From V098Q3NV@ubvms.cc.buffalo.edu Fri Dec 3 01:52:36 1993 Received: from ubvmsc.cc.buffalo.edu for V098Q3NV@ubvms.cc.buffalo.edu by www.ccl.net (8.6.4/930601.1506) id BAA28947; Fri, 3 Dec 1993 01:06:29 -0500 Received: from ubvms.cc.buffalo.edu by ubvms.cc.buffalo.edu (PMDF V4.2-13 #3449) id <01H60WAYZUJK8WY34D@ubvms.cc.buffalo.edu>; Fri, 3 Dec 1993 01:09:18 EST Date: Fri, 03 Dec 1993 01:09:18 -0500 (EST) From: V098Q3NV@ubvms.cc.buffalo.edu Subject: how to get Amsterdam DFT code? To: chemistry@ccl.net Message-id: <01H60WAZ1Q2A8WY34D@ubvms.cc.buffalo.edu> Organization: University at Buffalo X-VMS-To: IN%"chemistry@ccl.net" MIME-version: 1.0 Content-type: TEXT/PLAIN; CHARSET=US-ASCII Content-transfer-encoding: 7BIT Hi! Anybody know how I might obtain a copy of the Amsterdam DFT code? Thanks! John Manchester Roswell Park Cancer Inst / Battelle PNL gg339@zot.pnl.gov ph 509/372-4660 fx 509/375-6631 From ferenc@rchsg8.chemie.uni-regensburg.de Fri Dec 3 03:52:37 1993 Received: from rrzs1.rz.uni-regensburg.de for ferenc@rchsg8.chemie.uni-regensburg.de by www.ccl.net (8.6.4/930601.1506) id DAA29425; Fri, 3 Dec 1993 03:20:53 -0500 Received: from rchsg8.chemie.uni-regensburg.de by rrzs1.rz.uni-regensburg.de (4.1/URRZ-relay (1.4)) id AA17957; Fri, 3 Dec 93 09:20:33 +0100 Received: by rchsg8.chemie.uni-regensburg.de (920330.SGI/BelWue-1.0SG(subsidiary)) (for CHEMISTRY@ccl.net) id AA18862; Fri, 3 Dec 93 09:21:28 +0100 Date: Fri, 3 Dec 93 09:21:28 +0100 From: ferenc@rchsg8.chemie.uni-regensburg.de (Ferenc Molnar) Message-Id: <9312030821.AA18862@rchsg8.chemie.uni-regensburg.de> To: CHEMISTRY@ccl.net Subject: A&T bug ? Dear Netters, some weeks ago I posted requests for literature on constraints in MD-calculations. Yesterday I finished programming an algorithm for this problem. In order to compare some results, I wanted to use the "RATTLE"-scheme as implemented in one of the subroutines (called "f.9") from the book of Allen & Tildesley. Part of the "RATTLE" algorithm of the subroutine "f.9" (part: MOVEA) that I have does not lead to convergence! I think that the reason for this is a bug in the sourcecode. At the point where the intermediate positions and velocities are updated the corrections seem to have the wrong sign. e.g.: . PXI(A)=PXI(A)+RMA*DX . . PXI(B)=PXI(B)-RMA*DX . should read: . PXI(A)=PXI(A)-RMA*DX . . PXI(B)=PXI(B)+RMA*DX . Has anyone else made the same experience or is my code for "f.9" corrupt? Another question on a different topic: Does anybody know about parameters for Argon (or other rare gas atoms) in semiempirical schemes like AM1, PM3, or MNDO etc.? I will report to the net if anyone is interested in these topics. Thank you very much in advance, Ferenc Ferenc Molnar --------------------------------------------------------------------------- Institut fuer Physikalische und Theoretische Chemie - Lehrstuhl Prof. Dick - Tel.: (+49) 941 943-4466 /-4486 Universitaet Regensburg Fax.: (+49) 941 943-4488 Universitaetsstrasse 31 D-93053 Regensburg Deutschland / Germany --------------------------------------------------------------------------- EMail (SMTP): ferenc@rchsg8.chemie.uni-regensburg.de c5071@rchs1.chemie.uni-regensburg.de ferenc@rchnw2.ngate.uni-regensburg.de --------------------------------------------------------------------------- :-) There is more to live than increasing its speed. -- Ghandi ;-) --------------------------------------------------------------------------- From