA16906; Tue, 8 Oct 1996 11:38:06 +0100 Date: Tue, 8 Oct 1996 11:38:04 +0100 (WET DST) From: Pablo Vitoria Garcia X-Sender: qibvigap@lgdx02 To: ccl Subject: G94 Methods and basis for coordination compounds Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear colleagues, I've been using G94 and GAMESS for a while now, and I'm more or less familiar with their methods, but only for organic molecules. Now I need to do some energy calculations on diethylentriamine complexes of Co(III), Ni(II) and several other metals, and I am quite lost, due to SCF convergence problems. Could anybody give mesom einformation about the 'best' methods and basis for these kind of chemical compounds? Or point me to some literature about it? I've read the books by Tim Clark and Hehre, but since they are quite 'old' they deal mostly with small organic molecules. Thanks a lot Pablo -------------------------------------------------------------------------------- Pablo Vitoria Garcia Departamento de Quimica Inorganica, Facultad de Ciencias Universidad del Pais Vasco (UPV/EHU) Apartado 644, E-48080 Bilbao SPAIN e-mail: qibvigap@lgdx02.lg.ehu.es Phone: +34 4 4647700 Ext. 2450 -------------------------------------------------------------------------------- From cdac.ernet.in!gadre@parcom.ernet.in Thu Oct 3 04:56:46 1996 Received: from sangam.ncst.ernet.in for cdac.ernet.in!gadre@parcom.ernet.in by www.ccl.net (8.7.5/950822.1) id EAA07800; Thu, 3 Oct 1996 04:04:13 -0400 (EDT) Received: (from root@localhost) by sangam.ncst.ernet.in (8.7.5) id NAA08025 for CHEMISTRY@www.ccl.net; Thu, 3 Oct 1996 13:37:07 +0530 (GMT+05:30) >Received: from parcom.UUCP by iucaa (4.1/SMI-4.1) id AA29663; Wed, 2 Oct 96 18:40:50+050 Received: from parcom by sangam.ncst.ernet.in; Thu, 3 Oct 1996 13:37 GMT Received: from parcom.UUCP by iucaa (4.1/SMI-4.1) id AA29663; Wed, 2 Oct 96 18:40:50+050 Received: by parcom.cdac.ernet.in (4.1/SMI-4.1) id AA08216; Wed Oct 2 18:22:25 1996 (GMT + 0530) Date: Wed Oct 2 18:22:25 1996 (GMT + 0530) From: gadre@cdac.ernet.in Message-Id: <9610021252.AA08216@parcom.cdac.ernet.in> To: CHEMISTRY@www.ccl.net Dear Sirs: We have recently published an interesting article entitled "Steric Enhancement of Resonance: An Electron Localization Perspective". This article has probed a phenomenon termed as 'steric enhancement of resonance' (SER) discovered by an Indian organic chemist, Professor V. Baliah around 1960. It was also discussed by Professor Kamlet around the same time. We have found that the so-called 'steric' effects do have their electronic counterparts. We will be grateful to know of any other studies related to SER (either theoretical or experimental) or the sister phenomenon of Steric Inhibition of Resonance (SIR). We will also be glad to mail you a copy of our article [Curr. Sci. 71, 131 (1996)]. It could be of broad general interest to chemists. Thank you very much. Shridhar R. Gadre. From ccl@www.ccl.net Thu Oct 3 11:56:49 1996 Received: from bedrock.ccl.net for ccl@www.ccl.net by www.ccl.net (8.7.5/950822.1) id LAA10609; Thu, 3 Oct 1996 11:43:10 -0400 (EDT) Received: from euch4e.chem.emory.edu for qiang@euch4e.chem.emory.edu by bedrock.ccl.net (8.7.6/950822.1) id LAA14151; Thu, 3 Oct 1996 11:43:05 -0400 (EDT) From: Received: from localhost by euch4e.chem.emory.edu (AIX 3.2/UCB 5.64/4.03) id AA31587; Thu, 3 Oct 1996 11:43:06 -0400 Date: Thu, 3 Oct 1996 11:43:05 -0400 (EDT) To: CCLink Subject: Virial theorem... Message-Id: Hi, dear CCL members: I've noticed that in some cases, the -V/T given in the output of Gaussian94 is way off the correct value 2. I do know that in the usual ab initio theory, virial theorem doesn't hold exactly (even though quite many people are working along this line..), so a value close to 2 is good enough. But in some of my calculations, I've got values around 4!! What does this mean? Does this mean my calculation is not correct? I do notice that in those cases, there are close lying states, I wonder how is this related to my huge -V/T value. Any suggestions? Tons of thanks. ______________________________________________________________ Qiang Cui Dept. of Chem. Emory Univ. 508 Webster Dr. Apt.