From fox@saga.ucsf.EDU Sat Jan 15 01:50:09 1994 Received: from cgl.ucsf.EDU for fox@saga.ucsf.EDU by www.ccl.net (8.6.4/930601.1506) id BAA09589; Sat, 15 Jan 1994 01:45:06 -0500 Received: from saga.ucsf.EDU by cgl.ucsf.EDU (8.6.4/GSC4.24) id WAA16223 for ; Fri, 14 Jan 1994 22:45:05 -0800 Received: by saga.ucsf.EDU (1.37.109.8/GSC4.21) id AA23102; Fri, 14 Jan 1994 22:43:46 -0800 From: fox@saga.ucsf.EDU (Thomas Fox) Message-Id: <9401150643.AA23102@saga.ucsf.EDU> Subject: radical calc's on toluene derivatives To: CHEMISTRY@ccl.net Date: Fri, 14 Jan 94 22:43:46 PST Cc: fox@saga.ucsf.EDU Mailer: Elm [revision: 70.85] Hi Netters, to understand the substrate specifity of the enzym chloroperoxidase a litte better and to get some insight into the reaction mechanism, I'm presently performing ab-initio calculations on various toluene derivatives. I'm especially interested in the relative energies of the closed shell molecules and those with an electron or a proton abstracted. Now my questions: - how reliable are UHF/6-31G* or MP2-UHF/6-31G* energies for these systems. I have no feeling how good(?) MP2 is for radical energies. Any experiences out on the net? - Does anyone know some good references for radical calculations that I could look up? - Any experience with nitrobenzene or nitrotoluene? I see a rather high effect on the energies when turning on correlation, and I also get a rather high spin contamination (S**2 about 1.8) for nitrotoluene. Any references that cover this topic? Thanks for your help, posted or directly mailed. If there is enough interest, I will post a summary. Th. Fox __________________________________________________________________ Thomas Fox e-mail: fox@saga.ucsf.edu Dept. of Pharmaceutical Chemistry University of California San Francisco, CA 94143-0446 ------------------------------------------------------------------ From noy@tci002.uibk.ac.at Sat Jan 15 08:50:16 1994 Received: from uibk.ac.at for noy@tci002.uibk.ac.at by www.ccl.net (8.6.4/930601.1506) id IAA11106; Sat, 15 Jan 1994 08:36:32 -0500 Received: from tci002.uibk.ac.at by uibk.ac.at with SMTP id AA27225 (5.65c/IDA-1.4.4 for ); Sat, 15 Jan 1994 14:36:28 +0100 Received: by tci002.uibk.ac.at (AIX 3.2/UCB 5.64/CFIBK-2e.AIX) id AA18084; Sat, 15 Jan 1994 14:36:26 +0100 From: noy@tci002.uibk.ac.at (Teerakiat Kerdcharoen) Message-Id: <9401151336.AA18084@tci002.uibk.ac.at> Subject: on-line document for MD To: chemistry@ccl.net Date: Sat, 15 Jan 1994 14:36:26 +0100 (NFT) X-Mailer: ELM [version 2.4 PL21] Content-Type: text Content-Length: 1466 Dear Netters, I am about to write a document titled, "Internet Resource Guide for Molecular Dynamics," which I intend to have it available on-line somewhere. The main aim is to provide helpful informations for beginners in molecular dynamics who are lacking of programs. Apart from Allen's and Tildesley's book, the newscomer in MD will know how and where to access those resources on internet. In addition, I will also compile some relevant resources into this document, i.e., database in molecular biology, protein, etc. Now, I have some informations in hand but I would appreciate anywhom could send me what you know relating to this stuff, FTP sites, on-line services, introductory references in MD, useful books, and so on. Please send e-mail directly to me at noy@tci2.uibk.ac.at ( I have configured the field Reply-to: already, so you can use "reply" command ). Thanks a lot in advance. best wishes, Teerakiat ---------------------------------------------------------------------------- Teerakiat Kerdcharoen (NOY) Institute of General and Inorganic and Theoretical Chemistry Innrain 52a, A-6020 Innsbruck AUSTRIA e-mail: noy@tci.uibk.ac.at, noy@tci2.uibk.ac.at, c72454@cx.uibk.ac.at : noy@atc.atccu.chula.ac.th, noy@atc2.atccu.chula.ac.th ( Bangkok ) Research : Molecular Dynamics simulations : Computer Aided Molecular/Material Designs ----------------------------------------------------------------------------- From raman@bioc01.uthscsa.edu Sat Jan 15 11:50:15 1994 Received: from thorin.uthscsa.edu for raman@bioc01.uthscsa.edu by www.ccl.net (8.6.4/930601.1506) id LAA12076; Sat, 15 Jan 1994 11:40:46 -0500 Received: from bioc01.uthscsa.edu by thorin.uthscsa.edu with SMTP; Sat, 15 Jan 1994 10:41:33 -0600 (CST) Received: by bioc01.uthscsa.edu (4.1/SMI-4.1) id AA17114; Sat, 15 Jan 94 10:41:13 CST From: raman@bioc01.uthscsa.edu (C.S.RAMAN) Message-Id: <9401151641.AA17114@bioc01.uthscsa.edu> Subject: Re: SB Drug Design from a Model Binding Site To: chiremv!andromeda!jeffb@uunet.UU.NET (Jeff Blaney) Date: Sat, 15 Jan 1994 10:41:12 -0600 (CST) Cc: chemistry@ccl.net In-Reply-To: <9401130520.AA14919@andromeda> from "Jeff Blaney" at Jan 12, 94 09:20:55 pm X-Mailer: ELM [version 2.4 PL3] Content-Type: text Content-Length: 918 There is a very nice program called DOCK (V 3.0) available for doing docking simulations from Tack Kuntz's group. Cheers -raman P.S. There is no fee for academia! -- C.S.Raman raman@bioc01.uthscsa.edu - Internet UNIX Programming & Administration 70412.2354@compuserve.com - CIS SPARC & SGI Systems raman@hermes.chpc.utexas.edu - CHPC Department of Biochemistry c.raman@launchpad.unc.edu UTHSCSA 7703 Floyd Curl Dr. (210) 567-6623 [Tel] San Antonio, TX 78284-7760 (210) 567-6595 [Fax] ****************************************************************************** If a man's wit be wandering, let him study the Mathematics -Francis Bacon ****************************************************************************** From AHOLDER@VAX1.UMKC.EDU Sat Jan 15 12:50:16 1994 Received: from VAX1.UMKC.EDU for AHOLDER@VAX1.UMKC.EDU by www.ccl.net (8.6.4/930601.1506) id LAA11918; Sat, 15 Jan 1994 11:10:37 -0500 From: Received: from VAX1.UMKC.EDU by VAX1.UMKC.EDU (PMDF V4.2-11 #4431) id <01H7PHR661AO9M1PRN@VAX1.UMKC.EDU>; Sat, 15 Jan 1994 10:10:32 CST Date: Sat, 15 Jan 1994 10:10:32 -0600 (CST) Subject: Hypervalent sulfur (and other heavy main group elements) and SE methods To: CHEMISTRY@ccl.net Message-id: <01H7PHR67DIQ9M1PRN@VAX1.UMKC.EDU> X-VMS-To: IN%"CHEMISTRY@ccl.net" MIME-version: 1.0 Content-transfer-encoding: 7BIT Sorry to send this again, but I put the wrong subject heading and I know I sort messages this way.... --------------------------------------------------------------------- Hello Netters. Daniel Glossman asked some interesting questions about hypervalent sulfur species computed by semiempirical methods. It's an excellent question in that none of the "mainline" (i.e. Dewar-style) methods up til the recent advent of SAM1 has included an explicit treatment of d-orbitals. This precluded the old standard sp3d2 hybridization pattern that we all know from Cootn and Wilkinson. It was shown how- ever that successful results could be obtained within this limitation in a method using Gaussian corrections to the core-core replusion term in the approximation (PM3 : J. J. P. Stewart, J. Comput. Chem. 10, 221 (1989); AM1 : M. J. S. Dewar, Y.-C. Yuan, Inorg. Chem. 29, 3881 (1990)). MNDO's performance was substantially poorer than AM1 or PM3, especially for hypervalent systems. Which brings us to an intertesting question: Is it really sp3d2 hybrid- ization or are the d-orbitlas used as some sort of extra flexibility (polarization?)