acroft@chemistry.adelaide.edu.au Fri Dec 3 04:52:38 1993 Received: from pene.science.adelaide.edu.au for acroft@chemistry.adelaide.edu.au by www.ccl.net (8.6.4/930601.1506) id EAA29724; Fri, 3 Dec 1993 04:08:07 -0500 Received: by pene.science.adelaide.edu.au (5.61+IDA+MU/UA-5.26) id AA29183; Fri, 3 Dec 1993 19:38:05 +1030 From: Anna Croft Message-Id: <9312030908.AA29183@pene.science.adelaide.edu.au> Subject: Cartesian to Zmatrix To: chemistry@ccl.net Date: Fri, 3 Dec 1993 19:38:05 +1100 (EST) X-Mailer: ELM [version 2.4 PL3] Mime-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Length: 560 This is probably a FAQ but anyway, Is there a publically available program which will convert a set of cartesian coordinates into a simple Z matrix, especially when given a symmetry to work with. I know gaussian does the reverse but I would prefer to cut my time writing Z matricies down so I can get on with some real work ... (especially as I am working with rather large molecules) Thanks a lot, Anna Croft /* ** #include ** #define CHEMIST acroft@chemistry.adelaide.edu.au ** #define UNIVERSITY university_of_adelaide */ From ZSYAMP01@PUIGMAL.CESCA.ES Fri Dec 3 04:53:31 1993 Received: from phem3 for ZSYAMP01@PUIGMAL.CESCA.ES by www.ccl.net (8.6.4/930601.1506) id DAA29524; Fri, 3 Dec 1993 03:52:52 -0500 Received: from PUIGMAL.CESCA.ES (MAILER@EBCESCA1) by phem3.acs.ohio-state.edu (PMDF V4.2-13 #3557) id <01H6122WGOCG95PK62@phem3.acs.ohio-state.edu>; Fri, 3 Dec 1993 03:52:46 EST Received: from EBCESCA1 (NJE origin ZSYAMP01@EBCESCA1) by PUIGMAL.CESCA.ES (LMail V1.2a/1.8a) with BSMTP id 2469; Fri, 3 Dec 1993 09:42:34 +0000 Date: Fri, 03 Dec 1993 09:35:53 +0100 (CET) From: ZSYAMP01%EBCESCA1.BITNET@phem3.acs.ohio-state.edu Subject: IMIM + Ferran Sanz To: CCL Message-id: <01H6122WGOCI95PK62@phem3.acs.ohio-state.edu> Content-transfer-encoding: 7BIT Dear netters, I think this should 'fix' definitely the 'IMIM problem' (sorry, Juanjo, but the '93' prefix doesn't work from outside Spain). The right data is: Dr. Ferran Sanz or Dr. Francesc Manaut or Dr. Juanjo Lozano Institut Municipal d'Investigacio Medica (IMIM) c/ Doctor Aiguader, 80 08003 Barcelona Spain phone: (34) (3) 2211009 fax : (34) (3) 2213237 Internet: sistema@imim.es (or jlozano@imim.es) /Alicia ------------------------------------------------------------------------ Alicia Martinez Supercomputation Center of Catalonia (CESCA) Phone: (34)(3) 4914014 Avda. Diagonal 645 Fax: (34)(3) 4904635 08028 Barcelona BITNET: ZSYAMP01@EBCESCA1 SPAIN Internet: zsyamp01@puigmal.cesca.es ------------------------------------------------------------------------ From ipcakc@vigyan.ernet.in Fri Dec 3 06:52:39 1993 Received: from relay1.UU.NET for ipcakc@vigyan.ernet.in by www.ccl.net (8.6.4/930601.1506) id GAA00583; Fri, 3 Dec 1993 06:37:07 -0500 Received: from spool.uu.net (via LOCALHOST) by relay1.UU.NET with SMTP (5.61/UUNET-internet-primary) id AA00545; Fri, 3 Dec 93 06:37:05 -0500 Received: from sangam.UUCP by uucp5.uu.net with UUCP/RMAIL (queueing-rmail) id 063558.11544; Fri, 3 Dec 1993 06:35:58 EST Received: from vigyan.UUCP by sangam.ncst.ernet.in (4.1/SMI-4.2-ERNET-relay) with UUCP id AA10520; Fri, 3 Dec 93 15:06:02+0530 Received: by iisc.ernet.in (ERNET-IISc/AT&T UNIX SYS V.3.2) id AA01836; Fri, 3 Dec 93 13:56:44 EST Received: by vigyan.iisc.ernet.in (smail2.3) id AA20952; 3 Dec 93 13:50:04 EST (Fri) To: CHEMISTRY@ccl.net Subject: thanks Date: 3 Dec 93 13:50:04 EST (Fri) From: ipcakc@vigyan.iisc.ernet.in Message-Id: <9312031350.AA20952@vigyan.iisc.ernet.in> Dear Netters, Thanks to everybody who all sent me the details regarding Journal of Physical Organic Chemistry. Sridhar From ADAMO@CHEMNA.DICHI.UNINA.IT Fri Dec 3 07:52:40 1993 Received: from CHEMNA.DICHI.UNINA.IT for ADAMO@CHEMNA.DICHI.UNINA.IT by www.ccl.net (8.6.4/930601.1506) id HAA00840; Fri, 3 Dec 1993 07:05:51 -0500 From: Received: from CHEMNA.DICHI.UNINA.IT by CHEMNA.DICHI.UNINA.IT (PMDF V4.2-11 #3559) id <01H61LCVYV4W0002EN@CHEMNA.DICHI.UNINA.IT>; Fri, 3 Dec 1993 13:05:21 CET Date: Fri, 03 Dec 1993 13:05:21 +0100 (CET) Subject: MOLCAS package To: chemistry@ccl.net Message-id: <01H61LCW0H020002EN@CHEMNA.DICHI.UNINA.IT> X-VMS-To: IN%"chemistry@ccl.net" X-VMS-Cc: ADAMO MIME-version: 1.0 Content-type: TEXT/PLAIN; CHARSET=US-ASCII Content-transfer-encoding: 7BIT Dear netters, do you have some information on MOLCAS program and how to get it? Thank Ciao Carlo ------------------------------------------------------------------------------- Carlo Adamo | tel. +39-81-5476504 Dipartimento di Chimica | fax +39-81-5527771 via Mezzocannone 4 | e-mail ADAMO@CHEMNA.DICHI.UNINA.IT I-80134 Napoli | Italy | ________________________________________________________________________________ From ZSYAMP01@PUIGMAL.CESCA.ES Fri Dec 3 07:53:27 1993 Received: from phem3 for ZSYAMP01@PUIGMAL.CESCA.ES by www.ccl.net (8.6.4/930601.1506) id GAA00645; Fri, 3 Dec 1993 06:53:21 -0500 Received: from PUIGMAL.CESCA.ES (MAILER@EBCESCA1) by phem3.acs.ohio-state.edu (PMDF V4.2-13 #3557) id <01H618DO4I5C95PKTE@phem3.acs.ohio-state.edu>; Fri, 3 Dec 1993 06:53:15 EST Received: from EBCESCA1 (NJE origin ZSYAMP01@EBCESCA1) by PUIGMAL.CESCA.ES (LMail V1.2a/1.8a) with BSMTP id 2750; Fri, 3 Dec 1993 12:50:25 +0000 Date: Fri, 03 Dec 1993 12:42:48 +0100 (CET) From: ZSYAMP01%EBCESCA1.BITNET@phem3.acs.ohio-state.edu Subject: migrating QCPE 333 to other platforms To: CCL Message-id: <01H618DO4I5E95PKTE@phem3.acs.ohio-state.edu> Content-transfer-encoding: 7BIT Dear netters, some users here are interested in ordering a certain program (QCPE 333, CNDUV99: Computation of Electronic Transitions SCF-CNDO-CI Method Including Singly and Doubly Excited Configurations). The documentation says 'FORTRAN IV (CDC)', just for a computer we haven't got here. Has anybody tried (successfully or not) to port it to other platforms? Is such CDC FORTRAN version a serious inconvenience to migration to other computers? In particular, I'd like to install it in UNIX and VM environment. Any comments will be appreciated. Thanks in advance, Alicia ------------------------------------------------------------------------ Alicia Martinez Supercomputation Center of Catalonia (CESCA) Phone: (34)(3) 4914014 Avda. Diagonal 645 Fax: (34)(3) 4904635 08028 Barcelona BITNET: ZSYAMP01@EBCESCA1 SPAIN Internet: zsyamp01@puigmal.cesca.es ------------------------------------------------------------------------ From rwoods@biop.ox.ac.uk Fri Dec 3 07:54:00 1993 Received: from lmb.biop.ox.ac.uk for rwoods@biop.ox.ac.uk by www.ccl.net (8.6.4/930601.1506) id HAA01009; Fri, 3 Dec 1993 07:44:21 -0500 From: Received: by biop.ox.ac.uk (MX V3.3 VAX) id 12365; Fri, 03 Dec 1993 12:44:19 +0000 Date: Fri, 03 Dec 1993 12:43:46 +0000 To: cletner@remcure.bmb.wright.edu CC: chemistry@ccl.net Message-ID: <00976762.8199B820.12365@biop.ox.ac.uk> Subject: RE: RE:Protein force fields Dear Chuck, As it happens I have just reviewed the Rao and Teeter paper for our journal club. I chose the paper for 3 reasons: a) It was being presented to biochemists, b) I am a computational chemist, c) I liked the practicality of the approach. Martha Teeter is a crystalographer who has a long standing interest in proteins related to a-purothionin (eg crambin which she also solved), but has limited access to computing facilities (Microvax II). She clearly wants to find a method that gives a good guess for solving protein structures by x-ray methods. The paper presents a VERY rudimentary MD simulation using the AMBER UA force field, in vacuo, with much of the structure constrained. This is a very simple and unsophysticated approach, and in some ways it is perhaps pleasantly surprising that it worked. However, there are a few notable points: 1) This is a purely anecdotal report. 2) Alpha-PT is highly homologous to Crambin and so a very good guess for the MM/MD calculations was already available. 3) The MD was performed on a very small subset of the atoms (6 out of 46 residues only). 4) Because of the particular nature of this protein (and its homologs) the ends of the critical loop-region could be assumed to be in the correct conformation, therefore extensive conformational restraints could be invoked. 5) The authors report that an unconstrained MD simulation (epsilon=1,in vacuo) resulted in [hydrogen] bond breaking, but apparently did not test the stability with (epsilon=4) which they went on to use for the partial MD. 6) Although the authors refer to a 2ps equilibration period, there PE data clearly shows equilibration was not reached until about 30 ps. This is unimportant in context of their analysis, but without continuing the trajectory for a longer period it is not possible to say how stable their loop conformation really is. The results are however interesting, particularly the sequential nature of the changes in the backbone conformation. I think that if the system can be modelled based on similar high homology the UA approach looks very interesting, but it is very system dependant. It worked in this case but I think solvation would have to be considered for more general studies. Hope this sparks other comments and answers some of your questions, Best wishes, Rob Woods Robert J. Woods, Ph.D. Glycobiology Institute Department of Biochemistry University of Oxford South Parks Road Oxford, OX1 3QU England From rwoods@biop.ox.ac.uk Fri Dec 3 09:54:00 1993 Received: from lmb.biop.ox.ac.uk for rwoods@biop.ox.ac.uk by www.ccl.net (8.6.4/930601.1506) id JAA02127; Fri, 3 Dec 1993 09:52:01 -0500 From: Received: by biop.ox.ac.uk (MX V3.3 VAX) id 12484; Fri, 03 Dec 1993 14:52:30 +0000 Date: Fri, 03 Dec 1993 14:52:23 +0000 To: chemistry@ccl.net Message-ID: <00976774.794D85E0.12484@biop.ox.ac.uk> Subject: Correction to Crambin Authorship (RE:Protein...) The crystal structure of Crambin was solved by Wayne Hendrickson in collaboration with M. Teeter as kindly pointed out to me by Bob Williams. Sorry for any inaccuracy or misplaced credit. Robert J. Woods, Ph.D. Glycobiology Institute Department of Biochemistry University of Oxford South Parks Road Oxford, OX1 3QU England From shaoweng@helix.nih.gov Fri Dec 3 10:53:29 1993 Received: from helix.nih.gov for shaoweng@helix.nih.gov by www.ccl.net (8.6.4/930601.1506) id JAA02225; Fri, 3 Dec 1993 09:55:01 -0500 Received: from localhost by helix.nih.gov (8.6.4/1.35(helix-1.0)) id JAA12540; Fri, 3 Dec 1993 09:54:52 -0500 Date: Fri, 3 Dec 1993 09:54:52 -0500 From: shaoweng@helix.nih.gov (Shaomeng Wang) Message-Id: <199312031454.JAA12540@helix.nih.gov> To: acroft@chemistry.adelaide.edu.au, chemistry@ccl.net Subject: Re: Cartesian to Zmatrix MOPAC does. If you run MOPAC with keyword 0SCF, it will convert Cartesian to Zmatrix, or vice versa. hope this will be helpful. -Shaomeng From Patrick.Bultinck@rug.ac.be Fri Dec 3 10:56:47 1993 Received: from mserv.rug.ac.be for Patrick.Bultinck@rug.ac.be by www.ccl.net (8.6.4/930601.1506) id KAA02704; Fri, 3 Dec 1993 10:34:05 -0500 Received: from allserv.rug.ac.be by mserv.rug.ac.be with SMTP id AA09620 (5.65c/IDA-1.4.4 for ); Fri, 3 Dec 1993 16:33:33 +0100 Received: by allserv.rug.ac.be (5.0/SMI-SVR4) id AA22762; Fri, 3 Dec 93 16:31:15 +0100 Date: Fri, 3 Dec 1993 16:14:35 +0100 (MET) From: Patrick Bultinck Subject: POPULATION ANALYSIS To: CHEMISTRY@ccl.net Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Content-Length: 1554 I have performed some population analysis calculations on covalent molecules using ab initio Hartree-Fock. I performed MPA and LPA (mulliken and lowdin). The results were often miles apart. The reason, I think, is the fact that every value for n in S^nPS^(1-n) will do for defining a population analysis formula. I do no longer believe very much in the use of population analysis for determining atomic charges for atoms in a certain molecule. This disbelieve became bigger when last year, during my graduation thesis, I studied calculations of dipole moments. Indeed I remembered the formula DIP. MOM.=sum(atomic charge*R), sum over all atoms. I thought I could see how good PA was by using the PA results to determine the dipole moment (apart from the one calculated with the wavefunction). I calculated the different cartesian components of the DM, since PA gave me the charges and I knew from my input what the cart. coordinates of the atoms were. By putting together the cart. comp. of the DM I got to a value of the total dipole moment. Needless to say that the value was sometimes miles apart from experiment and from the wave-function derived dipole moment...(using RHF and RHF defined PA formulas) My question is : What is the use of the S^nPS^(1-n) derived population analysis ? Is there something crazy about my argumentation to say that PA is not to be trusted very much ? (esp. where I used the formula for the DM using the PA results...) Thanks for replies.... Patrick Bultinck University of Ghent E-Mail : Patrick.Bultinck@rug.ac.be From slee@ccl.net Fri Dec 3 12:52:43 1993 Received: from mail.uunet.ca for slee@ccl.net by www.ccl.net (8.6.4/930601.1506) id MAA04203; Fri, 3 Dec 1993 12:14:16 -0500 Received: from hyper by mail.uunet.ca with UUCP id <56271(2)>; Fri, 3 Dec 1993 12:05:08 -0500 Received: by hyper.hyper.com (920330.SGI/890607.SGI) (for ccl.net!chemistry) id AA05390; Fri, 3 Dec 93 12:04:04 -0500 From: slee@ccl.net (Thomas Slee) Message-Id: <9312031704.AA05390@hyper.hyper.com> Subject: Re: new parameters To: chemistry@ccl.net Date: Fri, 3 Dec 1993 12:04:03 -0500 X-Mailer: ELM [version 2.3 PL9] Dear netters, Slawomir Filipek recently posted a note to the list suggesting that he was unable to simulate certain molecules with any of HyperChem's