#2 Atlanta, GA 30322. Decatur, GA 30033. (404)-727-2381 (404)-636-6149 http://tswww.cc.emory.edu/~qcui ______________________________________________________________ From underhil@hp.rmc.ca Thu Oct 3 12:56:54 1996 Received: from sv2.rmc.ca for underhil@hp.rmc.ca by www.ccl.net (8.7.5/950822.1) id MAA10747; Thu, 3 Oct 1996 12:08:57 -0400 (EDT) Message-Id: <199610031608.MAA10747@www.ccl.net> Received: from underhill.rmc.ca by sv2.rmc.ca with SMTP (1.37.109.15/16.2) id AA153318906; Thu, 3 Oct 1996 12:08:26 -0400 Date: Thu, 3 Oct 1996 12:08:26 -0400 X-Sender: underhil@137.94.5.141 X-Mailer: Windows Eudora Version 1.4.3 To: chemistry@www.ccl.net From: underhil@hp.rmc.ca (Ross Underhill) Subject: IR freeware I'm looking for freeware that can be used for displaying and manipulating IR spectra in Windows. I've managed to find programs for NMR and mass spectra but nothing suitable for IR. Could someone please point me in the right direction. Thanks Dr. Ross Underhill Royal Military College of Canada Kingston, Ontario K7K 5L0 (613) 541-6000 X6175 From ccl@www.ccl.net Thu Oct 3 21:56:51 1996 Received: from bedrock.ccl.net for ccl@www.ccl.net by www.ccl.net (8.7.5/950822.1) id VAA13653; Thu, 3 Oct 1996 21:32:08 -0400 (EDT) Received: from meshsv02.tk.mesh.ad.jp for yoshicad@mxa.meshnet.or.jp by bedrock.ccl.net (8.7.6/950822.1) id VAA28277; Thu, 3 Oct 1996 21:32:05 -0400 (EDT) From: Received: from yoshitomi.mxa.meshnet.or.jp (kitk1DU04.fo.mesh.ad.jp [133.205.164.5]) by meshsv02.tk.mesh.ad.jp (8.6.12+2.4W/3.3W8-) with SMTP id KAA28827; Fri, 4 Oct 1996 10:32:03 +0900 Message-ID: <325469A2.5FE2@mxa.meshnet.or.jp> Date: Fri, 04 Oct 1996 10:34:26 +0900 X-Mailer: Mozilla 2.01I [ja] (Win95; I) To: chemistry@ccl.net CC: yoshicad Subject: GAMESS:partial geometry optimization Dear All, I would like to partial geometry optimization by GAMESS. but I could not find the keywords for it. Would you help me? Thanks for any comments. Koji Kanzaki -- KANZAKI KOJI( Yoshitomi Pharmaceutical Industries, LTD ) 955 Koiwai, Yoshitomi-cho, Chikujo-gun, Fukuoka, JAPAN 871 e-mail: yoshicad@mxa.meshnet.or.jp Fax: +81-979-24-3127 Phone: +81-979-23-8974(direct) From qibvigap@lgdx02.lg.ehu.es Sat Oct 5 05:57:07 1996 Received: from lgsx01.lg.ehu.es for qibvigap@lgdx02.lg.ehu.es by www.ccl.net (8.7.5/950822.1) id FAA19868; Sat, 5 Oct 1996 05:06:16 -0400 (EDT) Received: from lgdx02.lg.ehu.es by lgsx01.lg.ehu.es (4.1/4.7 ) id AA16820; Sat, 5 Oct 96 11:05:40 +0100 Received: from lcmx94.lc.ehu.es by lgdx02.lg.ehu.es (5.65/4.7) id AA20889; Sat, 5 Oct 1996 11:13:49 +0100 X-Sender: qibvigap@lgdx02.lg.ehu.es (Unverified) Message-Id: Date: Sat, 5 Oct 1996 11:11:52 +0000 To: chemistry@www.ccl.net From: qibvigap@lgdx02.lg.ehu.es (Pablo Vitoria) Subject: Error message in AIM calculation in G94 Dear colleagues, While doing an AIM (Atoms in Molecules) calculation for pyridazinium cAtion with the program G94, the following error message appeared when the program was trying to locate the 6-membered ring critical point: >>> Irreparable ring damage: the gap cannot be bridged >>> Error termination via Lnk1e in /usr/local/g94/l609.exe. The funny thing is that in a identical calculation with pyrazinium there was no problem at all in locating the ring point. Any suggestions about which the cause of this error may be? Thank you very much for your help Pablo Vitoria -------------------------------------------------------------------------------- Pablo Vitoria Garcia Departamento de Quimica Inorganica, Facultad de Ciencias Universidad del Pais Vasco (UPV/EHU) Apartado 