From pc1@pctc.chemie.uni-erlangen.de Fri Jan 22 10:23:08 1993 Message-Id: <9301220823.AA19746@pc1.chemie.uni-erlangen.de> To: chemistry@ccl.net Subject: Test of program Date: Fri, 22 Jan 93 09:23:08 +0100 From: Inst.f.Phys.Chem. I Hello, Thanks to everyone who replied. I think there are now enough volunteers to test my program. Peter Gedeck From rafapa@obelix.cica.es Fri Jan 22 10:33:41 1993 Date: Fri, 22 Jan 1993 10:33:41 UTC+0100 From: rafapa@obelix.cica.es Subject: Re: Looking for people who would like to test a program. To: chemistry@ccl.net, pc1@pctc.chemie.uni-erlangen.de Message-Id: <9301220933.AA08014@obelix.cica.es> >X-Envelope-to: chemistry@ccl.net, pc1@pctc.chemie.uni-erlangen.de Dear Sir, if your program does not require a colour screen I would be happy to test it. I have a 386SL portable. My address is: rafapa@obelix.cica.es Yours Sincerely Dr. Rafael R. Pappalardo Dept. Physical Chemistry Univ. of Seville (SPAIN) From DEWINDT@FRSAC11.bitnet Fri Jan 22 13:27:12 1993 Message-Id: <199301221233.AA05396@oscsunb.ccl.net> Date: Fri, 22 Jan 93 13:27:12 GMT From: "D. Mathieu" Subject: force constant symmetry and Gaussian90 To: chemistry@ccl.net Didier MATHIEU DSM - DRECAM - SRSIM Bat 462 CE Saclay F-91191 Gif-sur-Yvette Cedex FRANCE MAT at FRSAC11.BITNET Dear Sir, I would like to use the cartesian force constants provided by Gaussian90. I suppose the indexes of the force constant matrix are numbered according to the usual convention : x1 y2 z1 x2 y2 z2 .... xN yN zN But my main concern stems from the fact that molecular symmetry is not mirrored in the force constants. For instance, in the Gaussian90 User's Guide, the frequency job on H2O seems to be performed in the standard orientation, in that case, many force constants should have identical values, which is not the case. If somebody knows what are exactly the values provided by Gaussian90, I am very grateful to him for his help. Thanks a lot. Didier MATHIEU From cgch!x400!/PN=alain.dietrich/OU=chcgbs21/OU=ph224/@chsun.chuug.ch Fri Jan 22 13:06:32 1993 Date: 22 Jan 93 13:06:32 UT From: "BDIEAL" To: CHEMISTRY@ccl.net Subject: Re: PDB on the Mac Message-Id: <"23603122103991/26437 X400"*@x400.is.ciba-geigy.ch> For those who needed to display PDB mol. on the Mac, you can use: Chem3D Plus. You can even rotate the molecule ! Then if you need a PostScript file, first write it in a PICT format, and read it back in ChemDraw 2.1.3, and finally write it in PostScript format. Ciao. From cramer@chemsun.chem.umn.edu Fri Jan 22 02:33:16 1993 From: "Christopher Cramer" Message-Id: <9301221433.AA00850@chemsun.chem.umn.edu> Subject: Journal font trivia To: chemistry@ccl.net Date: Fri, 22 Jan 93 8:33:16 CST On p. 76 of the ACS style guide ab initio is specifically mentioned as an example of a common latin phrase or abbreviation that is _not_ italicized. Me, I'm just delighted that the ACS thinks "ab initio" is as common as "in situ" and "status quo"! CJC -- Christopher J. Cramer University of Minnesota Department of Chemistry 207 Pleasant St. SE Minneapolis, MN 55455-0431 (612) 624-0859 From tony@wucmd.wustl.edu Fri Jan 22 03:36:22 1993 Date: Fri, 22 Jan 93 09:36:22 -0600 From: tony@wucmd.wustl.edu (Tony Dueben) Message-Id: <9301221536.AA12953@wucmd> To: chemistry@ccl.net Subject: Xlisp information After I complete my sabbatical year here at Washington Univ., I'll be returning to my regular academic job at Southeast Missouri State Univ in Cape Girardeau. Included in my fall teaching assignment is a course on Programming Languages. Does anyone on the net have any information about XLisp, a Lisp-like interpreted for which the source code in C is available? I tried downloading it from WUARCHIVE, but I cannot uncompress the files. I need either the uncompressed files and documentation or compressed versions that really can be restored to fullness. Even an address where I could get one or the other would be help. Anthony J. Duben Center for Molecular Design Washington University Campus Box 1099 -- One Brookings Drive St. Louis MO 63130-4899 314-935-4672 tony@wucmd.wustl.edu From shenkin@still3.chem.columbia.edu Fri Jan 22 06:14:44 1993 Date: Fri, 22 Jan 93 11:14:44 -0500 From: shenkin@still3.chem.columbia.edu (Peter Shenkin) Message-Id: <9301221614.AA00420@still3.chem.columbia.edu> To: fisher@scripps.edu (Cindy Fisher), chemistry@ccl.net Subject: Re: Settle a Bet? Cindy Fisher, fisher@scripps.edu, writes: > According to "The ACS Style Guide" (1986) .... ab initio