From chemistry-request@ccl.net Mon Jul 27 12:46:52 1992 Date: Mon, 27 Jul 92 10:35:03 EDT From: "Robert L. Feldman" Subject: Survey on neural networks in medicine To: CHEMISTRY@ccl.net Status: R Date: Sun, 26 Jul 1992 18:04:00 GMT-0200 From: SABBATINI@CCVAX.UNICAMP.BR Subject: Survey on Neural Networks in Medicine To: Robert Feldman Date: Mon, 27 Jul 1992 11:12 CST From: C1790@slvaxa.umsl.edu Subject: NEED INFO ON CLARK STILL'S SOLVATION MODEL To: CHEMISTRY@ccl.net Status: R DEAR NETTERS, CAN SOMEONE RECOMMEND A RECENT PUBLICATION WHICH DESCRIBES AN APPLICATION OF CLARK STILL'S SOLVATION MODEL (W.C. STILL, et al., "SEMIANALYTICAL TREATMENT OF SOLVATION FOR MOLECULAR MECHANICS AND DYNAMICS", JACS, 112, 6127 (1990)? WE HAVE JUST COMPLETED A STUDY OF CONFORMATIONAL ENERGIES OF COMPLEX IONS, BOTH WITH AND WITHOUT INCLUSION OF CLARK'S SOLVATION TERMS. WE HAVE SOME QUESTIONS ABOUT SEPARATING THE "ELECTROSTATIC" COMPONENTS FROM THE "SOLVATION" COMPONENTS OF THE TOTAL CALCULATED ENERGY. WE WOULD LIKE TO SEE HOW OTHERS MAY HAVE HANDLED THIS ASPECT. AN REFERENCES ARE MUCH APPRECIATED. SEND TO BILL WELSH AT C1790@UMSLVAXA. --- Administrivia: The rest of this message is automatically appended by the mail exploder. CHEMISTRY@ccl.net --- everybody; CHEMISTRY-REQUEST@ccl.net --- coordinator only OSCPOST@ccl.net : send something from chemistry; FTP: www.ccl.net --- From chemistry-request@ccl.net Mon Jul 27 14:38:57 1992 Date: Mon, 27 Jul 1992 11:02 CST From: C1790@slvaxa.umsl.edu Subject: BILL WELSH To: CHEMISTRY@ccl.net Status: RO DEAR NETTERS, I WANT TO ADVERTISE A POSTDOCTORAL POSITION HERE PRIOR TO ITS APPEARANCE IN C&E NEWS. I AM LOOKING TO FILL A 2-3 YEAR POSTDOCTORAL POSITION ON A PROJECT FUNDED BY THE US FOOD AND DRUG ADMINISTRATION. SALARY IS NEGOTIABLE, BUT I EXPECT IT WILL BE $20K+ IN ADDITION TO FRINGE BENEFITS (I.E., MEDICAL, ETC.). THE APPLICANT MUST HAVE SOME EXPERTISE/ EXPERIENCE IN THE USE OF ARTIFICIAL INTELLIGENCE WITH AN EMPHASIS IN NEURAL NETWORKS. THE SPECIFIC APPLICATION INVOLVES USING NEURAL NETWORKS FOR ANALYSIS OF CHROMATOGRAPHIC SCANS OF DRUG FORMULATIONS, SO THE APPLICANT SHOULD HAVE A PHD IN CHEMISTRY OR RELATED AREA WITH AN EMPHASIS IN ANALYTICAL TECHNIQUES, COMPUTATIONAL METHODS OF ANALYSIS, AND DRUG ANALYSIS. PREVIOUS EXPERIENCE IN USING NEURAL NETS IN THE FIELD OF CHEMISTRY IS A BIG PLUS. A SECONDARY ASPECT OF THIS PROJECT INVOLVES COMPUTATIONAL CHEMISTRY, MOLECULAR MODELLING, AND COMPUTER-AIDED DESIGN. THUS SOME BACKGROUND IN APPLIED MOLECULAR MECHANICS AND DYNAMICS, MONTE CARLO, MOLECULAR ORBITAL METHODS, AND COMMERCIAL PACKAGES (E.G., INSIGHT/DISCOVER, SYBYL, SPARTAN, GAUSSIAN, AMPAC/MOPAC, MM3) IS AN ADDITIONAL PLUS FOR THE APPLICANT. INTERESTED PEOPLE SHOULD ARRANGE TO SEND VITA WITH COVER LETTER PLUS AT LEAST TWO LETTERS OF REFERENCE TO DR. BILL WELSH, DEPT. OF CHEMISTRY, UNIVERSITY OF MISSOURI, 8001 NATURAL BRIDGE RD., ST. LOUIS, MO 63121. A STARTING DATE BEFORE DECEMBER, 1992, IS DESIRABLE. THE UNIVERSITY OF MISSOURI IS AN AFFIRMATIVE ACTION/EQUAL OPPORTUNITY EMPLOYER. THANKS, BILL WELSH (C1790@UMSLVAXA). --- Administrivia: The rest of this message is automatically appended by the mail exploder. CHEMISTRY@ccl.net --- everybody; CHEMISTRY-REQUEST@ccl.net --- coordinator only OSCPOST@ccl.net : send something from chemistry; FTP: www.ccl.net --- From chemistry-request@ccl.net Mon Jul 27 17:38:50 1992 Date: Mon, 27 Jul 1992 12:16:44 -0700 (PDT) From: F0418950@JAGUAR.CSC.WSU.EDU Subject: Periodic Boundary Conditions in DISCOVER To: chemistry@ccl.net Status: R Help! Has anyone successfully carried out a MD simulation with peroidic boundary conditions (pbc) using the AMBER ff in DISCOVER 2.8.0 (by Biosym)? I would like to solvate a molecule I have and carry out a pbc md simulation . At the moment I have been just trying to get a pdc md simulation to work on a 10 angstrom cubic box without success. The directions in the manual are sketchy at best, especially in its description of the requirements for a pbc calculation( i.e. it states that after a pdc solvation has occured the replicate molecules must be made into real molecules and all replicates of the solvated molecule must be placed explicitly in the unit cell - - - say what?). Any help or examples(and clairification) would be greatly appreciated. Thanks in advance, Andrew f0418950@jaguar.csc.wsu.edu Washington State University Dept. of Biochemistry --- Administrivia: The rest of this message is automatically appended by the mail exploder. CHEMISTRY@ccl.net --- everybody; CHEMISTRY-REQUEST@ccl.net --- coordinator only OSCPOST@ccl.net : send something from chemistry; FTP: www.ccl.net --- From chemistry-request@ccl.net Mon Jul 27 19:46:10 1992 Date: Mon, 27 Jul 1992 15:53:26 EDT From: JOHNSON@CMCHEM.CHEM.CMU.EDU (Benny Johnson) Subject: Experimental values for molecular properties To: chemistry@ccl.net Status: RO Fellow netters, Can anyone give me references which collect together reliable, up-to-date experimental values of various molecular properties -- geometries, dipole moments, vibrational frequencies? I'm interested in these values mainly for small neutral systems with first-row atoms. Thanks in advance, Benny Johnson Carnegie Mellon University --- Administrivia: The rest of this message is automatically appended by the mail exploder. CHEMISTRY@ccl.net --- everybody; CHEMISTRY-REQUEST@ccl.net --- coordinator only OSCPOST@ccl.net : send something from chemistry; FTP: www.ccl.net --- From chemistry-request@ccl.net Mon Jul 27 20:53:18 1992 To: CHEMISTRY@ccl.net Organization: University of Illinois at Chicago Date: Monday, 27 Jul 1992 16:56:54 CDT From: Alan Hinds Subject: G90 installation in IBM VM/CMS Status: RO I am installing G90 in VM/CMS on an IBM 3090. The installation materials say the program is supported for IBM VS Fortran version 2.3 and 2.4, both old versions. Has anyone installed G90 using the current VS Fortran version 2.5? If so, did you encounter problems? Thank you for any assistance. - Alan Hinds --- Administrivia: The rest of this message is automatically appended by the mail exploder. CHEMISTRY@ccl.net --- everybody; CHEMISTRY-REQUEST@ccl.net --- coordinator only OSCPOST@ccl.net : send something from chemistry; FTP: www.ccl.net --- From chemistry-request@ccl.net Mon Jul 27 21:34:51 1992 Date: 27 Jul 1992 17:30:51 -0400 (EDT) From: "Joseph E. Bitar" Subject: CASSCF orbitals assignment. To: chemistry@ccl.net Status: RO I am