644, E-48080 Bilbao SPAIN e-mail: qibvigap@lgdx02.lg.ehu.es Phone: +34 4 4647700 Ext. 2450 ---------------------------------------------------------------------------- ---- From ccl@www.ccl.net Sat Oct 5 16:57:13 1996 Received: from bedrock.ccl.net for ccl@www.ccl.net by www.ccl.net (8.7.5/950822.1) id QAA21449; Sat, 5 Oct 1996 16:43:43 -0400 (EDT) Received: from mtigwc01.worldnet.att.net for JeffAyres@postoffice.worldnet.att.net by bedrock.ccl.net (8.7.6/950822.1) id QAA22527; Sat, 5 Oct 1996 16:43:43 -0400 (EDT) Received: from LOCALNAME ([207.147.237.226]) by mtigwc01.worldnet.att.net (post.office MTA v2.0 0613 ) with SMTP id AAA8693 for ; Sat, 5 Oct 1996 20:43:12 +0000 X-Sender: JeffAyres@postoffice.worldnet.att.net (Unverified) X-Mailer: Windows Eudora Light Version 1.5.2 To: chemistry@ccl.net From: Jeffrey J Ayres Subject: Re:PDB format Date: Sat, 5 Oct 1996 20:43:12 +0000 Message-ID: <19961005204310.AAA8693@LOCALNAME> Attn: M. Dooley, In response to your question dated Sept. 2, 1996. CAVEAT, or Verification/Validation/Value Control Authority is used to indicate entries known to be incorrect. The information is added by the PDB. For help with the exact format of a NMR pdb file, format descriptions should be available at the pdb internet site. Previous experience was successful in locating the exact format requirements of x-ray crystal pdb file format. Sorry can't be of more help. Jeff Ayres From shubin@email.unc.edu Sun Oct 6 17:13:52 1996 Received: from login3.isis.unc.edu for shubin@email.unc.edu by www.ccl.net (8.7.5/950822.1) id QAA03078; Sun, 6 Oct 1996 16:18:59 -0400 (EDT) Received: by email.unc.edu id <4301-103962>; Sun, 6 Oct 1996 16:18:44 -0400 Date: Sun, 6 Oct 1996 16:18:32 -0400 (EDT) Sender: Shubin Liu From: Shubin Liu X-Sender: shubin@login3.isis.unc.edu To: chemistry@www.ccl.net Subject: How to extract Ex and J values in G94 HF calculation? In-Reply-To: <3256CF7D.446B@cc.ic.ac.uk> Message-ID: Hi, All: Does anyone know how to obtain the exchange energy Ex and the classical Coulomb repulsion energy J in a G94 Hartree-Fock calculation? If you do, would you please drop me a line? Thank you very much! Shubin ............................................................................. Shubin Liu Department of Chemistry Email: shubin@email.unc.edu Kenan Hall A207, CB# 3290 sliu@mulliken.chem.unc.edu University of North Carolina Home Page: http://www.unc.edu/~shubin Chapel Hill, NC 27599-3290 Tel : (919) 962-0150 (Office) USA Fax : (919) 962-2388 ............................................................................. From son@cc.nifhi.ac.ru Mon Oct 7 08:14:03 1996 Received: from netserv1.free.net for son@cc.nifhi.ac.ru by www.ccl.net (8.7.5/950822.1) id HAA08695; Mon, 7 Oct 1996 07:45:37 -0400 (EDT) Received: from cc.nifhi.ac.ru by netserv1.free.net (8.6.12.C2.1/8s) with ESMTP id OAA16950 for ; Mon, 7 Oct 1996 14:45:25 +0300 Received: from [193.233.8.21] (5t62.nifhi.ac.ru [193.233.8.21]) by cc.nifhi.ac.ru (8.6.11/8.6.9) with SMTP id PAA09935 for ; Mon, 7 Oct 1996 15:54:50 GMT Date: Mon, 7 Oct 96 03:22:22 CST From: "Irina K. Vorontsova" Message-Id: <27723.son@cc.nifhi.ac.ru> Reply-To: To: chemistry@www.ccl.net Subject: Heats of adsorption of simple molecules Dear colleagues, I'm intresting in some experimental value of heats of adsorption of simple molecules (H2O, N2, O2, CO2, NH3) on the ionic crystals (NaCl or MgO type). Could somebody help me please with information of this type. Thanks a lot in advance, Irina Vorontsova e-mail son@cc.nifhi.ac.ru From toukie@zui.unizh.ch Mon Oct 7 11:14:03 1996 Received: from zzmkgtw.zzmk.unizh.ch for toukie@zui.unizh.ch by www.ccl.net (8.7.5/950822.1) id KAA09359; Mon, 7 Oct 1996 10:25:14 -0400 (EDT) Received: by zzmkgtw.zzmk.unizh.ch; (5.65v3.2/1.3/10May95) id AA08715; Mon, 7 Oct 1996 15:29:35 +0100 Message-Id: <1.5.4.32.19961007142609.0066d4c4@zui.unizh.ch> X-Sender: toukie@zui.unizh.ch (Unverified) X-Mailer: Windows Eudora Light Version 1.5.4 (32) Date: Mon, 07 Oct 1996 15:26:09 +0100 To: chemistry@www.ccl.net From: "Hr. Dr. S. Shapiro" Subject: Calc'n of delta G of solvation Dear Colleagues; Re FIELD, M. J. & HILLIER, I. H., Non-dissociative proton transfer in 2- pyridone-2-hydroxypyridine. An ab initio molecular orbital study. JCS Perkin II, 617-22 ('87) a formula for the delta G of solvation by bulk water is given involving the polarisability ("alpha"), dipole moment ("mu"), and spherical cavity of radius _a_ ("a"). I would very much appreciate hearing from anyone who has had experience using this or related equations for the calculation of delta G of solvation in which the values of alpha, mu, and a were calculated using MOPAC or a similar semi-empirical quantum mechanical scheme. Thanks in advance to all responders. Sincerely, S. Shapiro toukie@zui.unizh.ch From ccl@www.ccl.net Mon Oct 7 14:53:57 1996 Received: from bedrock.ccl.net for ccl@www.ccl.net by www.ccl.net (8.8.0/950822.1) id NAA00494; Mon, 7 Oct 1996 13:57:48 -0400 (EDT) Received: from rani.chem.yale.edu for lim@rani.chem.yale.edu by bedrock.ccl.net (8.8.0/950822.1) id NAA27197; Mon, 7 Oct 1996 13:47:49 -0400 (EDT) Received: by rani.chem.yale.edu; Mon, 7 Oct 96 13:47:50 -0400 From: Dongchul Lim Message-Id: <9610071747.AA16116@rani.chem.yale.edu> Subject: Gaussian cube visualization To: chemistry@ccl.net (Computational Chemistry) Date: Mon, 7 Oct 96 13:47:47 EDT X-Mailer: ELM [version 2.3 PL11] There have been many questions regarding visualization of the data generated by Gaussian CUBE. One way to visualize the CUBE data, e.g., isoelectron density and electrostatic potential, is to use the PSI88 package, although it's noninteractive. That is, you convert 3D volume data from a cube file into a format suitable for PSICON. Then, PSICON generates contour data, which can be displayed/printed on various devices. For more information about the PSI88 package, you may want to look at our web pages at http://zarbi.chem.yale.edu/programs/psi88.html Detailed procedure follows: 1. Rename a cube file as "kubsub.f17". Compile the following program and run it. (NOTE: This was written by Dan Severance, dan@sage.Syntex.Com) --------------- CUT HERE --------------------------- Program kubconv double precision input(51) character*80 junk real output(51,51,51) integer ia(30) double precision c(30),x(30),y(30),z(30) Real cr(30),xr(30),yr(30),zr(30) double precision x1,y1,z1,xo,yo,zo double precision x2,y2,z2,x3,y3,z3 C toang = 0.52917715 open(7,file='FOR007',form='unformatted') open(8,file='kubsub.f17',form='unformatted') read(7)Junk read(7)Junk read(7)Nat,xo,yo,zo write(*,*)' end of first',Nat,xo*toang,yo*toang,zo*toang read(7)I1,x1,y1,z1 write(*,*)' end of second',I1,x1*toang,y1*toang,z1*toang read(7)I2,x2,y2,z2 write(*,*)' end of third',I2,x2*toang,y2*toang,z2*toang read(7)I3,x3,y3,z3 write(*,*)' end of four lines ',i3,x3*toang,y3*toang,z3*toang read(7)(IA(I),c(I),x(I),y(I),z(I),I=1,nat) xo = xo * toang yo = yo * toang zo = zo * toang x1 = x1 * toang y1 = y1 * toang z1 = z1 * toang x2 = x2 * toang y2 = y2 * toang z2 = z2 * toang x3 = x3 * toang y3 = y3 * toang z3 = z3 * toang do I = 1, NAT c xr(I) = x(I)*toang c yr(I) = y(I)*toang c zr(I) = z(I)*toang xr(I) = x(I) yr(I) = y(I) zr(I) = z(I) Enddo write(*,'(i2,8x,3F10.6)')(IA(I),xr(I),yr(I),zr(I),I=1,nat) write(*,*)' end of atom input ' DO I = 1, I3 DO J = 1, I2 read(7)(input(k),K=1,i1) do K = 1, I1 output(k,j,i) = input(k)*toang enddo C write(*,*) I,J enddo enddo close(7) xmn = xo ymn = yo zmn = zo xmx = xmn + I1*x1 ymx = ymn + I2*y2 zmx = zmn + I3*z3 write(8)i1,nat write(8)(IA(I),I=1,NAT) write(8)(Xr(I),Yr(I),Zr(I),I=1,NAT) write(8)(((output(i,j,k),k=1,I1),j=1,I2),i=1,I3) write(8)xmn,xmx,ymn,ymx,zmn,zmx