From tblee@camd.soongsil.ac.kr Wed Aug 5 01:38:52 1998 Received: from camd.soongsil.ac.kr (camd.soongsil.ac.kr [203.253.24.201]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with SMTP id BAA08586 Wed, 5 Aug 1998 01:38:40 -0400 (EDT) From: tblee@camd.soongsil.ac.kr Received: from camdrc2.soongsil.ac.kr (camdedu22.soongsil.ac.kr [203.253.24.227]) by camd.soongsil.ac.kr (950413.SGI.8.6.12/950213.SGI.AUTOCF) via SMTP id OAA06216 for ; Wed, 5 Aug 1998 14:38:30 +0900 Message-Id: <3.0.2.32.19980805143728.0069a898@camd.soongsil.ac.kr> X-Sender: tblee@camd.soongsil.ac.kr X-Mailer: QUALCOMM Windows Eudora Light Version 3.0.2 (32) Date: Wed, 05 Aug 1998 14:37:28 +0900 To: chemistry@www.ccl.net Subject: charge & multiplicity for ab-initio calc. Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Dear CCLers, I would like to know the setting of charge & multiplicity for benzene ring - metal atom(Al, Mg, Cu.....) system. As I know, the cation-pi electron interaction is strong, the starting structure is the binding between metal cation and benzene ring. My query is the value of charge & multiplicity for this non-neutral strcuture. In this case, the system is neutral or charged? >From the geometry optimization calculation of the OH- ion, ---------------------------------------------------------------------------- ------------ INPUT : Gaussian generated by Cerius2 ----------------------------- Symbolic Z-matrix: Charge =-1 Multiplicity = 2 OUTPUT : THE SPECIFIED CHARGE AND MULTIPLICITY ARE IMPOSSIBLE IN THIS MOLECULE. THE SUM OF THE ATOMIC NUMBERS IS 10, NATOMS IS 2 ATOMIC NUMBER VECTOR 8 1 Error termination via Lnk1e in /usr/people/guest/g94/l301.exe. -------------------------------------------- --------------------------------------------- I didn't know the proper value for this system and was very confused by this charged system! If some example about the charged system or the other calculation technique exist, it will be very helpful for me. From hjj@dou.dk Wed Aug 5 06:03:45 1998 Received: from gamma.dou.dk (gamma.dou.dk [130.225.130.6]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id GAA09402 Wed, 5 Aug 1998 06:03:43 -0400 (EDT) Received: from dou.dk (hjallese.chem.ou.dk [130.225.149.146]) by gamma.dou.dk (8.8.6/8.8.4) with ESMTP id MAA15066; Wed, 5 Aug 1998 12:03:38 +0200 (METDST) Message-ID: <35C82ED2.37476DE@dou.dk> Date: Wed, 05 Aug 1998 12:07:58 +0200 From: "Hans Joergen Aa. Jensen" Reply-To: hjj@dou.dk Organization: Department of Chemistry, Odense University X-Mailer: Mozilla 4.04 (Macintosh; I; PPC) MIME-Version: 1.0 To: chaudash@aston.ac.uk CC: chemistry@www.ccl.net Subject: Re: CCL:RMS gradient References: Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit chaudash@aston.ac.uk wrote: > > Hi everyoone, > Just a quick question, > When performing geomtry optimisations via GAMESS > (semi-empirical/ab-initio), the RMS gradient gradually decreases as > the calculation progresses, however even though the equilibrium > geometry is eventually located, the RMS gradient every so often > 'jumps up'. > Can anyone enlighten me as to why this occurs? > Hi, if you walk down a hillside you will in some cases observe that it at one point is fairly steep, a little further down it is less steep (smaller gradient), then it becomes more steep again (larger gradient) and you have been walking downhill all the time! -- Hans Joergen. From huesser@physik.unizh.ch Wed Aug 5 06:35:45 1998 Received: from caprice.physik.unizh.ch (caprice.physik.unizh.ch [130.60.164.12]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id GAA09473 Wed, 5 Aug 1998 06:35:44 -0400 (EDT) Received: by caprice.physik.unizh.ch (8.7.3cf2.18) id MAA20950; Wed, 5 Aug 1998 12:35:43 +0200 From: Peter Huesser Message-Id: <199808051035.MAA20950@caprice.physik.unizh.ch> Subject: cu+ pseudopotential needed To: chemistry@www.ccl.net Date: Wed, 5 Aug 1998 12:35:43 +0200 (MEST) X-Mailer: ELM [version 2.4 PL23] MIME-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Dear CCLers, does anybody knows a pseudopotential for cu+ and where to find it ? Thank's in advance for any help Peter Huesser Email: huesser@physik.unizh.ch From steven@hartree.quantchem.kuleuven.ac.be Wed Aug 5 08:48:12 1998 Received: from hartree.chem.kuleuven.ac.be (hartree.quantchem.kuleuven.ac.be [134.58.49.1]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id IAA10113 Wed, 5 Aug 1998 08:48:10 -0400 (EDT) Received: from localhost (steven@localhost) by hartree.chem.kuleuven.ac.be (8.9.0/8.9.0) with SMTP id OAA39848 for ; Wed, 5 Aug 1998 14:49:53 +0100 Date: Wed, 5 Aug 1998 14:49:53 +0100 (NFT) From: Steven Creve To: Computational Chemistry List Subject: CCL: modelling summary Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi all here is a preliminary summary