From dlim@minerva.cis.yale.edu Tue May 3 02:22:11 1994 Received: from minerva.cis.yale.edu for dlim@minerva.cis.yale.edu by www.ccl.net (8.6.4/930601.1506) id BAA16982; Tue, 3 May 1994 01:48:42 -0400 Received: by minerva.cis.yale.edu (5.0/SMI-SVR4) id AA08906; Tue, 3 May 1994 01:49:12 +0500 From: dlim@minerva.cis.yale.edu (Dongchul Lim) Message-Id: <9405030549.AA08906@minerva.cis.yale.edu> Subject: calculation of atomic charges (summary) To: chemistry@ccl.net Date: Tue, 3 May 1994 01:49:12 -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: 1800 I'd like to thank all who responded. Here is a summary (rather severe chop-off of all signatures was made...) -D.LIM (dlim@minerva.ycc.yale.edu) ------------------------------ >From connectivity information: ------------------------------ Johannes Gasteiger et al, 1993 or 1994 in J. Comp. Chem. or J. Chem. Inf. Comput. Sci. Steven Dixon and Peter Jurs J. Comp Chem, 1993 or 1994. Dave Elrod dwelrod@upj.com The Gasteiger-Marsili method (along with its variants) is the most popular The original reference is J. Gasteiger and M. Marsili, Tetrahedron, 3 6, 3219 - 3288 (1980), although there have been enhancements since. Tom Slee slee@hyper.com Skorczyk(Acta Cryst., A32, 447 (1976)) or Gasteiger and Marsili(Tetrahedron 36, 3219(1980)). Both methods are available in commercial software packages such as CHEM-X. Also most molecular modeling programs have some way of getting partial atomic charges from a look up table or computing them from dipole moment values. Jerry Perlstein lsaw00@risque.chem.rochester.edu ------------------------------------- >From electronegativity equilibration: ------------------------------------- Shen, Subramaniam, Wong, McCammon "Superoxide Dismutase: Fluctuations in the Structure and Solvation of the Active Site Channel Studied by Molecular Dynamics Simulation" Biopolymers 1989, 28, 2085-2096 - take a look at reference 19: Sanderson, R. T. "Polar Covalence", 1983, Academic Press, Orlando, FL.). Jim Briggs charge distribution in molecules; the Electronegativity Equalization Method. Huheey, J.E.; "Inorganic Chemistry: Principles of Structure and Reactivity", 3rd ed., Harper & Row, New York, 1983, 159. Mick Kappler A.K. Rappe and W.A. Goddard III, J. Phys. Chem. 95, 3358-3363 (1991) -Jim From srheller@asrr.arsusda.gov Tue May 3 10:22:15 1994 Received: from asrr.arsusda.gov for srheller@asrr.arsusda.gov by www.ccl.net (8.6.4/930601.1506) id KAA20112; Tue, 3 May 1994 10:06:49 -0400 Message-Id: <199405031406.KAA20112@www.ccl.net> Date: 3 May 94 09:44:00 EDT From: "STEPHEN R. HELLER" Subject: One software package for review To: "chemed-l" cc: "chminf-l" , "chemistry" , "orgchem" 3 May, 1994 Subject: Computer Software for Review As the Software Review Editor for the ACS Journal of Chemical Information and Computer Science (JCICS) I often get software for review in the journal. I now have one package in hand (see below) and I am looking for someone who is willing to review the software. In return for the review you get to keep the software. The review should be completed in 1-2 months. The length of the review is 4-10 double spaced typed pages. Sample reviews can be found in most of the recent issues of JCICS. Please try to give me some (short) reason to choose you over another person. DO NOT SAY YOU WILL REVIEW ANYTHING I HAVE AVAILABLE. Messages with such replies are trashed! I have tried this approach for about the past three years and it is working reasonably well. (REMINDER: For those who haven't finished your reviews of software sent months and months ago, this last sentence does not apply to you!) As