write(*,*)xmn,xmx,ymn,ymx,zmn,zmx stop end --------------- CUT HERE --------------------------- 2. A file named "FOR007" is generated in step 1. Create a file named, e.g., "psicon.in". Its contents may be ------ CUT HERE ------- PSICON INPUT FILE 1 1 0 1 0.075000 ------ CUT HERE ------- 3. Run PSICON. On UNIX, you would do % PSICON < psicon.in 4. Then run PSI2. From Jeffrey.Nauss@UC.Edu Tue Oct 8 10:54:00 1996 Received: from jazz.san.uc.edu for Jeffrey.Nauss@UC.Edu by www.ccl.net (8.8.0/950822.1) id KAA08003; Tue, 8 Oct 1996 10:25:49 -0400 (EDT) Received: from beryllium.crs.uc.edu by UCBEH.SAN.UC.EDU (PMDF V5.0-7 #15949) id <01IAEAT3VJBWI00RDO@UCBEH.SAN.UC.EDU> for chemistry@www.ccl.net; Tue, 08 Oct 1996 10:23:58 -0500 (EST) Received: by beryllium.crs.uc.edu (951211.SGI.8.6.12.PATCH1042/940406.SGI.AUTO) for chemistry@www.ccl.net id KAA07393; Tue, 08 Oct 1996 10:24:23 -0400 Date: Tue, 08 Oct 1996 10:24:21 -0400 From: Jeffrey.Nauss@UC.Edu (Jeffrey L. Nauss) Subject: Discover to AMBER trajectory conversion To: chemistry@www.ccl.net Reply-to: Jeffrey.Nauss@UC.EDU Message-id: <9610081024.ZM7391@beryllium.crs.uc.edu> Organization: Dept. Chemistry, University of Cincinnati MIME-version: 1.0 X-Mailer: Z-Mail (3.2.2 10apr95 MediaMail) Content-type: text/plain; charset=us-ascii Content-transfer-encoding: 7BIT X-Zm-Priority: Low Might anyone have handy a program to covert a Discover history file to an AMBER trajectory file? AMBER 4.1 has some nice analysis modules we would like to use on a Discover MD simulation. 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: Jeffrey.Nauss@UC.Edu * * CCCCCCC URL http://www.che.uc.edu/~nauss * *********************************************************************** From Jeffrey.Nauss@UC.Edu Tue Oct 8 11:08:47 1996 Received: from jazz.san.uc.edu for Jeffrey.Nauss@UC.Edu by www.ccl.net (8.8.0/950822.1) id KAA07980; Tue, 8 Oct 1996 10:23:43 -0400 (EDT) Received: from beryllium.crs.uc.edu by UCBEH.SAN.UC.EDU (PMDF V5.0-7 #15949) id <01IAEAQT4QMUI00RDO@UCBEH.SAN.UC.EDU> for chemistry@www.ccl.net; Tue, 08 Oct 1996 10:22:06 -0500 (EST) Received: by beryllium.crs.uc.edu (951211.SGI.8.6.12.PATCH1042/940406.SGI.AUTO) for chemistry@www.ccl.net id KAA07338; Tue, 08 Oct 1996 10:22:32 -0400 Date: Tue, 08 Oct 1996 10:22:30 -0400 From: Jeffrey.Nauss@UC.Edu (Jeffrey L. Nauss) Subject: Recommended reference for DELPHI To: chemistry@www.ccl.net Reply-to: Jeffrey.Nauss@UC.EDU Message-id: <9610081022.ZM7336@beryllium.crs.uc.edu> Organization: Dept. Chemistry, University of Cincinnati MIME-version: 1.0 X-Mailer: Z-Mail (3.2.2 10apr95 MediaMail) Content-type: text/plain; charset=us-ascii Content-transfer-encoding: 7BIT X-Zm-Priority: High I am looking for the recommended reference for the program Delphi out of Barry Honig's group. I have found five possibilities from the Biosym/MSI manual for Delphi but which one is the *recommended* or preferred reference? Thanks... -- 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: Jeffrey.Nauss@UC.Edu * * CCCCCCC URL http://www.che.uc.edu/~nauss * *********************************************************************** From 101626.1574@CompuServe.COM Tue Oct 8 11:15:20 1996 Received: from dub-img-4.compuserve.com for 101626.1574@CompuServe.COM by www.ccl.net (8.8.0/950822.1) id KAA07910; Tue, 8 Oct 1996 10:17:07 -0400 (EDT) Received: by dub-img-4.compuserve.com (8.6.10/5.950515) id KAA16007; Tue, 8 Oct 1996 10:16:37 -0400 Date: 08 Oct 96 10:15:06 EDT From: Guy DESMARQUETS <101626.1574@CompuServe.COM> To: CCL Subject: Biomolecules visualisation PC Soft Message-ID: <961008141506_101626.1574_JHP106-3@CompuServe.COM> WINMGM (1), a professional software package for visualisation, manipulation and analysis of biomolecules ( Proteins, Nucleic Acids, Lipids,...). * Visualisation capabilities include real-time manipulation of high-grade graphics (CPK, ribbons,...), manipulation