? This has been bandied about for quite some time. A rel- atively definitive article (A. E. Reed, P. v. R. Schleyer, J. Am. Chem. Soc. 112, 1434 (1990)) seems to suggest that its not d-orbitals, but d- functions. I tend to come down in this camp myself. Anyway, whether or not its "orbital" or "function" it seesm that computationally they are needed for a proper description of these systems. Next: How do sp only semiempirical methods treat these systems? Answer: Badly and non-systematically. It is my belief that the hypervalent systems that AM1 or PM3 might get correct are fortuitous. Basically, I would not trust these results for anything important. To really get these systems, we need d-functions/orbitals in the description. TA DA: SAM1 to the rescue. Michael Dewar has been working over a period of some 8 years I know of on a way to bring d-orbitals into semi- empirical theory. This was accomplished with the new SAM1 method (M. J. S. Dewar, C. Jie, G. Yu, Tetrahedron 23, 5003 (1993); A. J. Holder, R. D. Dennington, C. Jie, Tetrahedron in press, (1994)). Here in Kansas City we have finished up the sulfur param- eterization with SAM1 and the results for hypervalent systems are much better. (All of this will be published shortly. This is not meant to be a stall, as we are still working on some of this. SAM1 with sulfur will be available in AMPAC 5.0 from Semichem to be released in March at the ACS meeting in San Diego.) There is some selected data below to illustrate the point. SF4 --- SAM1 Exptl Heat of Formation -179.5 -182.4 SF(1) 1.53 1.54 SF(2) 1.68 1.65 FSF(1) 128.8 129.2 FSF(2) 96.7 93.4 Ioniz. Pot. 12.55 12.03 General Results for Sulfur with SAM1 ------------------------------------ (The following are unsigned average errors.) SAM1 AM1 PM3 Heat of Formation (76 molecs) 6.45 7.09 9.33 Dipole Moments (45 molecs) 0.40 0.49 0.59 Ioniz. Pot. (67 molecs) 0.39 0.33 0.39 The results for P are even more dramatic, with the average errors in heats of formation being HALVED over PM3 and AM1! As well as hypervalent heavy main group elements, we are working on transition metals and hope to have iron and copper available in the 5.0 release as well. Hope this wasn't too boring. And YES, Doug, I'm always listening. You'll get 5.0 when its ready and you can repeat the study you mentioned with SAM1. Cheerio, Andy Holder =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= DR. ANDREW HOLDER Assistant Professor of Computational/Organic Chemistry Department of Chemistry || BITNET Addr: AHOLDER@UMKCVAX1 University of Missouri - Kansas City || Internet Addr: aholder@vax1.umkc.edu Spencer Chemistry, Room 315 || Phone Number: (816) 235-2293 Kansas City, Missouri 64110 || FAX Number: (816) 235-5502 =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= From h.rzepa@ic.ac.uk Sat Jan 15 14:50:17 1994 Received: from punch.ic.ac.uk for h.rzepa@ic.ac.uk by www.ccl.net (8.6.4/930601.1506) id OAA13136; Sat, 15 Jan 1994 14:07:39 -0500 Received: from sg1.cc.ic.ac.uk by punch.ic.ac.uk with SMTP (PP) id <12057-0@punch.ic.ac.uk>; Sat, 15 Jan 1994 19:04:26 +0000 Received: from anxa03 by cscmgb.cc.ic.ac.uk (920330.SGI/4.0) id AA07577; Sat, 15 Jan 94 19:06:03 GMT Message-Id: <9401151906.AA07577@cscmgb.cc.ic.ac.uk> X-Sender: rzepa@129.31.80.14 Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Sat, 15 Jan 1994 19:09:38 +0000 To: CHEMISTRY@ccl.net From: h.rzepa@ic.ac.uk (Henry Rzepa) (Henry Rzepa) Subject: On-line chemistry and electronic publishing via www. I note with some interest Jan's information that Wiley and Springer-Verlag have released their contents pages to www.ccl.net Could I sound out opinions on the following: a) whether a www server might also be used for this purpose? For example, we already have some chemistry material on ours, and the ease of