From B130778@vax.csc.cuhk.hk Thu Dec 10 23:17:00 1992 Date: Thu, 10 Dec 1992 15:17 +0800 From: B130778@vax.csc.cuhk.hk Subject: Stability test in Gaussian 90 To: CHEMISTRY@ccl.net Message-Id: <01GS5LNCNUQ88WWR4R@vax.csc.cuhk.hk> Dear fellow Gaussian users, Sorry to waste the bandwidth. I have sent help to GAUSSIAN many many times but didn't get any reply. I would appreciate any input to my problem. I was checking for the stability of the RHF wavefunction for a closed-shell molecule with G90. The following is the output from G90: *********************************************************************** Matrix Lowest Root Major Pairs *********************************************************************** Internal RHF 0.1012485 Stable RRHF --> CRHF 0.0665675 Stable RRHF --> RUHF -0.0486567 11A=14B 10A=13B 11A=13B 10A=14B 9A=12B 7A=12B 10A= 18B 11A=17B 10A=22B 11A=21B Not stable. *********************************************************************** Does it mean my molecule is RHF -> UHF unstable? Ida N. L. Ma Research assistant Dept. of Chemistry Chinese University of Hong Kong From RWOODS@VAX.MOLECULAR-BIOPHYSICS.OXFORD.AC.UK Thu Dec 10 05:56:44 1992 Message-Id: <199212101037.AA21842@oscsunb.ccl.net> Date: Thu, 10 Dec 92 10:39 BST From: RWOODS@VAX.MOLECULAR-BIOPHYSICS.OXFORD.AC.UK To: CHEMISTRY Subject: Monosaccharides in MOPAC Dear Mary, In regard to your question about the heat of formation of glucose, I will send you an optimized structure for alpha-D-glucopyranose that was generated using AM1 and starting from the crystal geometry. The heat of formation is about 30 kcal lower that yours so I suspect there is indeed a problem with your geometry. Bear in mind though that the absence on a "bond" in the z-matrix may be completely irrelevant--as long as the atoms are positioned correctly. Such "unusual" connectivities can however lead to failures to optimize properly. You should also be concerned with conformational flexibibility in any monosaccharide. Specifically, the hydroxyl groups and hydroxymethyl groups must be varied in orientation and a boltzmann average used then to calculate the heat of formation. Lastly, here are a couple of our references that might be worth a look: J. Am. Chem. Soc. 112 (1990) 4732-4741 J. Chem. Soc., Chem Commun. (1991) 334-337 Sincerely, Rob Woods Robert J. Woods Glycobiology Institute University of Oxford South Parks Road Oxford, OX1 3QU FAX:011-44-865-275216 From braendle@iac.unibe.ch Thu Dec 10 13:25:42 1992 Date: Thu, 10 Dec 1992 12:25:42 +0100 From: Martin Braendle Message-Id: <63*/S=braendle/OU=iac/O=UNIBE/PRMD=SWITCH/ADMD=ARCOM/C=CH/@MHS> To: "Comput. Chem. mailing list" Subject: Literature about CoMFA and QSAR? Can anyone point me to introducing literature about Comparative Molecular Field Analysis (CoMFA) and QSAR methods? Thank you. Martin Braendle ------------------------------------------------------------------------------- Martin Braendle, Institut f. Anorganische u. Physikalische Chemie, Universitaet Bern, Freiestr. 3, CH-3012 Bern, Email braendle@iac.unibe.ch, Tel. xx41 31 65 42 25, Fax xx41 31 65 39 94 ------------------------------------------------------------------------------- From PCJ@PSUVM.PSU.EDU Thu Dec 10 03:45:00 1992 Message-Id: <199212101345.AA24254@oscsunb.ccl.net> Date: Thu, 10 Dec 92 08:45 EST From: Subject: Re: symposium on computer-enhanced analytical spectroscopy ? To: sam@ncsa.uiuc.edu CEAS92 was held this past June. The next meeting of the conference will be June 1994 at Snowbird. The conference chair will be Steve Brown, Chem Dept, Univ of Delaware. P.C. Jurs, Penn State Univ From AHOLDER@VAX1.UMKC.EDU Mon Dec 10 01:58:30 1992 Date: 10 Dec 1992 07:58:30 -0600 (CST) From: Andy Holder Subject: Optimized starting places. To: CHEMISTRY@ccl.net Message-Id: <01GS562FPWSI9UM35O@VAX1.UMKC.EDU> Dear Netters, A question was asked about which starting place was best for subsequent calculations of properties using AM1. I think that there is a general principle that needs to be addressed here: Strictly speaking, the calc- ulated properties of a molecule using a particular model are valid ONLY AT A MINIMA PREDICTED BY THAT MODEL. This goes for MM, semiempirical, and ab initio methods. It is relatively common practice to perform high level property computations on a lower level ab initio optimized struct- ure. This is due to time constraints (especially for the required freq- uency analysis). For semiempirical methods (especially for non-class- ical systems) I would ALWAYS use the AM1 geometry. In the case you cited, the