in relative or absolute coordinates of several molecules, rendering tools providing complex representations of " workstation quality ",... * Construction and optimization tools for peptides and proteins include systematic search using stereo-alphabet combinatorial methods, Monte Carlo calculations, side chain optimization,... * Analyzis tools include.properties calculation such as hydrophobic/ hydrophilic or electrostatic potentials (2), interdistance maps, Ramachandran maps, solvent accessible surfaces... Available on PC under MS-Windows 3.1, NT and 95 Demo version available on the following net adress : http://www.fsagx.ac.be/info_faculte/info_dep/info_bp/mehdi/winmgm/winmgmen.htm Product commercialized by : Ab Initio Technology , 1 place de l'Etoile F-67210 Obernai, France phone : +33 88.95.68.52 (after October 18/1996 : +33 03.88.95.68.52) Fax : +33 88.95.07.92 (after October 18/1996 : +33 03.88.95.07.92) email : 101626.1574@compuserve.com (1) & (2) publications in J. Mol. Graphics & J. Biol. Chim. Ask for details! From mark@DEC3600.boa.uni.torun.pl Tue Oct 8 12:54:03 1996 Received: from DEC3600.boa.uni.torun.pl for mark@DEC3600.boa.uni.torun.pl by www.ccl.net (8.8.0/950822.1) id MAA09472; Tue, 8 Oct 1996 12:43:13 -0400 (EDT) Received: by DEC3600.boa.uni.torun.pl; id AA16612; Tue, 8 Oct 1996 18:43:19 +0100 From: "Marek J. Smolinski" Message-Id: <9610081743.AA16612@DEC3600.boa.uni.torun.pl> Subject: Frequencies of the molecules in a crystal To: CHEMISTRY@www.ccl.net Date: Tue, 8 Oct 1996 18:43:18 +0100 (MET) X-Mailer: ELM [version 2.4 PL23] Content-Type: text Dear Netters, I am looking for the theoretical studies on the calculations of frequencies of the molecules in a crystal. I will appreciate it if anybody can inform me of the current publications. I am looking for programs that calculate the frequencies and intensities in Crystals, too. Thank you in advance for any help. Marek Smolinski -- +-----------------------------------------+ | Marek J. Smolinski | | E-mail: MARK@MAT.UNI.TORUN.PL | | OFFICE: NICHOLAS COPERNICUS UNIVERSITY | | DEPT. OF CHEMISTRY | | Gagarina 7/112 87-100 TORUN POLAND | | PHONE NO. (+48) (056) 14505 | | FAX NO. (+48) (056) 542477 | +-----------------------------------------+ From ferenc@rchsg8.chemie.uni-regensburg.de Tue Oct 8 13:04:35 1996 Received: from comsun.rz.uni-regensburg.de for ferenc@rchsg8.chemie.uni-regensburg.de by www.ccl.net (8.8.0/950822.1) id MAA09581; Tue, 8 Oct 1996 12:52:05 -0400 (EDT) Received: from rchsg8.chemie.uni-regensburg.de by comsun.rz.uni-regensburg.de with SMTP id AA16747 (5.65c/IDA-1.4.4 for ); Tue, 8 Oct 1996 18:53:02 +0100 Received: by rchsg8.chemie.uni-regensburg.de (931110.SGI/URRZ-Sub-1.5-irix) (for CHEMISTRY@www.ccl.net) id AA00631; Tue, 8 Oct 96 18:53:25 +0200 Date: Tue, 8 Oct 96 18:53:25 +0200 From: ferenc@rchsg8.chemie.uni-regensburg.de (Ferenc Molnar) Message-Id: <9610081653.AA00631@rchsg8.chemie.uni-regensburg.de> To: CHEMISTRY@www.ccl.net Subject: halomethanes Dear Netters: I would like to calculate the optimized structures and normal modes for a set of related compounds (halomethanes). Cl2-C-F2 (Dichlorodifluoromethane) / \ Cl-C-F2* Cl2-C-F2+ (radical) (cation) / \ Cl-C-F2+ C-F2 (cation) (carbene) \ C-F What type of basis-set would you recommend, that treats all of these species in a balanced way? My idea was to use polarization and diffuse functions to catch the ionic or radical character of these species. I belive, that Hartree-Fock (HF) will do a poor job for some of these molecules and one has to include electron-correlation even during optimization! Do you think that it is sensible to start from a HF minimum structure and to reoptimze with MP2? Calculating normal modes with MP2 will be quite expensive in terms of CPU and disk usage! Any idea about the "precision" that can be expected from such a