implementation suggests that growth might be explosive in this area! b) whether a method such as www might or should be used for say "graphical" abstracts of the type favoured by say Angew Chemie, or the RSC Perkin journals, even if the full versions cannot be submitted for eg copyright reasons. c) Whether www might be suitable for otherwise VERY expensive colour plates? I have just received a request from one publisher for $2200 for printing a small colour diagram in a paper. I gather the real cost is at least this. Mounting the thing on www (or gopher) would be a zero cost item. Do any commercial publishers listening favour this idea? My soundings are that they are in two minds about protocols such as www, feeling on the one hand threatened in their hitherto dominance and control over scientific publishing, and on the other hand severely worried about dropping journals sales. See http:/www.ch.ic.ac.uk/RSC/P2/3_07186C.html for an example of how it might be done! d) whether the chemical community should be actively lobbying those involved in www and gopher development. For example, my contacts with David Johnson of Minnesota have been highly useful in promoting gopher+ as a chemists tool. Now that the www is moving into html+ as a scripting language, we as chemists need to make our needs known! e) If we can all become publishers by mounting a www document (or preprint), how do we handle refereeing, long term archiving, quality control and proofing, and indeed time-stamping and preventing fraud! Could publishers exist solely for (and make money from) a role as "authentication agents"? Dr Henry Rzepa, Dept. Chemistry, Imperial College, London, SW7 2AY. Tel: +44 71 225 8339. Fax: +44 71 589 3869. E-mail: rzepa@ic.ac.uk http://www.ch.ic.ac.uk/rzepa.html. Sent via MacPPP/MacTCP using Eudora 2.01. From b_duke@lacebark.ntu.edu.au Sat Jan 15 19:50:20 1994 Received: from lacebark.ntu.edu.au for b_duke@lacebark.ntu.edu.au by www.ccl.net (8.6.4/930601.1506) id TAA14479; Sat, 15 Jan 1994 19:01:08 -0500 From: Received: by lacebark.ntu.edu.au (AIX 3.2/UCB 5.64/4.03) id AA10474; Sun, 16 Jan 1994 09:29:41 -0600 Message-Id: <9401161529.AA10474@lacebark.ntu.edu.au> Subject: Code to read G92 chk files. To: CHEMISTRY@ccl.net (chemistry) Date: Sun, 16 Jan 1994 09:29:37 -0600 (CST) X-Mailer: ELM [version 2.4 PL21] Content-Type: text Content-Length: 3804 Hi, Comp Chem Netters. This is particularly directed at people who write code that interfaces with GAUSSIAN. I am trying to get PSIG90 from the AIMPAC package of Bader's group working on a IBM RISC 6000 under AIX and reading G92 chk files. The AIMPAC manual says it works - just link with l401 and util from g92. It is not that easy. The common dimensions changed from g90 to g92. Anyway I think I fixed all that and I get a *.wfn file with the correct coefficients and energies (agrees with output from OUTPUT=WFN). However the atomic coordinates are stuffed up. The program below isolates the problem. It reads 997 off the chk files and prints the coordinates. ICHARG, MULTIP -- NBASIS are correct. IAN is correct. C is not. I know I can use OUTPUT=WFN but I want other information and I have a modified version of psig90 on the vax for g90 chk files. However I need some results that are only or best obtained with g92 and I have that on the unix machine. I want the modified version to go on the RS6K but all this problem is still with the non-modified psig90. A makefile, similar to the one needed for psig90 is also below along with results for NH3 and H2O. The program retains the structure of psig90 but strips off everything not required to show up this problem. PROGRAM MAIN IMPLICIT REAL*8(A-H,O-Z) Parameter (MAXATM=1000,MAXAT1=(MAXATM+1)) C MAXATM=1000 REQUIRED FOR G92. 