a result, I am continuing this new method to find reviewers using this e- mail/user group system. I reserve the right to abandon this if it is a problem, or inappropriate. I will not notify people if I have found a reviewer. If you don't hear from me within a few days I have chosen someone else to review the particular package. As I get many, many, (too many) replies to this message, please do not respond after 4 May, 1994 (Wednesday), as I am sure the software will be gone by then. I can be reached on Internet (SRHELLER@ASRR.ARSUSDA.GOV). PLEASE BE SURE TO INCLUDE AN STREET ADDRESS, PHONE, and FAX NUMBER!!! (I send the software by Federal Express.) Without this information I WILL NOT consider your request. Steve Heller The package I now have is: 1. SigmaStat for Windows from Jandel Scientific. This is a statistical package for the PC. From raeker@tc6.fi.ameslab.gov Tue May 3 12:23:33 1994 Received: from ISUMVS.IASTATE.EDU for raeker@tc6.fi.ameslab.gov by www.ccl.net (8.6.4/930601.1506) id LAA21515; Tue, 3 May 1994 11:36:07 -0400 Received: from 147.155.30.6 by ISUMVS.IASTATE.EDU; Tue, 3 May 94 10:35:37 CDT Received: by tc6.fi.ameslab.gov (920330.SGI/921111.SGI.AUTO) for @isumvs.iastate.edu:chemistry@ccl.net id AA26688; Tue, 3 May 94 10:35:08 -0500 From: raeker@tc6.fi.ameslab.gov (Todd J. Raeker) Message-Id: <9405031535.AA26688@tc6.fi.ameslab.gov> Subject: Bulk electronic densities needed To: chemistry@ccl.net Date: Tue, 3 May 1994 10:35:07 -0600 (CDT) X-Mailer: ELM [version 2.4 PL5] Content-Type: text Content-Length: 651 I have a need for atomic electron densities of 3d,4d,5d transition metals derived from DFT bulk calculations. I would prefer parameters for a Gaussian expansion. Does anyone know of a reference or, better yet, a program I could get and run myself? Any pointers would be greatly appreciated. Thanks in advance. Todd. -- Dr. Todd J. Raeker | 307B Wilhelm Hall | Money Talks !! raeker@tc4.fi.ameslab.gov | Iowa State University | Mine keeps Phone (515)-294-9927 | Ames Laboratory, USDOE | saying goodbye. FAX (515)-294-5204 | Ames, Iowa 50011 | From hwang@iris100.biosym.com Tue May 3 12:35:42 1994 Received: from bioc1.biosym.com for hwang@iris100.biosym.com by www.ccl.net (8.6.4/930601.1506) id LAA21604; Tue, 3 May 1994 11:43:34 -0400 Received: from iris100.biosym.com by bioc1.biosym.com (5.64/0.0) id AA02604; Tue, 3 May 94 08:43:03 -0700 Received: by iris100.biosym.com (931110.SGI.ANONFTP/920502.SGI) for @bioc1.biosym.com:chemistry@ccl.net id AA23753; Tue, 3 May 94 08:42:58 -0700 Date: Tue, 3 May 94 08:42:58 -0700 From: hwang@biosym.com (Ming-Jing Hwang) Message-Id: <9405031542.AA23753@iris100.biosym.com> To: chemistry@ccl.net Subject: Re: CCL:Development of new Force Fields Frank Jensen wrote: >...Why not simply select say, a Morse potential >instead? The Taylor expression contains four parameter >(r0 and a,b,c), the Morse only three. ... One reason, a practical one, to use power series instead of Morse function is to make parameterization easier when using quantum mechanical energy data. With a power series the entire energy function (i.e. force field) becomes linear with respect to the force field parameters (force constants) which are being sought, when reference values (bond and angle references) and nonbond parameters are held fixed. The parameters (k1, k2, k3, etc.) can then be solved analytically with one matrix operation. New bond and angle references can be projected from the linear force constants (k1) just solved, and optimal references (the so called "natural" bond lengths and bond angles of the hypothetical "unperturbed" state on the