trying to perform CASSCF calculations on the singlet of a cyclic cation, C6NH6 (+1) using the 3-21G basis set. Gaussian 90 and/or 92 is the program of choice. The active space we want to define includes the six pi electrons in the six pi and pi* orbitals plus the empty p orbital on the nitrogen. I plan to do both single points and geometry optimizations. I have already done the RHF/3-21G optimization and an MP2/3-21G//RHF/3-21G single point calculations. Analysis of the Mulliken population at the RHF/3-21G level suggests that the occupied orbitals of interest are 20, 22, and 24(HOMO), and the virtual orbitals are 25, 26, 29, and 30. These results were confirmed visually using the AVS Chemistry Viewer. The manual for GAUSSIAN 90 suggests performing a single point calculation using the flag GUESS=ONLY in order to determine the proper pi orbitals (in this case, seven (7) orbitals, three occupied and four virtual) to be included in the calculation. This GUESS=ONLY run using CASSCF suggested that the occupied pi orbitals that should be included are 15, 18 and 23(HOMO-1); the virtual orbitals 27, 32, 36, and 41 also contained significant p or pi contributions and would complete the active space. Since I don't have any experience with these type of calculations, I would like to know if I am overlooking something that should be considered, included, omitted,...? and to know which approach is more correct for determination of the proper orbitals of the CASSCF calculation, i.e those >from the RHF/3-21G optimization or the CAS(6,7)/RHF GUESS=ONLY run. Joseph Bitar Graduate Student, University of Toledo. Chemistry Dept. e-mail: jbitar@uoft02.utoledo.edu --- Administrivia: The rest of this message is automatically appended by the mail exploder. CHEMISTRY@ccl.net --- everybody; CHEMISTRY-REQUEST@ccl.net --- coordinator only OSCPOST@ccl.net : send something from chemistry; FTP: www.ccl.net --- From chemistry-request@ccl.net Mon Jul 27 22:34:58 1992 From: Dongchul Lim Subject: Re: Neural Nets summary (warrning - LONG STUFF) To: chemistry@ccl.net (Computational Chemistry) Date: Mon, 27 Jul 92 18:03:44 EDT Status: RO radomski@mond1.ccrc.uga.edu writes: > > Hello Netters, > > here goes summary and my own answers to questions about > artificial neural networks. I took me a little while but then the > Jan's ban put on chemistry@ccl.net was quite a something! [...] > FTP site at cattell.psych.upenn.edu contains back issues od > Neuron-Digest, excellent source on all sorts of subjects connected > with neural networks (mainly artificial, but not only). The archive > contains close to 3000 pages (my estimate) of stuff, heavy going > but well worth it!!! > Neuron-Digest is the moderated by Peter Marvit. > In additon to Neuron-Digest, a massive collection of neural networks papers is available from archive.cis.ohio-state.edu in the directory /pub/neuroprose via anon ftp. -dcl /* Dept. of Chemistry, Yale Univ. 225 Prospect Street, New Haven, CT 06511 */ --- Administrivia: The rest of this message is automatically appended by the mail exploder. CHEMISTRY@ccl.net --- everybody; CHEMISTRY-REQUEST@ccl.net --- coordinator only OSCPOST@ccl.net : send something from chemistry; FTP: www.ccl.net ---