400 FOR G90. INTEGER NATOMS,ICHARG,MULTIP,NAE,NBE,NE,NBASIS,IAN REAL*8 ATMCHG,C COMMON /MOL/ NATOMS,ICHARG,MULTIP,NAE,NBE,NE,NBASIS, $ IAN(MAXAT1),ATMCHG(MAXATM),C(3,MAXATM) CHARACTER*40 NAME INTEGER FILNUM DATA IRWMOL/997/ C 1000 FORMAT(' ATOMIC COORDINATES:') 1010 FORMAT(1X,I3,3F10.5) 1200 FORMAT(' Name of Input File: ',$) 1210 FORMAT(A40) C LENMOL = 4*MAXATM + INTOWP(8+MAXATM) IFUNIT = 2 WRITE (6,1200) READ (5,1210) NAME CALL FOPEN(IFUNIT,2,NAME,0,JUNK) CALL FILEIO(2,-FILNUM(IRWMOL,IFUNIT),LENMOL,NATOMS,0) WRITE(7,1000) DO 10 I = 1, NATOMS WRITE(7,1010) IAN(I),(C(J,I),J=1,3) 10 CONTINUE STOP END # Makefile for coord # FFLAGS = -qextname # To correctly call external routines in util.a. # OBJS = coord.o # LIBS = /var/g92/util.a # Points to where util.a resides. # coord: $(OBJS) xlf $(FFLAGS) -o coord $(OBJS) $(LIBS) The results for NH3 are below. The x and y coordinates are reversed, otherwise the numbers are OK. ATOMIC COORDINATES: 7 .00000 .00000 -.20633 1 1.76194 .00000 .48145 1 -.88097 1.52588 .48145 1 -.88097 -1.52588 .48145 For H2O the results below are crazy. ATOMIC COORDINATES: 8 -.19255 .00000 -.14510 1 -.19255 .00000 1.85801 1 1.73296 .00000 -.69723 The results on a VAX using G90 chk files and the same program but with MAXATM changed to 400 which is appropriate for G90, are:- ATOMIC COORDINATES: 7 0.00000 0.00000 0.23959 1 0.00000 1.71267 -0.55904 1 1.48322 -0.85634 -0.55904 1 -1.48322 -0.85634 -0.55904 ATOMIC COORDINATES: 8 0.00000 0.00000 0.24110 1 0.00000 1.59975 -0.96440 1 0.00000 -1.59975 -0.96440 These are correct in the standard deviation. (N.B. the actual Z-matrix on the VAX is slightly different from that on the RS6K.) Now, have I made a blunder (most likely) or is there something wrong in g92 about how it writes C to the chk file. I would welcome any help you can give me. Cheers, Brian. -- Associate Professor Brian Salter-Duke (Brian Duke) School of Chemistry and Earth Sciences, Northern Territory University, Box 40146, Casuarina, NT 0811, Australia. Phone 089-466702 e-mail: b_duke@lacebark.ntu.edu.au or b_duke@uncl04.ntu.edu.au From raman@bioc01.uthscsa.edu Sat Jan 15 22:33:06 1994 Received: from thorin.uthscsa.edu for raman@bioc01.uthscsa.edu by www.ccl.net (8.6.4/930601.1506) id LAA12076; Sat, 15 Jan 1994 11:40:46 -0500 Received: from bioc01.uthscsa.edu by thorin.uthscsa.edu with SMTP; Sat, 15 Jan 1994 10:41:33 -0600 (CST) Received: by bioc01.uthscsa.edu (4.1/SMI-4.1) id AA17114; Sat, 15 Jan 94 10:41:13 CST From: raman@bioc01.uthscsa.edu (C.S.RAMAN) Message-Id: <9401151641.AA17114@bioc01.uthscsa.edu> Subject: Re: SB Drug Design from a Model Binding Site To: chiremv!andromeda!jeffb@uunet.UU.NET (Jeff Blaney) Date: Sat, 15 Jan 1994 10:41:12 -0600 (CST) Cc: chemistry@ccl.net In-Reply-To: <9401130520.AA14919@andromeda> from "Jeff Blaney" at Jan 12, 94 09:20:55 pm X-Mailer: ELM [version 2.4 PL3] Content-Type: text Content-Length: 918 There is a very nice program called DOCK (V 3.0) available for doing docking simulations from Tack Kuntz's group. Cheers -raman P.S. There is no fee for academia! -- C.S.Raman raman@bioc01.uthscsa.edu - Internet UNIX Programming & Administration 70412.2354@compuserve.com - CIS SPARC & SGI Systems raman@hermes.chpc.utexas.edu - CHPC Department of Biochemistry c.raman@launchpad.unc.edu UTHSCSA 7703 Floyd Curl Dr. (210) 567-6623 [Tel] San Antonio, TX 78284-7760 (210) 567-6595 [Fax] ****************************************************************************** If a man's wit be wandering, let him study the Mathematics -Francis Bacon ******************************************************************************