calculation? I have little experience with the calculation of ionic or radical species and every comment, hint, or suggestion is very much appreciated! I will summarize all the responses. Thanx a lot in advance! Your sincerely, Ferenc Ferenc Molnar --------------------------------------------------------------------------- Institut fuer Physikalische und Theoretische Chemie - Lehrstuhl Prof. Dick - Tel.: (+49) 941 943-4466 /-4486 Universitaet Regensburg Fax.: (+49) 941 943-4488 Universitaetsstrasse 31 D-93053 Regensburg Deutschland / Germany --------------------------------------------------------------------------- EMail (SMTP): Ferenc.Molnar@chemie.uni-regensburg.de --------------------------------------------------------------------------- Those who do not archive the past are condemned to retype it! -- Garfinkel & Spafford, Practical Unix Security --------------------------------------------------------------------------- From dgregory@msi.com Tue Oct 8 13:12:40 1996 Received: from bioc1.msi.com for dgregory@msi.com by www.ccl.net (8.8.0/950822.1) id MAA09483; Tue, 8 Oct 1996 12:44:19 -0400 (EDT) Received: from biff.msi.com by bioc1.msi.com (5.64/0.0) id AA18216; Tue, 8 Oct 96 09:43:44 -0700 Received: from [146.202.16.11] by biff.biosym.com (4.1/SMI-4.1) id AA28940; Tue, 8 Oct 96 09:43:40 PDT X-Sender: dgregory@146.202.0.225 Message-Id: Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Tue, 8 Oct 1996 09:45:03 -0700 To: chemistry@www.ccl.net From: dgregory@msi.com (Don Gregory) Subject: Re: CCL:Recommended reference for DELPHI Hi Jeffery, Whereas some papers specifically describe an algorithmic package, and give it a name, it appears the earliest publications from Barry's lab didn't give a program name specifically. The earliers reference I could find, which describes the method and provides examples, is Proteins, vol 1 no. 1, p.47-59 (1986) Hope this helps! Don Gregory At 7:22 AM 10/8/96, Jeffrey L. Nauss wrote: >I am looking for the recommended reference for the program Delphi out of Barry >Honig's group. I have found five possibilities from the Biosym/MSI manual for >Delphi but which one is the *recommended* or preferred reference? > >Thanks... > > >-- > 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: Jeffrey.Nauss@UC.Edu * >* CCCCCCC URL http://www.che.uc.edu/~nauss * >*********************************************************************** > >-------This is added Automatically by the Software-------- >-- Original Sender Envelope Address: Jeffrey.Nauss@UC.Edu >-- Original Sender From: Address: Jeffrey.Nauss@UC.Edu >CHEMISTRY@www.ccl.net: Everybody | CHEMISTRY-REQUEST@www.ccl.net: Coordinator >MAILSERV@www.ccl.net: HELP CHEMISTRY or HELP SEARCH | Gopher: www.ccl.net 73 >Anon. ftp: www.ccl.net | CHEMISTRY-SEARCH@www.ccl.net -- archive search > Web: http://www.ccl.net/chemistry.html Dr. Don Gregory (dgregory@msi.com) Molecular Simulations Inc. 9685 Scranton Rd. San Diego, CA 92121 (619) 546-5331 http://www.msi.com From vgusev@triprinceton.org Tue Oct 8 14:54:13 1996 Received: from pluto.njcc.com for vgusev@triprinceton.org by www.ccl.net (8.8.0/950822.1) id OAA10387; Tue, 8 Oct 1996 14:19:10 -0400 (EDT) Received: from monako (crystal.njcc.com [199.224.2.122]) by pluto.njcc.com (8.7.6/8.6.12) with SMTP id OAA22549 for ; Tue, 8 Oct 1996 14:19:02 -0400 (EDT) Message-Id: <1.5.4.32.19961008181726.002b2c68@pop.njcc.com> X-Sender: vgusev@pop.njcc.com X-Mailer: Windows Eudora Light Version 1.5.4 (32) Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Tue, 08 Oct 1996 14:17:26 -0400 To: CHEMISTRY@www.ccl.net From: Vladimir Gusev Subject: Characterization of Porous Materials: from Angstroms to Millimeters Hello, This information may be of interest to those in the chemical community, who deals with porous materials. TRI/Princeton Workshop, March 24-26, 1997, Princeton, NJ, USA