MM and SE geometries were very close. Most fortunate, but don't count on it. Andy =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= 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) 235-1717 =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= From jabs@chemie.uni-halle.dbp.de Thu Dec 10 16:14:44 1992 Date: Thu, 10 Dec 1992 15:14:44 +0100 From: jabs@chemie.uni-halle.dbp.de Message-Id: <921210151444*/S=jabs/OU=chemie/PRMD=UNI-HALLE/ADMD=DBP/C=DE/@MHS> To: chemistry@ccl.net Subject: dimer Hi, has anybody experiences in ab initio calculations of the angle- and distance depending of the hydrogen bonding in water-dimer (surface angle-distance and energy) or references from the litera- ture about this problem? I am not only interested on the water dimer, also in dimers of other systems (alcohols) and their hydrogen bonding parameters. ANdreas Jabs e-mail: c=de;a=dbp;p=uni-halle;ou=chemie;s=jabs From mfrancl@cc.brynmawr.edu Thu Dec 10 05:02:28 1992 Date: Thu, 10 Dec 92 10:02:28 -0500 From: mfrancl@cc.brynmawr.edu (Francl Michelle M) Message-Id: <9212101502.AA07493@cc.brynmawr.edu> To: chemistry@ccl.net Subject: information on computing in chemical education conferences One of my colleagues has recently received a grant for improving the introductory course in chemistry. She is interested in particular in increasing the variety of computing offered in the course. Does anyone know of any upcoming conferences that might be relevant, or of any active lists or newsgroups that might be helpful? Thanks! Michelle M. Francl mfrancl@cc.brynmawr.edu Department of Chemistry Bryn Mawr College From rafapa@obelix.cica.es Thu Dec 10 16:25:45 1992 Date: Thu, 10 Dec 1992 16:25:45 UTC+0100 From: rafapa@obelix.cica.es Subject: Re: Newzmat: from xyz to z-matrix To: CHUCK@psipsy.uct.ac.za, rafapa@obelix.cica.es Message-Id: <9212101525.AA12490@obelix.cica.es> >X-Envelope-to: chemistry@ccl.net The newzmat prgram that I mentioned yesteday is in the Gaussian 92 distribution. Sorry for the omission R.R. Pappalardo From kazic@antares.mcs.anl.gov Thu Dec 10 03:57:51 1992 From: kazic@antares.mcs.anl.gov (Toni Kazic) Date: Thu, 10 Dec 92 09:57:51 CST Message-Id: <9212101557.AA21728@clone.mcs.anl.gov> To: mes@atlas.chemistry.uakron.edu Subject: MOPAC Mary Ellen, I'm not a chemist but interested in simple sugars. Could you provide a reference of trail to this Quanta/Mopac interface? Thanks, toni From rjb@qm.c-chem.siu.edu Thu Dec 10 04:01:11 1992 Message-Id: <00133.2806831141.9638@qm.c-chem.siu.edu> Organization: Southern Illinois University at Carbondale To: CHEMISTRY@ccl.net (ChemComp Discussion) From: rjb@qm.c-chem.siu.edu (Robert Brenstein) Date: Thu, 10 Dec 1992 10:01:11 CST Subject: Re: Fortran buffs.. Reply RE>Fortran buffs.. A simple solution is to make the repetition number to be large (but that the output line max is not exceeded). For example, if you can print max of 132 chars, make you program as follows: do i=1, a write(*,200) (tor(i,j), j=1, a) 200 format(11(1x,f10.4,',')) enddo This will work for all values of "a"--Fortran will just use the format for as many elements of a as needed. If a > 11, you will just get two output lines, which is probably what you want anyway (if a>22, you will get 3 output lines and so forth). If you don't want the last comma on the output, check whether your compiler supports colon, :, as format delimiter. If it does, change the format statement to: 200 format(11(1x,f10.4,:,',')) This should make a conditional stop after last value is printed (if I remember correctly --this is not a feature that I use that often). This also assumes that you really need a comma between all numbers. If you need to compose more complex format statements that depend on variables in your program, read about using "internal write" feature of Fortran77 to make format statements on the fly. Robert -------------------------------------- I have a question related to fortran (for comp. chem. code). I want to write a file in 'matrix format'. ie , an output for a 3x3 matrix: a b c d e f g h i The existing code simply is: do i=1, a write(*,200) (tor(i,j), j=1, a) 200 format(3(1x,f10.4,',')) enddo Where 'a' in this case is 3 and is user defined (for different sizes). The question is about the format statement '200' I have to set the size '3' then compile. Fortran wont let me use a variable (in this case 'a') in the format statement. The question, is there a work around to make the format statement variable and reflect the dimension of the matrix without re-editing and re-compiling?