From mm02191@murata.co.jp Mon Apr 11 03:56:43 1994 Received: from relay1.UU.NET for mm02191@murata.co.jp by www.ccl.net (8.6.4/930601.1506) id DAA18372; Mon, 11 Apr 1994 03:48:42 -0400 From: Received: from uucp6.UU.NET by relay1.UU.NET with SMTP (5.61/UUNET-internet-primary) id AAwldf01852; Mon, 11 Apr 94 03:48:40 -0400 Received: from kddlab.UUCP by uucp6.UU.NET with UUCP/RMAIL ; Mon, 11 Apr 1994 03:48:50 -0400 Received: from kddfuji by kddlab.kddlabs.co.jp (5.61/6.2Junet) id AA19195; Mon, 11 Apr 94 16:42:51 +0900 Received: from omrongw.wg.omron.co.jp by kddfuji.kddlabs.co.jp (5.67+1.6W/KDD-1.02MX) id AA17073; Mon, 11 Apr 94 16:42:34 JST Received: by omrongw.wg.omron.co.jp (8.6.8+2.4Wb/2.8Wb-omrongw) id QAA00426; Mon, 11 Apr 1994 16:32:29 +0900 Received: by hqbob0.murata.co.jp (5.57/6.4J.6-murata1) id AA10318; Mon, 11 Apr 94 16:27:27 +0900 Received: by murata.co.jp (5.65/DEC-Ultrix/4.3) id AA00487; Mon, 11 Apr 1994 16:27:08 +1000 Message-Id: <9404110627.AA00487@murata.co.jp> To: Gustavo Mercier Cc: chemistry@ccl.net Subject: Re: CCL:Car-Parrinello MD program is now available. In-Reply-To: Your message of "Fri, 08 Apr 94 00:05:18 EDT." Date: Mon, 11 Apr 94 16:27:08 +1000 X-Mts: smtp Dear Dr. Mercier: > like to know how long the manual is since we would have to have it > translated, a potentially expensive process. Could you tell us a ... uuhm, this has very severe linguistic problem ... Before talking about the manual, please note that developing the CAMP Atami code had been done on volunteer bases, even if it is sold from JCPE. Fee of the program is only a shipping cost. "Japanese Manual of CAMP Atami" is 74 pages long. ^^^^^^^^ Contents: preface and copyright notice 1. Outline of the program ............. 1 2. Theoretical bases ................... 3 3. Formats of input files .............. 9 4. Formats of output files ............. 11 5. Some results of calculations ........ 13 Si, GaAs, metallic Al, Cu (crystal) H2O, SiH4, CH4, H2, (molecule) poly Acetylene. (macro molecule) 6. Structure of the Code ............... 38 minute description of the codes. 7. References .......................... 62 Appendix 1. History of CAMP Atami ............ 65 2. Mailing list on "CAMP" ........... 71 Yes, English translation of the manual is one of the our main concerns of these days. We surely plan to do it. However it will take, I suppose, half a year or so to translate the whole manual. It becomes too large to handle at a time. These may help You: A. A file containing compiling instructions are attached to the file set in English. B. A sample input file is also attached. C. Descriptions of the output files may not be provided in English. I will be able to tell you about them in that cases. D. Mailing list which devoted only on CAMP Atami will start soon. This mailing list will be set on some BBS in Japan, but you can sent and read mails via Inter-net Mail system without registration to the BBS. You may contact to the developers through the list. Address of the list is written on the manual. Any comments and questions on manual as well as on CAMP are appreciated. Please feel free to resent this message to others. | K. Nishida | Tenjin, Nagaokakyo, Kyoto 617 JAPAN | | research engineer | phone: +81-75-951-9111 | | Research & Develop Div. | facsimile: +81-75-956-6259 | | Murata Mfg., Co. Ltd. | JUNET: mm02191@murata.co.jp | >> A Car-Parrinello[1] MD program "CAMP Atami" is available from JCPE[2]. >> Please contact to JCPE to purchase the program. >> Programing Language is FORTRAN77. >> It is working on various UNIX machines, SUN, IRIS, NEWS, IBM, TITAN, >> HP, ALLIANT, CRAY, SX etc. >> >> Program No.: P089 >> Program Name: CAMP Atami (ver.1.0) >> Medium : 3.5" 2DD MS-DOS format. >> (tar + compress + uuencoded) >> Fee : 2,500 yen. Including (Japanese) Manual. >> >> Purchasing information from JCPE Newsletter: >> | JCPE: >> | JCPE Office, c/o Japan Association for International Chemical >> | Information(JAICI), Nakai Bldg., 6-25-4 Honkomagome, Bunkyo-ku, >> | Tokyo 113 JAPAN >> | >> | Tel: +81-3-5978-3622 >> | Fax: +81-3-5978-3600 >> | >> |2. Purchase >> | Catalog is included in every issue of JCPE Newsletter. Specify >> | number and title of the program and include fee in international >> | money order or any other exchangeable note to the above address. >> | We send programs only in the same type of medium as received >> | from the author. One does not have to be a member of JCPE >> | when placing the order of purchase. [1] R. Car and M. Parrinello, Phys. Rev. Lett. 55, 2417 (1985). [2] JCPE ("Japanese Chemical Program Exchange") is a Japanese Organization like QCPE. From dlim@minerva.cis.yale.edu Mon Apr 11 04:05:16 1994 Received: from minerva.cis.yale.edu for dlim@minerva.cis.yale.edu by www.ccl.net (8.6.4/930601.1506) id DAA18325; Mon, 11 Apr 1994 03:26:55 -0400 Received: by minerva.cis.yale.edu (5.0/SMI-SVR4) id AA07243; Mon, 11 Apr 1994 03:27:10 +0500 From: dlim@minerva.cis.yale.edu (Dongchul Lim) Message-Id: <9404110727.AA07243@minerva.cis.yale.edu> Subject: EPS to EPSI (bug fix) To: chemistry@ccl.net Date: Mon, 11 Apr 1994 03:27:09 -0400 (EDT) X-Mailer: ELM [version 2.4 PL23] Mime-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Content-Length: 5914 Sorry about posting this again, but this fixes some serious bugs in the previous posting. *** Usage *** Let's say you have a PostScript file called 'file.eps'. 1) This step is not necessary, unless you want to find out the exact bounding box. 