hypersurface of the training set molecules) can be obtained within a few iterations (when all the linear force constants vanish or are essentially zero). This advantage of using the linear-least-squares fitting is lost if a Morse potential is used. Note also there is no structure minimization during the paramterization since the data fitted are direct energy surface properties (configurational energy differences, and energy 1st and 2nd derivatives, etc. from ab initio calculations) and not the geometric parameters (equilibrium bonds, angles, and torsions) or vibrational frequencies commonly used in the traditional methods. This facilitates automation of many parts of the parameterization procedures in the derivation of CFF93 force field. Efficient fitting procedures make it possible to use large amount of quantum mechanical data to fit detailed (Class II) force fields and obtain reliable results. Ming-Jing Hwang hwang@biosym.com From R1JJH@VM1.CC.UAKRON.EDU Tue May 3 15:22:19 1994 Received: from phem3 for R1JJH@VM1.CC.UAKRON.EDU by www.ccl.net (8.6.4/930601.1506) id OAA24165; Tue, 3 May 1994 14:54:35 -0400 Received: from VM1.CC.UAKRON.EDU (MAILER@AKRONVM) by phem3.acs.ohio-state.edu (PMDF V4.2-13 #5888) id <01HBWN5GZEE899HXF8@phem3.acs.ohio-state.edu>; Tue, 3 May 1994 14:53:55 EDT Received: from AKRONVM (NJE origin R1JJH@AKRONVM) by VM1.CC.UAKRON.EDU (LMail V1.1d/1.7f) with BSMTP id 7160; Tue, 3 May 1994 14:35:29 -0400 Date: Tue, 03 May 1994 14:27:26 -0400 (EDT) From: Jack Houser Subject: Gaussian 90 on Tungsten To: Supercomputer bulletin board Message-id: <01HBWN5S9KBI99HXF8@phem3.acs.ohio-state.edu> Content-transfer-encoding: 7BIT Dear Netters: I, a humble organic chemist, have been asked by a colleague to run an ab initio calculation on W(CO)6 and its radical cation. Never having run a calculation on an inorganic compound before, I looked in the Gaussian 90 manual and found that there were two basis sets, LANLIMB and LANL1DZ which were usable for H through Bi. Does anybody know whether one of these is better than the other for my purposes, and is there anything else I should add to the route card? Thanks for the help. Jack Houser Department of Chemistry The University of Akron Akron Ohio 44325-3601 From LONCHARICH_RICHARD_J@Lilly.com Tue May 3 17:23:28 1994 Received: from Lilly.com for LONCHARICH_RICHARD_J@Lilly.com by www.ccl.net (8.6.4/930601.1506) id QAA25116; Tue, 3 May 1994 16:27:20 -0400 Received: from DECNET-MAIL (RX82788@MCVAX0) by INET.D48.LILLY.COM (PMDF V4.3-8 #6224) id <01HBWO95HQ740007Y7@INET.D48.LILLY.COM>; Tue, 3 May 1994 15:26:44 EST Date: Tue, 03 May 1994 15:26:44 -0500 (EST) From: Rick Loncharich Subject: mixed parameters in semiempirical methods To: chemistry@ccl.net Message-id: <01HBWO95JC2A0007Y7@INET.D48.LILLY.COM> X-VMS-To: MCDEV1::IN%"chemistry@ccl.net" MIME-version: 1.0 Content-transfer-encoding: 7BIT SUBJ: mixed parameters in semiempirical methods Douglas Smith and co-workers published a structural study of some aromatic amines in which they document the hazards of using mixed AM1-MNDO parameters. (J. Comp. Chem. 1992, 13(5), 640-650.) Has anyone else published on the hazards of using mixed parameters in semi-empirical calculations? I would appreciate any additional references that document the hazards of doing this. Thanks Rick Loncharich internet: rjl@lilly.com From: LONCHARICH RICHARD J (MCVAX0::RX82788) To: FOREIGN TRANSPORT ADDRESSEE (MCDEV1::IN%"chemistry@ccl.net") From longshot@chem.duke.edu Tue May 3 20:22:22 1994 Received: from duke.cs.duke.edu for longshot@chem.duke.edu by www.ccl.net (8.6.4/930601.1506) id TAA26973; Tue, 3 