is explicitly > given as an example of a common Latin phrase that should not be italicized. Grammar dicates that "ab initio" be hyphenated when used as an adjective, since it is a compound form. Thus: "We used ab-initio methods to derive these results", but "We derived these results ab initio." Just as in: "I spent a week in New York, and while there visited the New-York Historical Society." Similarly, "The ligand field splits the d-orbital degeneracy", whereas "Ligand-field effects lift the degeneracy of the d orbitals", where both "ligand field" and "d orbital" are hyphenated when used as compound adjectives, but unhyphenated when used as . Then again, I still use "data" and "media" as plural nouns... :-) -P. ************************f*u*cn*rd*ths*u*cn*gt*a*gd*jb************************ Peter S. Shenkin, Box 768 Havemeyer Hall, Dept. of Chemistry, Columbia Univ., New York, NY 10027; shenkin@still3.chem.columbia.edu; (212) 854-5143 ******* ...ghostlier demarcations, keener sounds. (Wallace Stevens) ******** From surya@flyer.ncsc.org Fri Jan 22 06:07:01 1993 Date: Fri, 22 Jan 93 11:07:01 -0500 From: Dr. Surya Panigrahy Message-Id: <9301221607.AA15618@flyer.ncsc.org> To: chemistry@ccl.net Subject: Stable Recurrence Subject: Stable Recurrence relations. Dear Netters, It would be of great help if any one can give me references to stable recurrence relations for Associated Legendre polynomial and its derivative in the region : theta =0 to 90 degrees. Note: I have tried the recurrence relation given in the NUMERICAL RECIPES book. The recurrence relations are not stable in entire region of theta. surya@cardinal.ncsc.org Dr. Surya N. Panigrahy, chem. Dept., Duke Univ. , Durham, NC 27705, ----- End of the message ----- . From youkha@iris75.biosym.com Fri Jan 22 01:29:49 1993 Date: Fri, 22 Jan 93 09:29:49 -0800 From: youkha@biosym.com Message-Id: <9301221729.AA22570@iris75.biosym.com> To: chemistry@ccl.net Subject: Nomenclature: Internals & Non-Bonds I am looking for a good word that describes BOTH : - Internal Coordinates or simply "INTERNALS": (bond, valence angle, out-of-plane angle, dihedral displacements) representing 1-2, 1-3, 1-4 interactions. - Non-Bond Distances or simply "NON-BONDS" representing 1-4...n interactions. Since we use them both in the analytical form of the Potental Energy, I would like to use one word only to refer to that coordinate system as a whole. One solution is to use simply the word Internals, in adopting a wider meaning, since after non-bond interactions are both intra-molecular and inter-molecular. The problem is that there is no convention here and confusion may arise. There is not even a convention about internal coordinates themselves ! Any thoughts ? I'll summarize for the list if responses come directly to me. Thank you. Philippe Youkharibache Biosym Technologies Inc. youkha@biosym.com From jle@world.std.com Fri Jan 22 08:23:36 1993 Date: Fri, 22 Jan 1993 13:23:36 -0500 From: jle@world.std.com (Joe M Leonard) Message-Id: <199301221823.AA12499@world.std.com> To: chemistry@ccl.net Subject: Looking for references for MNDO/AM1/PM3 parameters Netters... (specifically Jimmie Stewart, Walter Thiel and Andy Holder) I'm looking to complete my reference collection for the various sets of parameters used in semi-empirical calculations of the NDDO type. I have a bunch, but seek anybody with the "complete" list for these methods - including accepted alternatives. Naturally, if I get the references, I'll summarize to the list, but in this case it seems quite appropriate that those in the know post such information themselves. In case the stuff's unpublished, perhaps a simple list of supported elements and associated code/method would be useful... Joe Leonard jle@world.std.com From topper@haydn.chm.uri.edu Fri Jan 22 10:21:51 1993 Date: Fri, 22 Jan 93 15:21:51 -0500 From: topper@haydn.chm.uri.edu (Robert Q. Topper) Message-Id: <9301222021.AA00665@haydn.chm.uri.edu> To: surya@flyer.ncsc.org, chemistry@ccl.net Subject: Re: Stable Recurrence Re: your question about recurrence relations for the Associated Legendre polynomial: May I ask whether you are looking in the old (1986) or new (1992) edition of Numerical Recipes? Perhaps the new edition has an algorithm which will be more suitable. The first edition has some known errors in certain subroutines, which were apparently repaired in the new version. Also, have you looked at Abramowitz and Stegun's "Handbook of Mathematical