From dave@carbon.chem.csiro.au Tue Feb 23 11:28:11 1993 Message-Id: <199302230527.AA00546@shark.mel.dit.csiro.au> Date: Tue, 23 Feb 93 16:28:11 EST From: (Dr.) Dave Winkler Subject: List of Asian/Pacific comp chemists/modellers To: chminf-l@iubvm.ucs.indiana.edu, chemistry@ccl.net, Thanks to those who responded to my call for information on people in the Asia/Pacific region. I encourage anyone else who hasn't replied to me to do so. I will keep those people informed of events of interest in this area. __________________________________________________________________________ Dr. David A. Winkler Voice: 61-3-542-2244 Principal Research Scientist Fax: 61-3-543-8160 CSIRO Division of Chemicals and Polymers Private Bag 10 Clayton, Australia. "Life is what happens to you while you're making other plans" From jbundens@cc.brynmawr.edu Tue Feb 23 06:42:44 1993 Message-Id: <9302231642.AA05528@cc.brynmawr.edu> Subject: Koopmans? To: chemistry@ccl.net Date: Tue, 23 Feb 93 11:42:44 EST From: Bundens Jeanne W Would anyone happen to know T. Koopmans' first name or whether Koopmans was a man or a woman? From Physica 1933,1,104, Koopmans' theorem gives a way of calculating approximate ionization potentials and electron affinities. thanks, J. Bundens jbundens@cc.brynmawr.edu From vincent@retina.chem.psu.edu Tue Feb 23 08:37:44 1993 Date: Tue, 23 Feb 93 13:37:44 -0500 From: vincent@retina.chem.psu.edu (Jim Vincent) Message-Id: <9302231837.AA12997@retina.chem.psu.edu> To: CHEMISTRY@ccl.net Subject: Parallel AMBER summary Here is a very distilled summary of responses to the question: Has anyone implemented a parallel version of AMBER? Parallel Implementations of AMBER: Machine Group/Person Visionary Systems Computer Dave Evans (SIMD board for PC) Visionary Systems SGI RS3000 Mark Berger Roberto Gomperts SGI (UCSF does not confirm this) PVM on Indigo RS3000 Terry Lybrand and IBM RS6000 550 U of Washington, Seattle (Should run on any machines that run PVM) nCUBE Stephen DeBolt Peter Kollman UCSF Many people suggested AMBER has been implemented in parallel on various other machines such as Cray YMP, CM-5, and CM-2, however I have received no specific responses - only vague recollections. Work in progress is not included in this summary Jim Vincent vincent@retina.chem.psu From hogue@mosquito.den.mmc.com Tue Feb 23 06:08:29 1993 Date: Tue, 23 Feb 93 13:08:29 MST From: hogue@mosquito.den.mmc.com (Pat Hogue 1-2183) Message-Id: <9302232008.AA01433@mosquito.den.mmc.com> To: chemistry@ccl.net Subject: Methylene Could anyone offer an opinion on a small dilemma I am facing? The version of AM1 I have (GEOMOS, QCPE #584) gave singlet methylene with a slight negative charge on carbon ----- Begin Included Message ----- From chemistry-request@ccl.net Tue Feb 16 15:30:15 1993 Date: Tue, 16 Feb 93 10:04:11 -0800 From: wrinn@biosym.com Message-Id: <9302161804.AA01375@iris104.biosym.com> To: CHEMISTRY@ccl.net Subject: dmol electrostatic potentials There is a bug in DMol version 2.2 in the calculation of electrostatic potentials, as reported by Grzegorz Bakalarski. This has been corrected in version 2.3, which is (as of this week) the current version. DMol users may report bugs directly to rcenter@biosym.com. Michael Wrinn --- Administrivia: This message is automatically appended by the mail exploder: CHEMISTRY@ccl.net --- everyone CHEMISTRY-REQUEST@ccl.net --- coordinator OSCPOST@ccl.net send help from chemistry Anon. ftp www.ccl.net CHEMISTRY-SEARCH@ccl.net --- search the archives, read help.search file first --- ----- End Included Message ----- and small positive charges on the two hydrogen atoms, this is opposite to the example given in Tim Clark's handbook of computational chemistry. I think Tim's structure is correct because insertion requires a bridging intermediate, and because singlet methylene is probably considered "hot" because the hydrogens have a high negative valence. Thanks in advance to any or all offering help. From mbasd@seqnet.daresbury.ac.uk Tue Feb 23 18:29:59 1993 From: "A. Sheppard" Date: Tue, 23 Feb 93 18:29:59 GMT Message-Id: <23831.9302231829@s-crim1.dl.ac.uk> To: chemistry@ccl.net Subject: Connolly Surface Modelling Programs... Regular readers will remember I asked a few weeks ago about getting in touch with Michael Connolly with the intention of finding out more about his suite of surface modelling programs. Lisa Balbes (balbes@osiris.rti.org) was kind enough to give me his address: Michael L. Connolly Computational Scientist 2269 Chestnut Street, Suite 279 San Francisco CA 94123 USA (Tel. 010-1-415-346-3505) Michael then replied to my letter with a manual and some reprints describing his Molecular Surface Package (MSP). The various programs, briefly described below, are distributed as C source on Macintosh disks for a fee. I have not yet got the MSP package so these notes are my observations on reading the manual. PQMS (piecewise quartic molecular surface): an improvement of Connolly's original MS program (MS is available from QCPE, No. 429 I think). SRF - renders the PQMS output to show a smooth _solid_ surface rather than a dot surface. Also draws ball+stick and tube diagrams. A separate display program (e.g. Ribbons) is required. The surface can have a degree of transparency. TRB - reads file from PQMS and triangulates it, i.e. the dot surface >from PQMS is now represented as a triangular mesh. Needs a separate display program. Presumably the output could be used as input to a ray-tracing program. Omega - computes the curvature of the triangle surface from TRB DS - seems to be similar to the original MS program, except written in C instead of Fortran (=> is a lot faster ?). CPF - computes contours for a function defined at the vertices of a polyhedron. PDB2MS - converts atomic coordinates from PDB format to the format required by MS et al. Seems like a very well written and useful package. Hope this is of some use to you. Andy Sheppard mbasd@seqnet.daresbury.ac.uk -------------------------------------------- From AHOLDER@VAX1.UMKC.EDU Tue Feb 23 09:08:25 1993 Date: 23 Feb 1993 15:08:25 -0600 (CST) From: Andy Holder Subject: Carl Jug To: CHEMISTRY@ccl.net Message-Id: <01GV2D5QYS4I9EG42K@VAX1.UMKC.EDU> Does anyone have an e-mail for Carl Jug or even a regular mail? We are interested in SINDO. Andy P.S. Yes, I asked Jan first. =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= 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 wsonnen@rcf.usc.edu Tue Feb 23 07:08:43 1993 Date: Tue, 23 Feb 93 15:08:43 PST From: wsonnen@alnitak.usc.edu (Wayne Sonnen) Message-Id: <9302232308.AA19689@alnitak.usc.edu> To: chemistry@ccl.net Subject: dna base charges Dear CC netters, I am interested in obtaining electrostatic potential-derived charges with solvation effects included for dna bases: adenine, guanine, cytosine and thymine. My intention is to use these derived charges in some molecular dynamics studies. I understand that Guassian 92 can perform such calculations using a reaction-field model for the solvent and solving the problem in an iterative procedure. (1) Does anyone have any references in which such calculations have been done for the above dna bases? (2) How realistic are the derived charges on the above bases? I am interested in the charge distribution on the bases as they exist as isolated molecules in water and as they exist in both single and double stranded dna. (3) How would the counterions effect the charge distribution of the bases? Comments and/or opinions are very welcome. I will summarize responses and post it on the network. Although for discussion purposes, it might be best to reply to chemistry@ccl.net. Thank you, Wayne Sonnen wsonnen@alnitak.usc.edu