'bbfig' can be found in calypso-2.oit.unc.edu in the directory of /pub/packages/TeX/dviware/dvips/dvips/contrib/bbfig. % bbfig file.eps > file.bbfig 2) Open 'file.eps' or 'file.bbfig' with 'xpsview'. % xpsview file.eps or % xpsview file.bbfig 3) Cut the image within the bounding box with 'snapshot'. Save the image into 'file.rgb'. % snapshot 4) Convert RGB image to PostScript image and insert it in 'file.eps'. % rgb2pv file.eps file.rgb > file.epsi -Dongchul Lim ------------- CUT HERE (rgb2pv.c) ----------------------------------- /***************************************************************** * When you have a RGB image of a PostScript file, this program * * can be used to put a preview image into the PostScript file. * * * * Compilation: cc -o rgb2pv rgb2pv.c -limage -lm * * Usage: rgb2pv PSfile RGBfile * * Author: Dongchul Lim * * Department of Chemistry, Yale University * * lim@rani.chem.yale.edu (April, 1994) * ******************************************************************/ #include #include #include #include #define READLINE(fp, str) fgets((str), sizeof((str)), (fp)) static void image_error(char *msg) { fprintf(stderr, "%s\n", msg); } static void insert_preview (FILE *fp, unsigned long *pv_data, int pv_width, int pv_height) { int x, y, col, shift; int pv_depth, pv_lines; unsigned long *pixel, p; if (!fp || !pv_data || pv_width <= 0 || pv_height <= 0) return; /* count the number of Preview lines */ pv_lines = 0; for(y=pv_height-1,col=0;y>=0;y--) { for(x=0;x 80) {pv_lines++; col = 0;} } pv_lines++; col = 0; } /* actual writing of preview image */ pv_depth = 8; fprintf(fp, "%%%%BeginPreview: %d %d %d %d\n", pv_width, pv_height, pv_depth, pv_lines); for(y=pv_height-1,col=0;y>=0;y--) { pixel = pv_data + y * pv_width; fprintf(fp, "%%%%"); for (x=0;x>16)&0XFF))+(151*((p>>8)&0XFF))+(28*(p&0XFF))) >> 8)); col += 2; if (col > 80) { fprintf(fp, "\n"); fprintf(fp, "%%%%"); col = 0; } } fprintf(fp, "\n"); col = 0; } fprintf(fp, "%%%%EndPreview\n"); } int main (int argc, char *argv[]) { IMAGE *image; FILE *ifp, *ofp, *tmpfp; char *psfile, *imagefile, str[256]; int pv_width, pv_height, pv_lines; register int y, width; register unsigned short *sp, *rp, *gp, *bp, *ap, *rbuf, *gbuf, *bbuf, *abuf; register unsigned long *lp, *base; if (argc < 3) { fprintf(stderr, "Usage: %s psfile imagefile\n", argv[0]); exit(1); } psfile = argv[1]; imagefile = argv[2]; i_seterror(image_error); if (!(image = iopen(imagefile, "r"))) exit(1); if (image->xsize <= 0 || image->ysize <= 0 || image->zsize <= 0) { fprintf(stderr, "size of image is zero.\n"); iclose(image); exit(1); } /* read in pixel values */ base = (unsigned long *)malloc(image->xsize * image->ysize * sizeof(unsigned long)); rbuf = (unsigned short *)malloc(image->xsize * sizeof(unsigned short)); gbuf = (unsigned short *)malloc(image->xsize * sizeof(unsigned short)); bbuf = (unsigned short *)malloc(image->xsize * sizeof(unsigned short)); abuf = (unsigned short *)malloc(image->xsize * sizeof(unsigned short)); if (!base || !rbuf || !gbuf || !bbuf) { iclose(image); fprintf(stderr, "not enough memory.\n"); exit(1); } lp = base; for (y=0;yysize;y++) { width = image->xsize; rp = rbuf; gp = gbuf; bp = bbuf; ap = abuf; switch (image->zsize) { case 1: case 2: getrow(image, rbuf, y, 0); while (width--) *lp++ = 0x00010101 * (*rp++); break; case 3: getrow(image, rbuf, y, 0); getrow(image, gbuf, y, 1); getrow(image, bbuf, y, 2); while (width--) *lp++ = *rp++ | ((*gp++)<<8) | ((*bp++)<<16); break; default: getrow(image, rbuf, y, 0); getrow(image, gbuf, y, 1); getrow(image, bbuf, y, 2); getrow(image, abuf, y, 3); while (width--) *lp++ = *rp++ | ((*gp++)<<8) | ((*bp++)<<16) | ((*ap++)<<24); break; } } pv_width = image->xsize; pv_height = image->ysize; iclose(image); free(rbuf); free(gbuf); free(bbuf); free(abuf); /* open input PostScript, output PostScript and tmp scractch files */ if (!(ifp = fopen(psfile, "r"))) { fprintf(stderr, "Can't open file %s.\n", psfile); free(base); exit(1); } tmpfp = tmpfile(); ofp = stdout; /* get rid of previous preview image */ rewind(ifp); READLINE(ifp, str); if (strncmp(str, "%!", 2) != 0) { fprintf(stderr, "%s is not a PostScript file.\n", psfile); fclose(ifp); fclose(ofp); fclose(tmpfp); free(base); exit(1); } fprintf(tmpfp, "%!PS-Adobe-3.0 EPSI-3.0\n"); while (READLINE(ifp, str)) { if (strncmp(str, "%%BeginPreview:", 15) == 0) { sscanf(str+15, "%*d %*d %*d %d", &pv_lines); while (pv_lines-- > 0) READLINE(ifp, str); continue; } fprintf(tmpfp, "%s", str); } /* insert preview image */ rewind(tmpfp); while (READLINE(tmpfp, str)) { if (str[0] != '%') { /* insert preview image */ insert_preview(ofp, base, pv_width, pv_height); fprintf(ofp, "%s", str); break; } fprintf(ofp, "%s", str); } free(base); /* concatenate the rest of the PostScript file to the output */ while (READLINE(tmpfp, str)) fprintf(ofp, "%s", str); /* close all files */ fclose(ifp); fclose(ofp); fclose(tmpfp); exit(0); } ------------------ CUT HERE ----------------------------------------- From inoue@greencross.co.jp Mon Apr 11 04:56:46 1994 Received: from uucp0.iij.ad.jp for inoue@greencross.co.jp by www.ccl.net (8.6.4/930601.1506) id EAA18785; Mon, 11 Apr 1994 04:56:32 -0400 Received: from wincgw1.winc.ad.jp (wincgw1.winc.ad.jp [202.15.200.1]) by uucp0.iij.ad.jp (8.6.8+2.4Wb/3.3Wb-UUCP) with SMTP id RAA12399 for ; Mon, 11 Apr 1994 17:56:29 +0900 Received: by wincgw1.winc.ad.jp (5.67+1.6W/4.18:3.7:winc:931216) id AA23359; Mon, 11 Apr 94 17:56:48 JST Received: by gccss2.greencross.co.jp (4.1/6.4J.6-agu4) id AA14806; Mon, 11 Apr 94 17:11:17 JST Date: Mon, 11 Apr 94 17:11:17 JST From: inoue@greencross.co.jp (Y. Inoue) Message-Id: <9404110811.AA14806@gccss2.greencross.co.jp> To: chemistry@ccl.net Subject: Re: Sybyl spl Hi Chuck, There are many Sybyl spl examples under /sybyl601/spl. But some spl does not work properly. I am interested in your idea, but most spl are not so long programs, and I think limited researchers wrote spl. So I do not mind if Tripos always collect spl and send us correct ones in CD-ROM. And because we cannot use "ftp", we are not interested in the site. I am going to bring two spl for Tripos Users' Meeting. One is getesp.spl, corrected