force fields. I have since been in touch with Dr. Filipek and he has now let me know that HyperChem's MM+ force field does indeed handle the molecules in question 'very well.' Tom Slee From major@dino.qci.bioch.bcm.tmc.edu Fri Dec 3 13:12:13 1993 Received: from bcm.tmc.edu for major@dino.qci.bioch.bcm.tmc.edu by www.ccl.net (8.6.4/930601.1506) id MAA04308; Fri, 3 Dec 1993 12:32:55 -0500 Received: from dino.qci.bioch.bcm.tmc.edu by bcm.tmc.edu (LAA17389); Fri, 3 Dec 1993 11:32:54 -0600 Received: by dino.qci.bioch.bcm.tmc.edu; Fri, 3 Dec 93 11:32:00 -0800 Date: Fri, 3 Dec 93 11:32:00 -0800 From: Joe Major - Tannox Message-Id: <9312031932.AA08618@dino.qci.bioch.bcm.tmc.edu> To: chemistry@ccl.net Subject: modelling peptides near lipid interface Netters: I am interested in modelling peptides near the aqueous/lipid bilayer interface. Experimental studies indicated that this region presents a different environment than that found in the "normal" aqueous milieu or in the lipid bilayer. For example some studies indicate a dielectric of 25-35 within 10-30 A outside the bilayer. Although several groups have explicity modelled bilayers and membrane proteins, I am unaware of MM/MD as well as electrostatic potential studies on peptides near the bilayer. Can anyone give any helpful suggestions, useful parameters, references and/or names of individuals working on this kind of problem. I will summarize responses to the net. Thank you in advance. Joe Major From EDGECOMK@QUCDN.QUEENSU.CA Fri Dec 3 13:52:47 1993 Received: from QUCDN.QueensU.CA for EDGECOMK@QUCDN.QUEENSU.CA by www.ccl.net (8.6.4/930601.1506) id MAA04591; Fri, 3 Dec 1993 12:54:58 -0500 Message-Id: <199312031754.MAA04591@www.ccl.net> Received: from QUCDN.QUEENSU.CA by QUCDN.QueensU.CA (IBM VM SMTP V2R2) with BSMTP id 2820; Fri, 03 Dec 93 12:53:39 EST Received: from QUCDN.QUEENSU.CA (NJE origin EDGECOMK@QUCDN) by QUCDN.QUEENSU.CA (LMail V1.1d/1.7f) with RFC822 id 7687; Fri, 3 Dec 1993 12:53:39 -0500 Date: Fri, 3 Dec 1993 12:52 EST From: EDGECOMK@QUCDN.QueensU.CA To: chemistry@ccl.net Subject: popln. analysis and dipoles Patrick B.'s comments on population analysis and dipole moments strike a cord. I have heard these complaints(and made some myself) for a number of years. 1) the choice of divison of the overlap population is arbitrary... various lines of thought have gone into the derivation of literally hundreds of methods of doing this but the bottem line is that you do not have a quantum mechanical operator for the population in an 'orbital' on a particular atom that 'belongs' to that atom. Perhaps the most attractive methods are those that arise through the use of quantum mechanics, do not use arbitrary boundaries and as well apply to the total density. (eg. Richard Bader et al's theory of mol. structure) 2) the 'charge' on an atom is not a point charge, this is a gross assumption that in itself can lead to large errors. It appears to arise from the conceptually appealing picture of nice spherical atoms in molecules. The density is, however, not spherical around each atom in a molecule. Thus, using a point charge model with populations calculated through arbitrary division of the overlap populations has a good chance of giving poor results. The above being said, these different methods of treating the problem of population analysis has led to a lot of chemical insight for various problems. You must keep the