From eslone@mason1.gmu.edu Sun Oct 2 13:16:38 1994 Received: from mason1.gmu.edu for eslone@mason1.gmu.edu by www.ccl.net (8.6.9/930601.1506) id MAA21884; Sun, 2 Oct 1994 12:36:38 -0400 Received: by mason1.gmu.edu (5.65/DEC-Ultrix/4.3/GMUv3) id AA07723; Sun, 2 Oct 1994 12:36:37 -0400 Message-Id: <9410021636.AA07723@mason1.gmu.edu> Subject: Latest Chemistry Font file Available NOW! To: chemistry@ccl.net, CHEMED-L%UWF.BITNET@uga.cc.uga.edu Date: Sun, 2 Oct 1994 12:36:37 -0400 (EDT) From: "J. Eric Slone" X-Mailer: ELM [version 2.4 PL23] Mime-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Content-Length: 907 An updated Chemistry Font for Windows is now on www.ccl.net in the /incoming directory. If it is not there, it has been moved to its permanent home in /pub/chemistry/software/MS-WINDOWS. New features: Macro recall of fundamental constants with units Some new and some improved characters Newman Projections Lewis Dots ________________________________________________________________________________ J. Eric Slone Scientific Consulting Services Serving Government & Industry Since 1982 Internet: eslone@mason1.gmu.edu Compuserve: 73757,2776 "True science teaches, above all, to Fax: (703) 751-6639 doubt, and to be ignorant." Voice: (703) 461-7078 Miguel do Unamuno ________________________________________________________________________________ From elewars@alchemy.chem.utoronto.ca Sun Oct 2 14:16:40 1994 Received: from alchemy.chem.utoronto.ca for elewars@alchemy.chem.utoronto.ca by www.ccl.net (8.6.9/930601.1506) id NAA22115; Sun, 2 Oct 1994 13:22:26 -0400 Received: (from elewars@localhost) by alchemy.chem.utoronto.ca (8.6.9/8.6.9) id NAA01093 for chemistry@ccl.net; Sun, 2 Oct 1994 13:22:18 -0400 Date: Sun, 2 Oct 1994 13:22:18 -0400 From: "E. Lewars" Message-Id: <199410021722.NAA01093@alchemy.chem.utoronto.ca> To: chemistry@ccl.net Subject: CHARGES IN MOLECULES: A QUESTION 1994 Oct 2 It is said that atomic charges in molecules are not observables, and so there is no single right way to calculate them. Hence the fact we have several (many?) schemes, all of them giving different "answers". Are charges unobservable/unmeasurable because of fundamental quantum-mechanical reasons (e.g. there is no QM charge operator, in contrast to there being QM operators for, say, energy or dipole moment), or could an experiment be designed *en principe* to give an objective measure of the atomic charges in a molecule? When van't Hoff and Le Bell proposed shapes for molecules in the 1870's, these shapes were unobservables, but, we now know, not for fundamental reasons. From bhardy@convex.ox.ac.uk Sun Oct 2 15:16:39 1994 Received: from oxmail.ox.ac.uk for bhardy@convex.ox.ac.uk by www.ccl.net (8.6.9/930601.1506) id OAA22606; Sun, 2 Oct 1994 14:52:41 -0400 Received: from convex.ox.ac.uk by oxmail.ox.ac.uk with SMTP (PP) id <14535-0@oxmail.ox.ac.uk>; Sun, 2 Oct 1994 19:51:22 +0100 From: Barry Hardy Date: Sun, 2 Oct 94 19:49:07 +0100 Message-Id: <27583.9410021849@convex.ox.ac.uk> To: chemistry@ccl.net Subject: CHARMM/Amber File Conversion CCLers, Can anyone suggest a program/tool that can convert CHARMM input files (coordinates, parameters, topology) to Amber and vice-versa? If not, what is the most efficient work-around? Respond to me & I'll summarize. Barry J. Hardy From ross@cgl.ucsf.EDU Sun Oct 2 16:16:41 1994 Received: from socrates.ucsf.EDU for ross@cgl.ucsf.EDU by www.ccl.net (8.6.9/930601.1506) id QAA22977; Sun, 2 Oct 1994 16:10:31 -0400 Received: (from ross@localhost) by socrates.ucsf.EDU (8.6.9/GSC4.24) id NAA26682 for chemistry@ccl.net; Sun, 2 Oct 1994 13:10:29 -0700 Date: Sun, 2 Oct 1994 13:10:29 -0700 Message-Id: <199410022010.NAA26682@socrates.ucsf.EDU> From: ross@cgl.ucsf.edu (Bill Ross ) To: chemistry@ccl.net Subject: Charge From: "E. Lewars" It is said that atomic charges in molecules are not observables, ... Are charges unobservable/unmeasurable