version of esp_get.spl. The other is bond-rotation and CoMFA r2 validation spl for searching proper comformation, originally programmed by Dr.Tamiki Nishimura, Sumitomo Pharm., and modified by me. Hope this help. Yoshihisa INOUE the Green Cross Corp. 2-25-1 Shodai-ohtani, Hirakata,Osaka 573 JAPAN tel: +81-720-56-9328 fax: +81-720-57-5020 E-mail:inoue@greencross.co.jp From mbdtssg@hpb.ch.man.ac.uk Mon Apr 11 06:56:51 1994 Received: from nessie.mcc.ac.uk for mbdtssg@hpb.ch.man.ac.uk by www.ccl.net (8.6.4/930601.1506) id GAA19542; Mon, 11 Apr 1994 06:49:55 -0400 Received: from hpb.ch.man.ac.uk (actually mchhpb.ch.man.ac.uk) by nessie.mcc.ac.uk with SMTP (PP); Mon, 11 Apr 1994 11:49:28 +0100 From: Steve Greatbanks Message-Id: <2547.9404111049@hpb.ch.man.ac.uk> Subject: ps to eps conversion To: chemistry@ccl.net Date: Mon, 11 Apr 94 11:49:10 BST Mailer: Elm [revision: 70.85] Hi, for anybody out there with ghostscript, a more elegant solution is to use the following shell script ( which I hasten to add, I did not write, but found hiding on our system ) **********cut here*********** #!/bin/sh LOCALPATH=/usr/contrib/bin PATH=/bin:/usr/bin:/usr/ucb\:$LOCALPATH\ export PATH outfile if [ $# -lt 1 -o $# -gt 2 ]; then echo "Usage: pstoepsi file.ps [file.epsi]" 1>&2 exit 1 fi infile=$1 if [ $# -eq 1 ] then case "${infile}" in *.ps) base=`basename ${infile} .ps` ;; *.cps) base=`basename ${infile} .cps` ;; *.eps) base=`basename ${infile} .eps` ;; *.epsf) base=`basename ${infile} .epsf` ;; *) base=`basename ${infile}` ;; esac outfile=${base}.epsi else outfile=$2 fi gs -q -dNOPAUSE -dNODISPLAY ps2epsi.ps < ${infile} 1>&2 ( cat << BEGINEPS /InitDictCount countdictstack def gsave save mark newpath /showpage {} def BEGINEPS cat ${infile} cat << ENDEPS countdictstack InitDictCount sub { end } repeat cleartomark restore grestore ENDEPS ) >> ${outfile} exit 0 ********cut here*************** All you need to do is change the paths to whatever are appropraite for your system and all should be well. Steve Greatbanks. From jovinel@imiucca.csi.unimi.it Mon Apr 11 07:56:47 1994 Received: from imiucca.csi.unimi.it for jovinel@imiucca.csi.unimi.it by www.ccl.net (8.6.4/930601.1506) id GAA19669; Mon, 11 Apr 1994 06:57:22 -0400 Received: by imiucca.csi.unimi.it (1.37.109.4/15.6) id AA14593; Mon, 11 Apr 94 12:56:19 +0200 (GMT+1) From: Luca Jovine Message-Id: <9404111056.AA14593@imiucca.csi.unimi.it> Subject: Looking for RMS distance calculator To: CHEMISTRY@ccl.net (Computational Chemistry List) Date: Mon, 11 Apr 94 12:56:19 METDST Mailer: Elm [revision: 70.85] Dear Netters, I am looking for a program that could calculate a RMS distance matrix for a set of homologous molecular structures (possibly in PDB format). It would be even better if such program allowed to pick which parts of the structures to compare (for example, only P atoms, or all atoms of a subset of nts, etc. - as you can guess I need it for comparing some nucleic acid structures), without having to do it by hand by editing the PDB files. Does such a program exist, and, if so, how to get it? (I can use Macs or SGI or HP or Windows/DOS). Thank you very much in advance, Luca -------------------------------------------------------------------------------- Luca Jovine Dipartimento di Biologia e di Genetica dei Microrganismi Universita' degli Studi di Milano Via Celoria 26 I-20133 Milano ITALY Voice: +39.2.26605213 FAX: +39.2.2664551 E-Mail: jovinel@imiucca.csi.unimi.it "I'll give you a definitive maybe" (Sam Goldwyn) -------------------------------------------------------------------------------- From mizan@rz.engin.umich.edu Mon Apr 11 08:56:44 1994 Received: from rz.engin.umich.edu for mizan@rz.engin.umich.edu by www.ccl.net (8.6.4/930601.1506) id IAA20827; Mon, 11 Apr 1994 08:39:57 -0400 Received: by rz.engin.umich.edu (5.67/1.35) id AA12499; Mon, 11 Apr 94 12:39:57 GMT Date: Mon, 11 Apr 94 12:39:57 GMT From: "Tahmid I. Mizan" Message-Id: <9404111239.AA12499@rz.engin.umich.edu> To: CHEMISTRY@ccl.net Subject: self-diffusivity of supercritical water Hello, Does anybody know any references for experimental data for the self-diffusivity of supercritical water ? I am aware of some work by Jiri Jonas with NMR but I don't know of any specifiec journal papers. Could some kind soul enlighten me ? Thanks. Tahmid Mizan University of Michigan mizan@engin.umich.edu From chp1aa@surrey.ac.uk Mon Apr 11 09:56:47 1994 Received: from mail-server.surrey.ac.uk for chp1aa@surrey.ac.uk by www.ccl.net (8.6.4/930601.1506) id JAA21516; Mon, 11 Apr 1994 09:10:36 -0400 Received: from central.surrey.ac.uk by mail-server.surrey.ac.uk with SMTP using (PP) id <29210-0@mail-server.surrey.ac.uk>; Mon, 11 Apr 1994 14:10:25 +0100 Received: by central.surrey.ac.uk (1.37.109.8/16.2) id AA24031; Mon, 11 Apr 1994 14:10:23 +0100 From: Mr Andrew D Allen Message-Id: <9404111310.AA24031@central.surrey.ac.uk> Subject: Problem with SCF convergence in AMPAC To: chemistry@ccl.net Date: Mon, 11 Apr 94 14:10:23 BST Mailer: Elm [revision: 70.85] I am running AMPAC v2.1 and have run into problems with SCF convergence. I have a large, ~60 atoms, molecule which converges OK if carry out a geometry optimisation on all coordinates. The problem arises when I try to constrain the optimisation by flaging some of the bonds, angle and torsions to not be optimised. Has anyone experienced this problem with Semi-emp, or QM methods in general, and has anyone any possible ways to overcome the problem. I would like to avoid doing a full geometry optimisation for the molecule due to its size. Andy. -- ################################################################################ Structural and Computation Chemistry Group__________chp1aa@uk.ac.surrey - JANET. Department of Chemistry_____________________________phone__+44(483)-300800-2632. University of