weaknesses in mind when choosing an approach. Any other thoughts on this? Ken Edgecombe ----- End of the message ----- From ryan%phmms0.mms.smithkline.com@smithkline.com Fri Dec 3 15:54:01 1993 Received: from phmms0.mms.smithkline.com for ryan%phmms0.mms.smithkline.com@smithkline.com by www.ccl.net (8.6.4/930601.1506) id OAA06115; Fri, 3 Dec 1993 14:58:19 -0500 Received: by phmms0.mms.smithkline.com (920330.SGI/911001.SGI) for chemistry@ccl.net id AA23017; Fri, 3 Dec 93 14:57:43 -0500 Date: Fri, 3 Dec 93 14:57:43 -0500 From: ryan%phmms0.mms.smithkline.com@phinet.smithkline.com (Dominic Ryan) Message-Id: <9312031957.AA23017@phmms0.mms.smithkline.com> To: chemistry@ccl.net Subject: Population analysis Reply-To: ryan%phmms0.mms@sb.com As was pointed out, population analysis is not unique. There are a host of methods available for partitioning density between sites. One must ask what the charges will be used for. In a force field context an atomic charge is simply one more fudge factor available in the system for tuning to get the 'right' answer. Early days of force field development concentrated on intramolecular energies, in vacuo at that. After you make pretty good guesses at bond stretching and angle bending components (and cross terms when part of your flavor of force field) you are left with torsion terms, VDW terms and charges. Early work derived VDW terms from rare gas data in part and from crystal packing (making allowances for the differences one sees there in x-ray, electron and neutron diffraction). One is generally left then with torsions and charges (VDW terms are also modified and combining rules are modified in Tom Halgren's work). You try to assign chemically sensible charges and tweak the torsion terms until conformational energies reproduce your reference states (quantum mechanical, and experimental). More recently there has been greater emphasis on intermolecular energies (lets ignore solvation for now). These are dominated by electrostatic forces. Now one needs to worry more about getting both chemically sensible charges and charges that will give the 'correct' interaction energy which must be taken from high level QM where one needs to worry about basis set effects etc. A relatively recent method of defining atomic charges calculates the molecular electrostatic potential around a molecule and constrains the charges to reproduce this distribution as much as possible. This has the advantage of in principle reproducing the bulk of the interaction energy between two molecules, including the anisotropy. In practice there are limitations here as well, and in small molecules particularly (H2O) a set of atom-centered charges in not sufficient to adequately describe the potential. One advantage of using 'fitted' charges is that the dipole (and higher order molecular multipoles) are well reproduced. There is a *lot* of literature on this approch now. Check out Reviews in Computational Chemistry, vol. 2 for a recent review. Bader's method of partitioning charge is consistent but leads to a different picture of atomic charge from the fitted methods. Neither one is *wrong* but they look at different things. ___________________________________________________________________________ M. Dominic Ryan (215)-270-6529 SmithKline Beecham Pharmaceuticals Headers may be WRONG, do NOT use reply, use: ryan%phmms0.mms@sb.com From lipkowitz@chem.iupui.edu Fri Dec 3 