because of fundamental quantum-mechanical reasons ... or could an experiment be designed *en principe* to give an objective measure of the atomic charges in a molecule? One experimental approach is to use electron densities derived from X-ray diffraction data to derive point charges. See David Pearlman and Sung-Hou Kim, "Atomic Charges for DNA Constituents Derived from Single-crystal X-ray Diffraction Data," J. Mol. Biol. (1990) 211, 171-187. No matter how 'objective' the measure of point charges, they must allow other observables to be reproduced if they are to be of value in the molecular mechanical context. In practice, such factors as the convention of only considering pairwise interactions that is usually used for speed of calculation and the convenience of fixing charges for a range of confomers may dictate non-objective fitting. Bill Ross From sichelj@umoncton.ca Sun Oct 2 16:37:44 1994 Received: from bosoleil.ci.umoncton.ca for sichelj@umoncton.ca by www.ccl.net (8.6.9/930601.1506) id PAA22721; Sun, 2 Oct 1994 15:28:14 -0400 Received: by bosoleil.ci.umoncton.ca (1.38.193.5/16.2) id AA28912; Sun, 2 Oct 1994 16:29:13 -0300 Date: Sun, 2 Oct 1994 16:29:13 -0300 (ADT) From: John Sichel Subject: Re: CCL:CHARGES IN MOLECULES: A QUESTION To: "E. Lewars" Cc: chemistry@ccl.net In-Reply-To: <199410021722.NAA01093@alchemy.chem.utoronto.ca> Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Atomic charges are not well-defined because atoms in molecules are not well-defined. The QM charge operator is just the charge (= -e for electrons), so one can integrate -e x (psi)^2 over a volume which represents the atom, but this volume is not uniquely defined. Some quantum chemists use the method proposed by Richard Bader (McMaster University, Canada) which is based on analysis of the charge density. If this method is accepted, it does provide a unique partition of the electronic charge appropriate for Hartree-Fock quality wavefunctions. John Sichel Universite de Moncton Moncton, NB, Canada On Sun, 2 Oct 1994, E. Lewars wrote: > 1994 Oct 2 > > It is said that atomic charges in molecules are not observables, and so there > is no single right way to calculate them. Hence the fact we have several > (many?) schemes, all of them giving different "answers". > > Are charges unobservable/unmeasurable because of fundamental quantum-mechanical > reasons (e.g. there is no QM charge operator, in contrast to there being QM > operators for, say, energy or dipole moment), or could an experiment be > designed *en principe* to give an objective measure of the atomic charges in > a molecule? When van't Hoff and Le Bell proposed shapes for molecules in the > 1870's, these shapes were unobservables, but, we now know, not for fundamental > reasons. > > > ---Administrivia: This message is automatically appended by the mail exploder: > CHEMISTRY@ccl.net -- everyone | CHEMISTRY-REQUEST@ccl.net -- coordinator > MAILSERV@ccl.net: HELP CHEMISTRY | Gopher: www.ccl.net 73 > Anon. ftp www.ccl.net | CHEMISTRY-SEARCH@ccl.net -- archive search > http://www.ccl.net/chemistry.html | for info send: HELP SEARCH to MAILSERV > From rgab@trpntech.com Sun Oct 2 19:16:42 1994 Received: from netcomsv.netcom.com for rgab@trpntech.com by www.ccl.net (8.6.9/930601.1506) id TAA24336; Sun, 2 Oct 1994 19:15:58 -0400 Received: from trpntech.com by netcomsv.netcom.com with UUCP (8.6.4/SMI-4.1) id PAA28022; Sun, 2 Oct 1994 15:56:24 -0700 Message-Id: <199410022256.PAA28022@netcomsv.netcom.com> Date: 2 Oct 1994 15:38:22 -0800 From: "Richard Bone" Subject: Bader Atomic Charges To: "CCL" Subject: Bader Atomic Charges John Sichel wrote: > Some quantum chemists use the method proposed by Richard Bader (McMaster > University, Canada) which is based on analysis of the charge density. If > this method is accepted, it does provide a unique partition of the > electronic charge appropriate for Hartree-Fock quality