Surrey________________________________fax_________+44(483)-300803. Guildford, Surrey, GU2 5XH, UK______________________ftp____________131.227.110.2 ################################################################################ From hogue@canada.den.mmc.com Mon Apr 11 10:56:43 1994 Received: from canada.den.mmc.com for hogue@canada.den.mmc.com by www.ccl.net (8.6.4/930601.1506) id KAA22081; Mon, 11 Apr 1994 10:02:37 -0400 Received: by canada.den.mmc.com (4.1/1.34.a) id AA01622; Mon, 11 Apr 94 08:02:04 MDT Date: Mon, 11 Apr 94 08:02:04 MDT From: hogue@canada.den.mmc.com (Pat Hogue 1-2183) Message-Id: <9404111402.AA01622@canada.den.mmc.com> To: chemistry@ccl.net Subject: Nitrite anion Dear Netters: I need help with references that discuss life times and mechanisms for anion, cation and radicals generated during the combustion of nitrate propellants (e.g., hydroxyl ammonium nitrate and triethanol ammonium nitrate). The nitrite anion NO2- appears to be especially catalytic in this regard. I would guess this is because it posses symmetry and orbital energies that allow optimum overlap with unreacted molecules. Right? Any help will be appreciated. I will post responses. Pat Hogue From herbert.homeier@rchs1.chemie.uni-regensburg.de Mon Apr 11 10:56:57 1994 Received: from comsun.rz.uni-regensburg.de for herbert.homeier@rchs1.chemie.uni-regensburg.de by www.ccl.net (8.6.4/930601.1506) id KAA22469; Mon, 11 Apr 1994 10:48:40 -0400 Received: from rchs1.chemie.uni-regensburg.de by comsun.rz.uni-regensburg.de with SMTP id AA26692 (5.65c/IDA-1.4.4 for ); Mon, 11 Apr 1994 16:48:03 +0200 Received: by rchs1.chemie.uni-regensburg.de (4.1/URRZ-sub (1.5)) id AA16315; Mon, 11 Apr 94 16:47:12 +0200 Date: Mon, 11 Apr 94 16:47:12 +0200 From: Herbert Homeier (t4720) Message-Id: <9404111447.AA16315@rchs1.chemie.uni-regensburg.de> To: CHEMISTRY@ccl.net Subject: Special issue of JOURNAL OF GLOBAL OPTIMIZATION Cc: pardalos@math.ufl.edu Hi, netters, the following should interest several members of the computational chemistry list. Best regards Herbert -------------------------------------------------------------- Dr. Herbert H. H. Homeier Institut fuer Physikalische und Theoretische Chemie Universitaet Regensburg D-93040 Regensburg, Germany Phone: +49-941-943 4720 FAX : +49-941-943 2305 email: herbert.homeier@chemie.uni-regensburg.de (preferred) homeier@vax1.rz.uni-regensburg.d400.de na.hhomeier@na-net.ornl.gov -------------------------------------------------------------- ------------- BEGIN INCLUDED MESSAGE ------------------------- From: Panos Pardalos Date: Thu, 7 Apr 94 22:35:08 EDT Subject: Contents, Journal of Global Optimization Table of Contents JOURNAL OF GLOBAL OPTIMIZATION (Kluwer Academic Publishers) Vol. 4 No. 2 (1994) Special issue: Advances in Computational Chemistry and Protein Folding co-editors: Panos M. Pardalos, and Guoliang Xue. Panos M. Pardalos, David Shalloway, and Guoliang Xue, Optimization Methods for Computing Global Minima of Nonconvex Potential Energy Functions, pp. 117-133. Costas D. Maranas and Christodoulos A. Floudas, Global Minimum Potential Energy Conformations of Small Molecules, pp. 135-170. Thomas Coleman, David Shalloway, and Zhijun Wu A Parallel Build-Up Algorithm for Global Energy Minimizations of Molecular Clusters Using Effective Energy Simulated Annealing, pp. 171-185. Guoliang Xue, Molecular Conformation on the CM-5 by Parallel Two-Level Simulated Annealing, pp. 187-208. David M. Ferguson, Amanda Marsh, Thomas Metzger, David G. Garrett, and Keith Kastella, Conformational Searches for the Global Minimum of Protein Models, pp. 209-227. Andrew T. Phillips and J. B. Rosen, A Quadratic Assignment Formulation of the Molecular Conformation Problem, pp. 229-241. ------------- END INCLUDED MESSAGE --------------------------- From herbert.homeier@rchs1.chemie.uni-regensburg.de Mon Apr 11 10:57:13 1994 Received: from comsun.rz.uni-regensburg.de for herbert.homeier@rchs1.chemie.uni-regensburg.de by www.ccl.net (8.6.4/930601.1506) id KAA22353; Mon, 11 Apr 1994 10:38:27 -0400 Received: from rchs1.chemie.uni-regensburg.de by comsun.rz.uni-regensburg.de with SMTP id AA26566 (5.65c/IDA-1.4.4 for ); Mon, 11 Apr 1994 16:38:15 +0200 Received: by rchs1.chemie.uni-regensburg.de (4.1/URRZ-sub (1.5)) id AA16306; Mon, 11 Apr 94 16:37:25 +0200 Date: Mon, 11 Apr 94 16:37:25 +0200 From: Herbert Homeier (t4720) Message-Id: <9404111437.AA16306@rchs1.chemie.uni-regensburg.de> To: CHEMISTRY@ccl.net Subject: 1995, 01: Computational Biology and Parallel Computing, Hawaii Hi, netters, the conference described below may be of interest to some of you. Best regards Herbert -------------------------------------------------------------- Dr. Herbert H. H. Homeier Institut fuer Physikalische und Theoretische Chemie Universitaet Regensburg D-93040 Regensburg, Germany Phone: +49-941-943 4720 FAX : +49-941-943 2305 email: herbert.homeier@chemie.uni-regensburg.de (preferred) homeier@vax1.rz.uni-regensburg.d400.de na.hhomeier@na-net.ornl.gov -------------------------------------------------------------- From: Timothy Mattson Date: Wed, 6 Apr 94 09:58:25 PDT Subject: Parallel Computational Biology Call For Papers and Referees Computational Biology and Parallel Computing for the BioTechnology Track of the 28th Hawaii International Conference on System Sciences, HICSS-28 Maui, Hawaii - January 3-6, 1995 The Hawaii International Conference on System Sciences traditionally attracts leading researchers in the both the biotechnology and parallel computing disciplines. This minitrack takes advantage of this unique overlap by creating a forum for papers that discuss the use of parallel and distributed computers in the biological sciences. This includes a wide range of problems, some of which are: * protein folding * sequence analysis * linkage analysis * molecular modeling * computational chemistry ^^^^^^^^^^^^^^^^^^^^^^^ (sic!) These papers will be carefully refereed, so please let us know if you are willing to referee -- even if you can't submit a paper. Contact either of the organizers if you have any questions. ORGANIZERS Timothy G. Mattson (Tim) L. Ridgway Scott Intel Supercomputer Systems Division Department of Mathematics Mail Stop CO6-09 University of Houston 14924 N.W. Greenbrier Pkwy Houston, TX 77204--3476 Beaverton, OR 97229 Phone: (503) 531-5627 Phone: 713-743-3445 FAX: (503) 531-5501 FAX: 713-743-3505 email: tgm@ssd.intel.com email: scott@uh.edu From kappler@SECS.UCSC.EDU Mon Apr 11 13:11:55 1994 Received: from MOLENG.UCSC.EDU for kappler@SECS.UCSC.EDU by www.ccl.net (8.6.4/930601.1506) id MAA24271; Mon, 11 Apr 1994 12:47:36 -0400 Received: by SECS.UCSC.EDU (MX V3.1C) id 17596; Mon, 11 Apr 1994 09:48:36 PDT Date: Mon, 11 Apr 1994 09:48:34 PDT From: Mick Kappler To: chemistry@ccl.net CC: kappler@SECS.UCSC.EDU Message-ID: <0097CCA8.67B81B80.17596@SECS.UCSC.EDU> Subject: MOPAC V6.00 ruthenium question Hi, Is it possible to study ruthnium using MOPAC V6.00? A more appropiate question is what element numbers do each of the Hamiltonians support? Mick Kappler Molecular Engineering Laboratory Univ. of California kappler@secs.ucsc.edu From cletner@remcure.bmb.wright.edu Mon Apr 11 13:26:07 1994 Received: from remcure.bmb.wright.edu for cletner@remcure.bmb.wright.edu by www.ccl.net (8.6.4/930601.1506) id MAA24254; Mon, 11 Apr 1994 12:46:15 -0400 Received: by remcure.bmb.wright.edu (920330.SGI/921111.SGI.AUTO) for CHEMISTRY@ccl.net id AA09008; Mon, 11 Apr 94 12:34:42 -0700 Date: Mon, 11 Apr 1994 12:01:03 -0700 (PDT) From: Charles Letner Subject: Sybyl SPL scripts Summary To: Computational Chemistry List Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hello all, Obviously I'm not the only person who thinks that a ftp site for SPL scripts is a good idea. I've been inundated with responses. All but one see a real need for such a site. The good news is that there is a site already. The bad news is that it doesn't contain any scripts yet. It is associated with the SYBYL mail exploder. The address for this site is: extreme.chem.rpi.edu Incoming scripts should go in the "incoming" directory and then will be made available in the /pub/sybyl directory. A number of issues have been brought up by respondents. Here is a summary of these issues: 1) Could other utilities that are only usefull to Sybyl users be deposited at this site? One respondent has some C programs that does various things with output from Sybyl that could be contributed. 2) What about acknowledgement for scripts that are used in work that is published. Clearly the "programmer" of script that is a major part of an project that is published should be acknowledged. But what about a utility that is only a small part of the project? Further, what level of acknowledgement would be required? 3) Then there are the mechanics of site deposition/management. What kind of assurances are that a script will work? Should sample data be include? How about descriptions and instructions on a particular script? Then there is the issue of a index file of the deposited scripts. 4) Finally, a couple of you where concerned with Tripos' reaction to this whole thing. I've already been in contact with them. They have no problem with this. I'm looking into seeing if there are any formal rules that address these concerns with the owner of the ftp site. In particular I'll look into getting a set of formal rules set up. Any comments on these issues above are welcome, but please reply to me. I'm sure many of the non-sybyl users on this list could care less about this discussion. I'll summarize info on this thread later. Thanks to all Chuck Charles Letner Wright State University Department of Biochemistry Dayton, OH 45435 e-mail: cletner@remcure.bmb.wright.edu From jig@qorg.unizar.es Mon Apr 11 15:12:36 1994 Received: from qorg.unizar.es for jig@qorg.unizar.es by www.ccl.net (8.6.4/930601.1506) id OAA25900; Mon, 11 Apr 1994 14:25:56 -0400 Message-Id: <199404111825.OAA25900@www.ccl.net> Received: by qorg.unizar.es (1.37.109.4/16.2) id AA18677; Mon, 11 Apr 94 20:25:12 GMT From: Jose Ignacio Garcia Subject: 1,3-dipolar cycloadditions To: chemistry@ccl.net Date: Mon, 11 Apr 94 20:25:11 MET Mailer: Elm [revision: 70.85] Dear netters, I intend to start a study about the reaction between diazomethane and a series of complex dipolarophiles. Given that the important size of these systems, I have planned to use semiempirical methods (AM1 and PM3). I have some references dealing with the use of these type of calculations to locate transition structures in this kind of reactions, but the conclusions seem some controversial. I would acknowledge any ideas or suggestions on this topic. Of course, I will summarize the responses to the net. ******************************************************************************* Dr. Jose Ignacio Garcia-Laureiro Phone : 34-(9)76-350475 Departamento de Quimica Organica Fax : 34-(9)76-567920 Instituto de Ciencia de Materiales de Aragon e-mail: jig@qorg.unizar.es C.S.I.C.