17:52:46 1993 Received: from indyvax.iupui.edu for lipkowitz@chem.iupui.edu by www.ccl.net (8.6.4/930601.1506) id RAA07081; Fri, 3 Dec 1993 17:09:22 -0500 Received: from macgw.chem.iupui.edu by INDYVAX.IUPUI.EDU (PMDF V4.2-12 #3694) id <01H61TVGS0DS0004H8@INDYVAX.IUPUI.EDU>; Fri, 3 Dec 1993 17:09:17 -0500 Date: Fri, 03 Dec 1993 17:12:42 +0930 From: Lipkowitz Subject: Population Analysis To: Comp Chem List Message-id: <01H61TVGSTBM0004H8@INDYVAX.IUPUI.EDU> Content-transfer-encoding: 7BIT Netters: There has been, and remains, controversy about how to partition electrons on atoms for population analysis. To help me understand what's going on, Don Boyd and I asked Steve Bachrach to write a book chapter on that topic. See Reviews in Computational Chemistry, Volume 5, eds. K. Lipkowitz and D.Boyd, VCH Publishers Inc., New York, 1994 ( available in January). Kenny From budong@chem.columbia.edu Fri Dec 3 17:57:16 1993 Received: from cucbs.chem.columbia.edu for budong@chem.columbia.edu by www.ccl.net (8.6.4/930601.1506) id RAA07130; Fri, 3 Dec 1993 17:25:43 -0500 Received: by cucbs.chem.columbia.edu id AA19688 (5.65c/IDA-1.4.4 for chemistry@ccl.net); Fri, 3 Dec 1993 17:25:20 -0500 Date: Fri, 3 Dec 1993 17:25:20 -0500 From: Budong Peng Message-Id: <199312032225.AA19688@cucbs.chem.columbia.edu> To: chemistry@ccl.net Subject: Excited States by GAMESS Dear netters; Currently I am working on the Formamide and Formamide-H2O complex with the GAMESS software. For Formamide HCONH2, I can reach the electronically excited states by UHF run with MULT=3. With the output from this I did a MCSCF OPTIMIZ(E)ation and get the total energy to be higher than the ground state (in MCSCF as well). The $DRT group for SCFTYP=MCSCF is GROUP=C1 FORS=.TRUE. IEXCIT=2 (I found that it doesn't matter how much is IEXCIT) NDOC=11 NVAL=0 NALP=2 When I tried to get to the excited singlet state, I replaced NALP=2 by NAOS=1 NBOS=1 However, the final energy is slightly LOWER than the ground state! Since I specified two singly occupied molecular orbitals, should this be an excited state? I am very puzzled by this. Another question I have is that how do I get to higher excited states with electron at a high orbital but leave lower orbitals empty? I couldn't figure out by reading the reference. For Formamide-H2O complex, I can't even specify MULT=3 and do a UHF calculation, the program will stop at the first NSERCH and say too many iterations before it can converge. Is it because that the complex has two molecules and the program is confused about how to get at the excited state? Is it quite different for one and two molecules? I would appreciate any advice and suggestionn. Thank you very much. Budong Peng From mercie@med.cornell.edu Fri Dec 3 23:52:50 1993 Received: from cumc.cornell.edu for mercie@med.cornell.edu by www.ccl.net (8.6.4/930601.1506) id XAA08430; Fri, 3 Dec 1993 23:33:03 -0500 Received: from localhost (mercie@localhost) by cumc.cornell.edu (8.6.4/ECH1.13) id XAA02680; Fri, 3 Dec 1993 23:31:13 -0500 Date: Fri, 3 Dec 1993 23:31:09 -0500 (EST) From: Gustavo Mercier Subject: Re: how to get Amsterdam DFT code? To: V098Q3NV@ubvmsb.cc.buffalo.edu cc: chemistry@ccl.net In-Reply-To: <01H60WAZ1Q2A8WY34D@ubvms.cc.buffalo.edu> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi! To get the Amsterdam DFT code: send e-mail to adf@chem.vu.nl or tevelde@chem.vu.nl good luck mercier mercie@cumc.cornell.edu