May 1994 19:26:05 -0400 Received: from london.chem.duke.edu by duke.cs.duke.edu (5.65/3.9G/4.1.3) id AA03170; Tue, 3 May 94 19:26:04 -0400 Received: from canada.chem.duke.edu by london.chem.duke.edu (5.64/1.19LP/4.1.1) id AA09565; Tue, 3 May 94 19:26:03 -0400 Received: by canada.chem.duke.edu (5.64/2.12L/4.1) id AA05648; Tue, 3 May 94 19:26:02 -0400 Date: Tue, 3 May 94 19:26:02 -0400 From: longshot@chem.duke.edu (Brad Isbister) Message-Id: <9405032326.AA05648@canada.chem.duke.edu> To: chemistry@ccl.net Subject: AMBER 4.0 help I'm going through the process of learning AMBER and I'm stuck at the minimization routine. I have created a record for MeOH and gotten through the prep, link, edit, and parm modules. I took the starting coordinates from a drawing out of SYBYL. I've put the molecule in a box of TIP3P water and would like to minimize for a couple hundred steps (but even one will do!). When I run the minimization, all of the support files get read in, the starting coords are written to output, and then it dies, apparently before any energy calculations. The error message says COORDINATE RESETTING CANNOT BE ACCOMPLISHED, DEVIATION IS TOO LARGE. What kinds of things might cause this problem? I've appended the relevant section of the .out file to to this message. I've varied several of the input settings, but in a random way since I don't understand the source of the problem. Any suggestions? Thanks, -Brad ---------------------------------Clip N Save------------------------------------ Brad Isbister Duke University longshot@chem.duke.edu Department of Chemistry Computational/Biophysical chemistry E.J. Toone group Now, the .out file: 3. ATOMIC COORDINATES AND VELOCITIES Methanol begin time read from input coords = 0.000 ps COORDINATE RESETTING CANNOT BE ACCOMPLISHED, DEVIATION IS TOO LARGE NITER, NIT, LL, I AND J ARE : 0 2 1 1 2 FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 0.000 0.000 154.738 H1A 1 BOND = 0.0000 ANGLE = 0.0000 DIHED = 0.0000 VDWAALS = 0.0000 ELECT = 0.0000 HBOND = 0.0000 1-4 NB = 0.0000 1-4 ELEC= 0.0000 CONST = 0.0000 %MINMD-F-ERSTOP, fatal error Routine Sec % -------------------------- Pairlist 0.00 0.00 Nonbond 0.00 0.00 Bond 0.00 0.00 Angle 0.00 0.00 Dihedral 0.00 0.00 Shake 0.18 1.57 Pol. der 0.00 0.00 Efielde 0.00 0.00 Indip 0.00 0.00 Matmul 0.00 0.00 Other 11.48 98.43 -------------------------- Total 11.67 0.00 Hours From news@nntp-server.caltech.edu Tue May 3 22:22:23 1994 Received: from piccolo.cco.caltech.edu for news@nntp-server.caltech.edu by www.ccl.net (8.6.4/930601.1506) id VAA27767; Tue, 3 May 1994 21:41:34 -0400 Received: from gap.cco.caltech.edu by piccolo.cco.caltech.edu with ESMTP (8.6.7/DEI:4.41) id SAA21788; Tue, 3 May 1994 18:41:30 -0700 Received: by gap.cco.caltech.edu (8.6.7/DEI:4.41) id SAA13160; Tue, 3 May 1994 18:41:21 -0700 To: mlist-chemistry@nntp-server.caltech.edu Path: news From: hpritcha@cco.caltech.edu Newsgroups: mlist.chemistry Subject: GAMESS on a PARAGON Date: 4 May 1994 01:41:20 GMT Organization: caltech Lines: 16 Distribution: usa Message-ID: <2q6ug0$cr5@gap.cco.caltech.edu> NNTP-Posting-Host: ostlund.caltech.edu X-Newsreader: Hello mlist.chemistry world, Has anybody out in the mlist chemistry world built an executable of the GAMESS electronic structure program for an Intel Paragon running OSF which actually works? I would appreciate hearing from any such persons, as I cannot get beyond building an exec which immediately gives a Segmentation fault when started in a compute partition. Not even a core file to help diagnose! Thanks in advance. Howard Pritchard 818-395-6537 hpritcha@ccosun.caltech.edu