-Universidad de Zaragoza jig@cc.unizar.es 50009 ZARAGOZA (SPAIN) jig@msf.unizar.es ******************************************************************************* "And all this science I don't understand it's just my job five days a week..." ELTON JOHN - Rocket man ******************************************************************************* From chp1aa@surrey.ac.uk Mon Apr 11 09:56:47 1994 Received: from mail-server.surrey.ac.uk for chp1aa@surrey.ac.uk by www.ccl.net (8.6.4/930601.1506) id JAA21516; Mon, 11 Apr 1994 09:10:36 -0400 Received: from central.surrey.ac.uk by mail-server.surrey.ac.uk with SMTP using (PP) id <29210-0@mail-server.surrey.ac.uk>; Mon, 11 Apr 1994 14:10:25 +0100 Received: by central.surrey.ac.uk (1.37.109.8/16.2) id AA24031; Mon, 11 Apr 1994 14:10:23 +0100 From: Mr Andrew D Allen Message-Id: <9404111310.AA24031@central.surrey.ac.uk> Subject: CCL:Problem with SCF convergence in AMPAC To: chemistry@ccl.net Date: Mon, 11 Apr 94 14:10:23 BST Mailer: Elm [revision: 70.85] I am running AMPAC v2.1 and have run into problems with SCF convergence. I have a large, ~60 atoms, molecule which converges OK if carry out a geometry optimisation on all coordinates. The problem arises when I try to constrain the optimisation by flaging some of the bonds, angle and torsions to not be optimised. Has anyone experienced this problem with Semi-emp, or QM methods in general, and has anyone any possible ways to overcome the problem. I would like to avoid doing a full geometry optimisation for the molecule due to its size. Andy. -- ################################################################################ Structural and Computation Chemistry Group__________chp1aa@uk.ac.surrey - JANET. Department of Chemistry_____________________________phone__+44(483)-300800-2632. University of Surrey________________________________fax_________+44(483)-300803. Guildford, Surrey, GU2 5XH, UK______________________ftp____________131.227.110.2 ################################################################################ From chp1aa@surrey.ac.uk Mon Apr 11 09:56:47 1994 Received: from mail-server.surrey.ac.uk for chp1aa@surrey.ac.uk by www.ccl.net (8.6.4/930601.1506) id JAA21516; Mon, 11 Apr 1994 09:10:36 -0400 Received: from central.surrey.ac.uk by mail-server.surrey.ac.uk with SMTP using (PP) id <29210-0@mail-server.surrey.ac.uk>; Mon, 11 Apr 1994 14:10:25 +0100 Received: by central.surrey.ac.uk (1.37.109.8/16.2) id AA24031; Mon, 11 Apr 1994 14:10:23 +0100 From: Mr Andrew D Allen Message-Id: <9404111310.AA24031@central.surrey.ac.uk> Subject: CCL:Problem with SCF convergence in AMPAC To: chemistry@ccl.net Date: Mon, 11 Apr 94 14:10:23 BST Mailer: Elm [revision: 70.85] I am running AMPAC v2.1 and have run into problems with SCF convergence. I have a large, ~60 atoms, molecule which converges OK if carry out a geometry optimisation on all coordinates. The problem arises when I try to constrain the optimisation by flaging some of the bonds, angle and torsions to not be optimised. Has anyone experienced this problem with Semi-emp, or QM methods in general, and has anyone any possible ways to overcome the problem. I would like to avoid doing a full geometry optimisation for the molecule due to its size. Andy. -- ################################################################################ Structural and Computation Chemistry Group__________chp1aa@uk.ac.surrey - JANET. Department of Chemistry_____________________________phone__+44(483)-300800-2632. University of Surrey________________________________fax_________+44(483)-300803. Guildford, Surrey, GU2 5XH, UK______________________ftp____________131.227.110.2 ################################################################################ From hogue@canada.den.mmc.com Mon Apr 11 10:56:43 1994 Received: from canada.den.mmc.com for hogue@canada.den.mmc.com by www.ccl.net (8.6.4/930601.1506) id KAA22081; Mon, 11 Apr 1994 10:02:37 -0400 Received: by canada.den.mmc.com (4.1/1.34.a) id AA01622; Mon, 11 Apr 94 08:02:04 MDT Date: Mon, 11 Apr 94 08:02:04 MDT From: hogue@canada.den.mmc.com (Pat Hogue 1-2183) Message-Id: <9404111402.AA01622@canada.den.mmc.com> To: chemistry@ccl.net Subject: CCL:Nitrite anion Dear Netters: I need help with references that discuss life times and mechanisms for anion, cation and radicals generated during the combustion of nitrate propellants (e.g., hydroxyl ammonium nitrate and triethanol ammonium nitrate). The nitrite anion NO2- appears to be especially catalytic in this regard. I would guess this is because it posses symmetry and orbital energies that allow optimum overlap with unreacted molecules. Right? Any help will be appreciated. I will post responses. Pat Hogue From herbert.homeier@rchs1.chemie.uni-regensburg.de Mon Apr 11 10:56:57 1994 Received: from comsun.rz.uni-regensburg.de for herbert.homeier@rchs1.chemie.uni-regensburg.de by www.ccl.net (8.6.4/930601.1506) id KAA22469; Mon, 11 Apr 1994 10:48:40 -0400 Received: from rchs1.chemie.uni-regensburg.de by comsun.rz.uni-regensburg.de with SMTP id AA26692 (5.65c/IDA-1.4.4 for ); Mon, 11 Apr 1994 16:48:03 +0200 Received: by rchs1.chemie.uni-regensburg.de (4.1/URRZ-sub (1.5)) id AA16315; Mon, 11 Apr 94 16:47:12 +0200 Date: Mon, 11 Apr 94 16:47:12 +0200 From: Herbert Homeier (t4720) Message-Id: <9404111447.AA16315@rchs1.chemie.uni-regensburg.de> To: CHEMISTRY@ccl.net Subject: CCL:Special issue of JOURNAL OF GLOBAL OPTIMIZATION Cc: pardalos@math.ufl.edu Hi, netters, the following should interest several members of the computational chemistry list. Best regards Herbert -------------------------------------------------------------- Dr. Herbert H. H. Homeier Institut fuer Physikalische und Theoretische Chemie Universitaet Regensburg D-93040 Regensburg, Germany Phone: +49-941-943 4720 FAX : +49-941-943 2305 email: herbert.homeier@chemie.uni-regensburg.de (preferred) homeier@vax1.rz.uni-regensburg.d400.de na.hhomeier@na-net.ornl.gov -------------------------------------------------------------- ------------- BEGIN INCLUDED MESSAGE ------------------------- From: Panos Pardalos Date: Thu, 7 Apr 94 22:35:08 EDT Subject: Contents, Journal of Global Optimization Table of Contents JOURNAL OF GLOBAL OPTIMIZATION (Kluwer Academic Publishers) Vol. 4 No. 2 (1994) Special issue: Advances in Computational Chemistry and Protein Folding co-editors: Panos M. Pardalos, and Guoliang Xue. Panos M. Pardalos, David Shalloway, and Guoliang Xue, Optimization Methods for Computing Global Minima of Nonconvex Potential Energy