From SOKALSKI%PLWRTU11.BITNET@phem3.acs.ohio-state.edu Mon Dec 13 02:55:21 1993 Received: from phem3 for SOKALSKI%PLWRTU11.BITNET@phem3.acs.ohio-state.edu by www.ccl.net (8.6.4/930601.1506) id CAA25926; Mon, 13 Dec 1993 02:14:35 -0500 Received: from PLWRTU11.CI-PWR.WROC.EDU.PL (MAILER@PLWRTU11) by phem3.acs.ohio-state.edu (PMDF V4.2-13 #3557) id <01H6EXJIR4Y895S6QL@phem3.acs.ohio-state.edu>; Mon, 13 Dec 1993 02:14:29 EST Received: from PLWRTU11.BITNET (SOKALSKI) by PLWRTU11.CI-PWR.WROC.EDU.PL (Mailer R2.10 ptf000) with BSMTP id 6727; Mon, 13 Dec 93 08:13:57 CET Date: Mon, 13 Dec 1993 08:13:41 +0100 (CET) From: Andrzej Sokalski Subject: RE: summary on population analysis To: "RE: summary on population analysis" Message-id: <931213.081341.CET.SOKALSKI@PLWRTU11.BITNET> Content-transfer-encoding: 7BIT X-Acknowledge-To: Let me add my 2c to the problem how to define atomic charge. > Patrick Bultinck writes: My question is : > What is the use of the S^nPS^(1-n) derived population analysis ? It is very useful to demonstrate the arbitrariness of popular definitions of atomic charge. I always recomend it to beginning students to realize that there is entire universe of population analyses besides Mulliken. Unfortunately, other known definitions (like Potential Derived, zero Charge Flux, etc.) are not much less arbitrary. Sooner or later someone demonstrates in the literature their arbitrariness or complains on their basis set dependence. How to correct this problem in general way ? Perhaps the easiest way out is substituting atomic charges by higher atomic multipole moments. As it has been already pointed out here by Anthony Stone numerous procedures developed since early 70's are known in literature. For example if someone insists to start multipole expansion from particular atomic charge definition one can use our Cumulative Atomic Multipole Moments (CAMM), (Chem.Phys.Lett.98,86(1983), which can be derived starting from any possible atomic charge definition (Theochem, 256,91(1992), J.Comp.Chem.,13,883 (1992)). It may be Mulliken, Lowdin, any arbitrary n value in general S^nPS^(1-n) charge definition, GATP, Potential Derived, assumed ZERO charge on each atom (or even your telephone number if you have such desire) ! The use od CAMM procedure to correct Mulliken and Lowdin charge definitions (also at short distances !) has been demonstrated recently by Koster, Koelle and Jug (J.Chem.Phys. 99,1224(1993). However, the most practical choice will be using definition maximizing monopole contribution, so the multipole expansion will quickly converge. Although it may depend on the case, PD charges recommended by Don Williams seem to be quite good in this respect. This topics is covered in Rev.Comp.Chem,2,219-271(1991). However, the higher multipole corrections to PD charges remain still significant, although better balanced than within Mulliken or Lowdin definitions. What is also important for those dealing with large molecules is that CAMM procedure does not involve expensive and arbitrary fitting process. For those who prefer dealing with point charges instead of multipoles, one may analytically decompose each atomic multipole into set of off-atom charges (see Comp.Phys. Comm.,52,397(1989) or Theor. Chim. Acta, 85,209(1993). Again this procedure does not involve arbitrary fitting and even works at short distances allowing to monitor intramolecular electrostatic interactions ! So in conclusion - we all are probably condemned to use arbitrary atomic charge definitions in building simple models of molecular charge distribution, but there are several ways to correct their deficiencies or estimate corresponding errors "a posteriori". W. Andrzej Sokalski Institute of Physical and Theoretical Chemistry, Wroclaw, Poland From pat@mercury.aichem.arizona.edu Mon Dec 13 15:57:24 1993 Received: from mercury.aichem.arizona.edu for pat@mercury.aichem.arizona.edu by www.ccl.net (8.6.4/930601.1506) id PAA20770; Mon, 13 Dec 1993 15:50:43 -0500 Received: by mercury.aichem.arizona.edu (5.57/Ultrix3.0-C) id AA17825; Mon, 13 Dec 93 13:43:29 -0700 Date: Mon, 13 Dec 1993 13:34:44 -0700 (MST) From: Pat Walters Subject: FREE File Conversion Software - Unix, DOS, Mac To: chemistry@ccl.net In-Reply-To: <9312121658.AA05883@bioc01.uthscsa.edu> Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII BABEL is a program designed to interconvert a number of file formats currently used in molecular modeling. The program is available for Unix (AIX, Ultrix, Sun-OS, Convex, SGI, Cray, Linux), MS-DOS, and Macs running at least System 7.0. Babel will currently read the following file formats : Mopac Cartesian Mopac Internal Mopac Output CSD GSTAT CSD CSSR Free Form Fractional Macromodel MM2 Ouput PDB Alchemy XYZ Mac Molecule Chem3D MicroWorld Ball and Stick MOLIN Babel will currently write the following formats : Mopac Cartesian Mopac Internal Gaussian Input IDATM Macromodel Mac Molecule MM2 Input MM2 Ouput PDB file Report of interatiomic distances, angles, and torsions Alchemy XYZ Ball and Stick Chem3D MicroWorld Babel is capable of assigning hybridization, bond order, connectivity when these elements are not present in the input file. Babel is also capable of adding and deleting hydrogens from a structure. HOW TO OBTAIN BABEL Babel is available by anonymous ftp from joplin.biosci.arizona.edu in the directory pub/Babel. Login as anonymous and give your e-mail address as a password. INSTALLATION OVERVIEW UNIX The Unix version is in the file babel.tar.Z 1. uncompress babel.tar.Z 2. tar -xvf babel.tar 3. follow the instructions in README.1ST ------------- Special note to those with Sun workstations --------------- Unfortunately many Sun workstations have non-ANSI C compliers. Those with Sun workstations have two choices: - compile Babel with gcc - download the file babel-sun.tar.Z which contains an executable binary compiled with gcc under SunOS 4.1.1 -------------------------------------------------------------------------- MAC The Mac version is in the file macbabel.sea.hqx 1. UnBixhex the file with StuffIt Expander, CompactPro or whatever. 2. Double click on the self extracting archive macbabel.sea 3. Follow the instructions in the file Babel Manual. DOS The DOS version is in the file dosbabel.zip 1. pkunzip dosbabel.zip 2. follow the instructions in README.1ST Any questions regarding BABEL should be directed to babel@mercury.aichem.arizona.edu _________________________________________________________________________ Pat Walters pat@mercury.aichem.arizona.edu Graduate Student Laboratory for Artificial Intelligence in Chemistry * Dept of Chemistry * * * University of Arizona, Tucson AZ 85721 * * * Voice : 602-621-6334 FAX : 602-621-8407 *** "At least it's a dry heat" * _______________________________________________________*__________________