Functions?" (Dover, New York, 1972). This is a standard sourcebook for algorithms for the computation of special functions like Legendre polynomials (associated or otherwise). -Robert ******************************** * Robert Q. Topper * * Department of Chemistry * * University of Rhode Island * * Kingston, RI 02881 * ******************************** * rtopper@chm.uri.edu OR * * topper@haydn.chm.uri.edu * * (401) 792-2597 [office] * * (401) 792-5072 [FAX] * ******************************** From Joel_Wolff@camsci.com Fri Jan 22 13:28:33 1993 Message-Id: <199301221336265710@mercury.camsci.com> Date: Fri, 22 Jan 1993 13:36:26 +0000 From: BDIEAL Subject: RE:: PDB on the Mac To: Comp Chem Date 1/22/93 Subject RE-- PDB on the Mac >From Joel Wolff To Comp Chem CC BDIEAL Reply to: RE:: PDB on the Mac BDIEAL Writes: >For those who needed to display PDB mol. on the Mac, you can use: > Chem3D Plus. >You can even rotate the molecule ! >Then if you need a PostScript file, first write it in a PICT format, >and read it back in ChemDraw 2.1.3, and finally write it in PostScript >format. >Ciao. I would like to correct his statement. There is no need to transfer the Chem3D Plus image to ChemDraw to get PostScript output. Chem3D Plus 3.1 supports PostScript, and files can be exported to an EPS (Encapsulated PostScript) file. Joel Wolff, Ph.D. Customer Support Manager Cambridge Scientific Computing 875 Massachusetts Avenue, Suite 61 Cambridge, MA 02139 Tel: 617/491-6862 Fax: 617/491-8208 Internet: support@camsci.com Compuserve: 76070,615 AppleLink: CSC.COM AOL: CamSci From system@alchemy.chem.utoronto.ca Thu Jan 21 17:30:39 1993 Date: Thu, 21 Jan 93 17:31:46 -0500 From: system@alchemy.chem.utoronto.ca (System Admin (Mike Peterson)) Message-Id: <9301212231.AA25780@alchemy.chem.utoronto.ca> To: chemistry-request@ccl.net Subject: Re: Normal coordinate analysis Programs written by Doug McIntosh and I are available from QCPE for this purpose, for both "big" IBM/UNIX systems and PCs. Sorry but I don't have the program numbers at hand. The programs build the G matrix from the internal coordinates, and will either do simple normal mode analysis, or will adjust the force constants to fit vibrational frequency data on isotopic substitutions (the more the merrier!). Mike. -- Mike Peterson, SysAdmin, U/Toronto Chemistry E-mail: system@alchemy.chem.utoronto.ca Tel: (416)978-7094 Fax: (416)978-8775 From shenkin@still3.chem.columbia.edu Fri Jan 22 14:32:48 1993 Date: Fri, 22 Jan 93 19:32:48 -0500 From: shenkin@still3.chem.columbia.edu (Peter Shenkin) Message-Id: <9301230032.AA03112@still3.chem.columbia.edu> To: youkha@biosym.com, chemistry@ccl.net Subject: Re: Nomenclature: Internals & Non-Bonds > I am looking for a good word that describes BOTH : > > - Internal Coordinates or simply "INTERNALS": > (bond, valence angle, out-of-plane angle, dihedral displacements) > representing 1-2, 1-3, 1-4 interactions. > > - Non-Bond Distances or simply "NON-BONDS" > representing 1-4...n interactions. > > Since we use them both in the analytical form of the Potental Energy, > I would like to use one word only to refer to that coordinate system ^^^^^^^^^^^^^^^^^ > as a whole. ^^^^^^^^^^ Philippe, I think you want to use a term like "force-field variables" to refer to this set of variables. What defines them is not that they correspond to a set of coordinates -- they do not -- but rather that they are the variables in terms of which the energy and forces are most simply expressed; computationally, they constitute the input to the function that calculates the energy and forces. For example, whether you choose to represent the molecule in Cartesian or in internal coordinates, the distances between all pairs of atoms are well defined once a complete set of coordinates has been assigned to the molecule. However, none of the non-bonded distances is equal to the value of any coordinate in either system. The non-bonded distances are redundant geometric variables which can be calculated from the coordinates; they are not coordinates themselves, unless you are working in distance space. Therefore I'd use a term like "force-field variables". (Note the hyphen. :-) ) -P. ************************f*u*cn*rd*ths*u*cn*gt*a*gd*jb************************ Peter S. Shenkin, Box 768 Havemeyer Hall, Dept. of Chemistry, Columbia Univ., New York, NY 10027; shenkin@still3.chem.columbia.edu; (212) 854-5143 ******* ...ghostlier demarcations, keener sounds. (Wallace Stevens) ********