Functions, pp. 117-133. Costas D. Maranas and Christodoulos A. Floudas, Global Minimum Potential Energy Conformations of Small Molecules, pp. 135-170. Thomas Coleman, David Shalloway, and Zhijun Wu A Parallel Build-Up Algorithm for Global Energy Minimizations of Molecular Clusters Using Effective Energy Simulated Annealing, pp. 171-185. Guoliang Xue, Molecular Conformation on the CM-5 by Parallel Two-Level Simulated Annealing, pp. 187-208. David M. Ferguson, Amanda Marsh, Thomas Metzger, David G. Garrett, and Keith Kastella, Conformational Searches for the Global Minimum of Protein Models, pp. 209-227. Andrew T. Phillips and J. B. Rosen, A Quadratic Assignment Formulation of the Molecular Conformation Problem, pp. 229-241. ------------- END INCLUDED MESSAGE --------------------------- From herbert.homeier@rchs1.chemie.uni-regensburg.de Mon Apr 11 10:57:13 1994 Received: from comsun.rz.uni-regensburg.de for herbert.homeier@rchs1.chemie.uni-regensburg.de by www.ccl.net (8.6.4/930601.1506) id KAA22353; Mon, 11 Apr 1994 10:38:27 -0400 Received: from rchs1.chemie.uni-regensburg.de by comsun.rz.uni-regensburg.de with SMTP id AA26566 (5.65c/IDA-1.4.4 for ); Mon, 11 Apr 1994 16:38:15 +0200 Received: by rchs1.chemie.uni-regensburg.de (4.1/URRZ-sub (1.5)) id AA16306; Mon, 11 Apr 94 16:37:25 +0200 Date: Mon, 11 Apr 94 16:37:25 +0200 From: Herbert Homeier (t4720) Message-Id: <9404111437.AA16306@rchs1.chemie.uni-regensburg.de> To: CHEMISTRY@ccl.net Subject: CCL:1995, 01: Computational Biology and Parallel Computing, Hawaii Hi, netters, the conference described below may be of interest to some of you. Best regards Herbert -------------------------------------------------------------- Dr. Herbert H. H. Homeier Institut fuer Physikalische und Theoretische Chemie Universitaet Regensburg D-93040 Regensburg, Germany Phone: +49-941-943 4720 FAX : +49-941-943 2305 email: herbert.homeier@chemie.uni-regensburg.de (preferred) homeier@vax1.rz.uni-regensburg.d400.de na.hhomeier@na-net.ornl.gov -------------------------------------------------------------- From: Timothy Mattson Date: Wed, 6 Apr 94 09:58:25 PDT Subject: Parallel Computational Biology Call For Papers and Referees Computational Biology and Parallel Computing for the BioTechnology Track of the 28th Hawaii International Conference on System Sciences, HICSS-28 Maui, Hawaii - January 3-6, 1995 The Hawaii International Conference on System Sciences traditionally attracts leading researchers in the both the biotechnology and parallel computing disciplines. This minitrack takes advantage of this unique overlap by creating a forum for papers that discuss the use of parallel and distributed computers in the biological sciences. This includes a wide range of problems, some of which are: * protein folding * sequence analysis * linkage analysis * molecular modeling * computational chemistry ^^^^^^^^^^^^^^^^^^^^^^^ (sic!) These papers will be carefully refereed, so please let us know if you are willing to referee -- even if you can't submit a paper. Contact either of the organizers if you have any questions. ORGANIZERS Timothy G. Mattson (Tim) L. Ridgway Scott Intel Supercomputer Systems Division Department of Mathematics Mail Stop CO6-09 University of Houston 14924 N.W. Greenbrier Pkwy Houston, TX 77204--3476 Beaverton, OR 97229 Phone: (503) 531-5627 Phone: 713-743-3445 FAX: (503) 531-5501 FAX: 713-743-3505 email: tgm@ssd.intel.com email: scott@uh.edu From herbert.homeier@rchs1.chemie.uni-regensburg.de Mon Apr 11 16:13:44 1994 Received: from comsun.rz.uni-regensburg.de for herbert.homeier@rchs1.chemie.uni-regensburg.de by www.ccl.net (8.6.4/930601.1506) id QAA27244; Mon, 11 Apr 1994 16:01:37 -0400 Received: from rchs1.chemie.uni-regensburg.de by comsun.rz.uni-regensburg.de with SMTP id AA29058 (5.65c/IDA-1.4.4 for ); Mon, 11 Apr 1994 22:01:30 +0200 Received: by rchs1.chemie.uni-regensburg.de (4.1/URRZ-sub (1.5)) id AA16489; Mon, 11 Apr 94 22:00:39 +0200 Date: Mon, 11 Apr 94 22:00:39 +0200 From: Herbert Homeier (t4720) Message-Id: <9404112000.AA16489@rchs1.chemie.uni-regensburg.de> To: bulldawg@oroites.ccqc.uga.edu Subject: Re: info on g orbitals and higher angular momentum orbitals Cc: CHEMISTRY@ccl.net Reply-To: Herbert.Homeier@chemie.uni-regensburg.de > From chemistry-request@ccl.net Sat Apr 2 03:22:46 1994 > Subject: CCL:info on g orbitals and higher angular momentum orbitals > To: chemistry@ccl.net > X-Mailer: ELM [version 2.4 PL20] > Content-Type> : > text> > Content-Length: 2149 > Sender: chemistry-request@ccl.net > X-Lines: 49 > > Hi Netters, > > After spending a good bit of an afternoon trying to find an article > that had pictures of g-functions in it, I only found one reference: > > "Order out of Chaos: Shapes of Hydrogen Orbitals" > by G. L. Breneman in J. Chem. Ed., Vol. 65, p.31 (1988). > > This is a pretty good article, but the pictures are of very poor > quality once I photocopy the article. Can anyone recommend any > other articles or even books that have nice looking pictures of > g-functions. I would also be interested in any pictures of > orbitals with higher angular momentum than 'g' or about any studies ..... (stuff deleted) .... > Russ > > -- > Russ Thomas > Center for Computational Quantum Chemistry > University of Georgia, Athens, Georgia 30602-2556 > bulldawg@xerxes.ccqc.uga.edu : Phone (706) 542-7747 : FAX (706) 542-0406 Russ, it is rather easy to generate nice plots of spherical harmonics for higher l values using for instance Maple V Release 2. Below, I include a short text file which shows how to do this. Best regards Herbert -------------------------------------------------------------- Dr. Herbert H. H. Homeier Institut fuer Physikalische und Theoretische Chemie Universitaet Regensburg D-93040 Regensburg, Germany Phone: +49-941-943 4720 FAX : +49-941-943 2305 email: herbert.homeier@chemie.uni-regensburg.de (preferred) homeier@vax1.rz.uni-regensburg.d400.de na.hhomeier@na-net.ornl.gov -------------------------------------------------------------- -------------------- cut here, call orbitals.txt, import as text file --------- #45678901234567890123456789012345678901234567890123456789012345678901234567890 # # author and copyright: Herbert H. H. Homeier, 1994 # email: na.hhomeier@na-net.ornl.gov # date: April 11, 1994 # # description: procedures to compute real and complex spherical harmonics # and to display them via three-dimensional polar diagrams # # include plots package with(plots); # define a procedure for a 3d polar diagram pointnr := 4000: # number of points in the plot polardiagram:=u -> sphereplot(abs(simplify(u)),phi=0..2*Pi,theta=0..Pi, axes=boxed,scaling=constrained,style=point,numpoints=pointnr); # define spherical coordinate functions (for r=1) x:=(phi,theta)->cos(phi) * sin(theta); y:=(phi,theta)->sin(phi)*sin(theta); z:=(phi,theta)->cos(theta); # plot some cartesian real angular functions d_xy:=polardiagram( (x(phi,theta)*y(phi,theta)) ): d_xy; p_x:=polardiagram(x(phi,theta)): p_x; f_xyz:=polardiagram( (x(phi,theta)*y(phi,theta)) *z(phi,theta) ):f_xyz; # define procedures for # associated Legendre function # of simple argument x assLeg:=(l,m,x)->1/2^l/l!*(1-x*x)^abs(m/2)* diff( (x*x-1)^l,seq(x,i=1..(l+abs(m)))); # of complicated argument (for instance z=cos(theta)) AssLeg:=proc(l,m,z) local x; simplify(subs(x=z,assLeg(l,m,x))); end; # complex spherical harmonics (Condon-Shortley phases) spherHarm:=proc(l,m,theta,phi) local mm,x; mm:=abs(m); I**(m+mm)* 1/2^l/l!*(sin(theta))^mm* simplify( subs(x=cos(theta), diff( (x*x-1)^l,seq(x,i=1..(l+mm))) ) )* exp(I*m*phi)* sqrt((2*l+1)*(l-mm)!/(l+mm)!/4/Pi); end; # real spherical harmonics ( m<0: sin function, else cos function) realSpherHarm:=proc(l,m,theta,phi) local mm,x; mm:=abs(m); if m<0 then AssLeg(l,mm,cos(theta))*sin(mm*phi)*sqrt((2*l+1)*(l-mm)!/(l+mm)!/2/Pi); else AssLeg(l,mm,cos(theta))*cos(mm*phi)*sqrt((2*l+1)*(l-mm)!/(l+mm)!/2/Pi); fi; end; # create 3d polar diagrams for some real spherical harmonics polardiagram(realSpherHarm(3,0,theta,phi)); # pointnr := 40000: # uncomment for higher resolution of next plot (slower!) polardiagram(realSpherHarm(5,2,theta,phi)); # calculate some complex spherical harmonics spherHarm(5,-5,theta,phi); spherHarm(5,-4,theta,phi);factor("); spherHarm(5,-3,theta,phi);factor("); spherHarm(5,-2,theta,phi);factor("); spherHarm(5,-1,theta,phi);factor("); spherHarm(5,0,theta,phi);factor("); spherHarm(5,1,theta,phi);factor("); spherHarm(5,2,theta,phi);factor("); spherHarm(5,3,theta,phi);factor("); spherHarm(5,4,theta,phi);factor("); spherHarm(5,5,theta,phi);factor("); # compare A. Lindner, Drehimpulse in der Quantenmechanik # (Teubner, Stuttgart, 1984), p. 97. spherHarm(3,3,theta,phi);factor("*sqrt(4*Pi/7)); spherHarm(3,-3,theta,phi);factor("*sqrt(4*Pi/7)); spherHarm(3,2,theta,phi);factor("*sqrt(4*Pi/7)); spherHarm(3,-2,theta,phi);factor("*sqrt(4*Pi/7)); spherHarm(3,1,theta,phi);factor("*sqrt(4*Pi/7)); spherHarm(3,-1,theta,phi);factor("*sqrt(4*Pi/7)); spherHarm(3,0,theta,phi);factor("*sqrt(4*Pi/7)); From pacahil@somnet.sandia.gov Mon Apr 11 19:12:23 1994 Received: from somnet.sandia.gov for pacahil@somnet.sandia.gov by www.ccl.net (8.6.4/930601.1506) id TAA29381; Mon, 11 Apr 1994 19:00:56 -0400 Received: (from pacahil@localhost) by somnet.sandia.gov (8.6.7/8.6.6) id RAA25984 for CHEMISTRY@ccl.net; Mon, 11 Apr 1994 17:01:16 -0600 Date: Mon, 11 Apr 1994 17:01:16 -0600 From: Paul A Cahill Message-Id: <199404112301.RAA25984@somnet.sandia.gov> To: CHEMISTRY@ccl.net Subject: JACS Gopher? Can't decode the TIFF files! Has anyone had any luck in downloading and then reading the files available on the American Chemical Society site? I'm trying to retrieve supplementary material which is apparently stored as a "Group 4 Fax" compressed TIFF file. The ftp or gopher transfers work fine, but I don't have a program that can read the compressed file. Please respond directly to me. I'll summarize to the net if there is interest. Thanks!!! Paul Cahill Sandia National Laboratories pacahil@somnet.sandia.gov P.S. I'm using a Mac, so I'd prefer such programs, but will summarize all responses... From billg@SCGROUP.BARRNET.NET Mon Apr 11 19:26:03 1994 Received: from mail.barrnet.net for billg@SCGROUP.BARRNET.NET by www.ccl.net (8.6.4/930601.1506) id SAA29203; Mon, 11 Apr 1994 18:19:23 -0400 Received: from fujitsu1.fai.com by mail.barrnet.net (5.67/1.37) id AA15967; Mon, 11 Apr 94 15:19:21 -0700 Received: from scg.scg.fai.com by fujitsu.fai.com (4.1/SMI-4.1) id AA03142; Mon, 11 Apr 94 15:19:18 PDT Received: by scg.scg.fai.com (4.1/SMI-4.1) id AA05482; Mon, 11 Apr 94 15:20:07 PDT Date: Mon, 11 Apr 94 15:20:07 PDT From: billg@scg.fai.com (Marketing) Message-Id: <9404112220.AA05482@scg.scg.fai.com> To: chemistry@ccl.net Subject: aqueous modeling code Netters, I am looking for a Windows-based PC software package that computes various properties of aqueous systems. Examples include properties such as free energies of solvation, pKa, partition coefficients, solubilities, diffusion coefficients, etc. My guess is that any such package would be rule-based, but perhaps there are some that include input from quantum-chemical calculations as well. I believe that MSI markets a code known as "Polaris" that fulfills a similar function on UNIX-based platforms. I would certainly appreciate any suggestions or comments that you may have. -Bill ********************************************************************* * William A. Glauser, Ph.D. | Internet: billg@scg.fai.com * * Computational Chemist | Voice: (610) 436-8125 * * SuperComputer Group | FAX: (610) 430-1526 * * Fujitsu America, Inc. | * *********************************************************************