http://pluto.njcc.com/~aneimark/copm_workshop Characterization of Porous Materials: from Angstroms to Millimeters The workshop will provide state-of-the-art approaches to characterize porous materials of different origin in the range over six decades of magnitude from angstroms to millimeters. Lectures by recognized leaders of science and technology will include both the theoretical principles and the methodology of modern experimental techniques. The workshop will also provide demonstrations of capabilities of advanced adsorption, mercury, and liquid porosimeters and related analytical instruments, including software programs for calculating pore structure parameters and predicting engineering properties of porous materials. Round table discussion sessions will be organized on typical applications, including microporous solids, nanoporous regular structures, disordered materials and fractals, soft and deformable fibrous materials. The workshop is intended for qualified scientists and engineers who are involved in research and development of processes where porous materials play a key role. Industrial implications include monitoring, control, design and manufacture of the adsorbents, catalysts, fibers, textiles, coatings, soils, etc. for optimal performance of catalysis, separations, paper-making and printing, oil-recovery, pollution control, soil/water remediation, drying, hemo-sorption, respiratory protection, powder, nonwovens and other technologies. The registration fee is $595 per person ($495 per person for registrants >from the TRI corporate/assosiate members and for multiple registrants from the same organization). The fee includes admission to all sessions, workshop materials, lunch and refreshments. Workshop chairman: Alexander V. Neimark Tel: 609 924 3150, ext.17; Fax: 609 6837149; E-mail: aneimark@triprinceton.org Sincerely, Vladimir Gusev TRI/Princeton 601 Prospect Ave, P.O. Box 625 Princeton, NJ 08542, USA Tel: (609) 924-3150 Fax: (609) 683-7149 http://pluto.njcc.com/~vgusev From MECHADV@concentric.net Tue Oct 8 21:54:06 1996 Received: from tribune.concentric.net for MECHADV@concentric.net by www.ccl.net (8.8.0/950822.1) id VAA13168; Tue, 8 Oct 1996 21:41:39 -0400 (EDT) Received: from cliff.cris.com (cliff.cris.com [199.3.12.45]) by tribune.concentric.net (8.7.5/(96/09/19 1.3)) id VAA02327; Tue, 8 Oct 1996 21:41:39 -0400 (EDT) [1-800-745-2747 The Concentric Network] Errors-To: Received: from crc3.concentric.net (cnc054039.concentric.net [206.173.78.39]) by cliff.cris.com (8.7.5) id VAA11211; Tue, 8 Oct 1996 21:41:37 -0400 (EDT) Message-ID: <325B2A28.7A2A@pop3.concentric.net> Date: Tue, 08 Oct 1996 21:29:28 -0700 From: Dale Young Organization: Mechanical Advantage X-Mailer: Mozilla 2.01 (Win95; U) MIME-Version: 1.0 To: chemistry@www.ccl.net Subject: Periodic Table for Windows 95 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Mechanical Advantage wishes to announce to the computational chemistry list that the latest release of the Periodic Table for Windows 95 is now available. This program is loaded with data on each element in both Standard and SI units. A click of the mouse over the desired element displays a data screen on the element. The user may print the data or cut and paste it from our program into technical documents or lab reports. The program will run on IBM compatible 486's or higher with at least 4 Megs of RAM. The program was written for Windows 95 and will not run on systems using Windows 3.1. Periodic Table version 2.1 retails for $19.99 for an individual license or $99.99 for an Unlimited Site License for business and Universities. Send check or money order to: Mechanical Advantage, P.O. Box 769 Kernersville, NC 27285-0769 Questions and inquiries are welcome at our e-mail address: mechadv@concentric.net (All prices include shipping, handling and applicable sales tax.)