wavefunctions. To be a little pedantic, in response: The Bader atomic definitions arise from the quantum mechanics of a subsystem, applicable when a subspace is defined to be one with a 'zero-flux' boundary condition. Bader partitions the charge-density in this way. It is a little facile to refer to the origin of such "atoms in molecules" as deriving from an analysis of the 'charge density'. Because the definition is based on the charge density it is not restricted to wavefunctions of 'Hartree Fock quality'. Given a charge density from any source, it is possible to split it up in this way. This atomic partitioning has been shown, by way of a number of examples, to retain certain desirable 'chemical' features, particularly loose 'transferability' of properties of a number of types. As an example, the contributions of -CH2- groups to the heats of formation of a homologous series of alkanes are well-replicated. One would argue that the success of this definition of a chemically bound atom in descr- ibing measurable properties augers well for the associated atomic charges (and higher multipoles) that result. I add, however, that the charges themselves often have magnitudes which are much larger than those typically employed in molecular modelling. This has given rise to a little skepticism of this approach. The atomic charge, per se, is rather an ambitious parameter with which to expect to replicate MEP's very well, except when using some fitting procedure. The Bader approach lends itself to the use of a self-consistent set of atomic multipole moments, i.e., not just charge, but dipole, quadrupole, etc. I am not aware of any study which has demonstrated the success (or otherwise) of Bader atomic properties in modelling the MEP of some 'relevant' molecule, though small-molecule studies have appeared in the past and there is by now a large body of literature on the charges them- selves. Recent papers by K. E. Laidig have addressed the issue of how to build up a molecular moment (of any order) from atomic contributions. Much of the theory behind atomic properties and subspace partitioning is covered in Bader's book ["Atoms in Molecules, A Quantum Theory" -OUP, now available in paperback.] This message is a comment, not a 'flame', and I am not seeking to open a sub-debate on the "Theory of Atoms in Molecules". I merely feel these aspects have some relevance to the current discussion of atomic charges, particularly today's posting. Richard Bone __________________________________________________________ Richard G. A. Bone, PhD. Computational Chemist Terrapin Technologies, Inc. South San Francisco USA E-mail rgab@trpntech.com From dok707@cvx12.inet.dkfz-heidelberg.de Sun Oct 2 21:16:44 1994 Received: from cvx12.inet.dkfz-heidelberg.de for dok707@cvx12.inet.dkfz-heidelberg.de by www.ccl.net (8.6.9/930601.1506) id UAA24932; Sun, 2 Oct 1994 20:28:58 -0400 Received: by cvx12.inet.dkfz-heidelberg.de id AA00694 (5.65c/IDA-1.4.4 for chemistry@ccl.net); Mon, 3 Oct 1994 01:26:33 +0100 Date: Mon, 3 Oct 1994 01:26:33 +0100 From: Frank Herrmann Message-Id: <199410030026.AA00694@cvx12.inet.dkfz-heidelberg.de> To: chemistry@ccl.net Subject: MOPAC: unreasonable structures Dear netters, when doing single point calculations (1SCF) on molecule conformations containing clashes ( non bonded distance ~= 1A ) the following problems occur: 1- either MOPAC do not terminate even when using T=... 2- or the energy is far below that of resonable structures MOPAC checks if the bond distance is < 0.8A. But the clashes should at least, if not resulting in an error, raise the energy. Is this a bug or is there an explanation ? Regards, -------------------------------------------------- Frank Herrmann, Dept. of Molecular Biophysics 0810 German Cancer Research Center Im Neuenheimer Feld 280, D-69120 Heidelberg Tel: (49) 6221-422336, FAX: (49) 6221-422333 email: F.Herrmann@dkfz-heidelberg.de