of the responses I received till now. Thanks to all people giving information! ------------------------------------------------------------------- for inorganic systems: Comba, Hambley, Molecular Modeling of Inorganic Compounds, VCH, NY, 1995 for bioinorganic systems: Zimmer, Chem. Rev., 1995, 95, 2629 Andrew R. Leach, "Molecular Modelling: Principles and Applications", Edited by Longman, Singapore in 1996 Encyclopedia of Computational Chemistry, P. v. R. Schleyer, N. L. Allinger, T. Clark, J. Gasteiger, P. Kollman, and H. F. Schaefer III, Eds., John Wiley & Sons. and some nice links: http://www.cooper.edu/engineering/chemechem/monte.html http://www.cup.cam.ac.uk/onlinepubs/ArtMolecular/ArtMoleculartop.html http://ct-cr6.chem.uva.nl/frenkel_smit/ http://www.msi.com/info/materials/general/erich/Main.htm http://antas.agraria.uniss.it -------------------------------------------------------------------------- Steven Creve steven.creve@chem.kuleuven.ac.be Labo Quantumchemie Celestijnenlaan 200F 3001-HEVERLEE tel: (32) (16) 32 73 93 BELGIUM fax: (32) (16) 32 79 92 From laurent@crypt.u-strasbg.fr Wed Aug 5 09:00:17 1998 Received: from crypt.u-strasbg.fr (crypt.u-strasbg.fr [130.79.34.5]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id JAA10221 Wed, 5 Aug 1998 09:00:14 -0400 (EDT) Received: (from laurent@localhost) by crypt.u-strasbg.fr (8.9.0/8.9.0) id OAA00984; Wed, 5 Aug 1998 14:57:23 +0200 (METDST) Date: Wed, 5 Aug 1998 14:57:21 +0200 (MET) From: Laurent TROXLER To: Peter Huesser cc: chemistry@www.ccl.net Subject: Re: CCL:cu+ pseudopotential needed In-Reply-To: <199808051035.MAA20950@caprice.physik.unizh.ch> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII On Wed, 5 Aug 1998, Peter Huesser wrote: > Dear CCLers, > > does anybody knows a pseudopotential for cu+ and where to > find it ? > Have a look on http://www.theochem.uni-stuttgart.de/pseudopotentiale/ > Thank's in advance for any help > > Peter Huesser > > Email: huesser@physik.unizh.ch > > -------This is added Automatically by the Software-------- > -- Original Sender Envelope Address: huesser@physik.unizh.ch > -- Original Sender From: Address: huesser@physik.unizh.ch > CHEMISTRY@www.ccl.net: Everybody | CHEMISTRY-REQUEST@www.ccl.net: Coordinator > MAILSERV@www.ccl.net: HELP CHEMISTRY or HELP SEARCH | Gopher: www.ccl.net 73 > Anon. ftp: www.ccl.net | CHEMISTRY-SEARCH@www.ccl.net -- archive search > Web: http://www.ccl.net/chemistry.html > Laurent ,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@/\@@/\@@/\@@@@ Laurent TROXLER / \/ \/ \ Lab. Modelisation et Simulations Moleculaires / /\/ /\/ /\ \ Universite Louis Pasteur \ \/ /\/ /\/ / 4, rue Blaise Pascal \ \/\ \/\ \/ 67070 Strasbourg (France) /\ \/\ \/\ \ E-mail: troxler@crypt.u-strasbg.fr / /\/ /\/ /\ \ Tel : (33) 3 88 41 62 87 \ \/ /\/ /\/ / @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@\@@/\@@/\@@/@@@ """"""""""""""""""""""""""""""""""""""""""""""""""\/""\/""\/"""" From dgao@chem.iupui.edu Wed Aug 5 09:34:16 1998 Received: from hydroxyl.chem.iupui.edu (hydroxyl.chem.iupui.edu [134.68.136.154]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with SMTP id JAA10714 Wed, 5 Aug 1998 09:34:15 -0400 (EDT) Received: from localhost by hydroxyl.chem.iupui.edu (950413.SGI.8.6.12/MSU-2.04) id NAA00689; Wed, 5 Aug 1998 13:34:15 GMT Date: Wed, 5 Aug 1998 08:34:15 -0500 (EST) From: Daquan Gao To: tblee@camd.soongsil.ac.kr cc: chemistry@www.ccl.net Subject: Re: CCL:G:charge & multiplicity for ab-initio calc. In-Reply-To: <3.0.2.32.19980805143728.0069a898@camd.soongsil.ac.kr> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII On Wed, 5 Aug 1998 tblee@camd.soongsil.ac.kr wrote: > Dear CCLers, > > I would like to know the setting of charge & multiplicity for benzene ring > - metal atom(Al, Mg, Cu.....) system. As I know, the cation-pi electron > interaction is strong, the starting structure is the binding between metal > cation and benzene ring. My query is the value of charge & multiplicity for > this non-neutral strcuture. In this case, the system is neutral or charged? > > >From the geometry optimization calculation of the OH- ion, > > ---------------------------------------------------------------------------- > ------------ > INPUT : > > Gaussian generated by Cerius2 > ----------------------------- > Symbolic > Z-matrix: > Charge =-1 Multiplicity = 2 > > OUTPUT : > > THE SPECIFIED CHARGE AND MULTIPLICITY ARE IMPOSSIBLE IN THIS MOLECULE. > > THE SUM OF THE ATOMIC NUMBERS IS 10, NATOMS IS 2 > ATOMIC NUMBER VECTOR > 8 1 > Error termination via Lnk1e in > /usr/people/guest/g94/l301.exe. > -------------------------------------------- > --------------------------------------------- > > I didn't know the proper value for this system and was very confused by > this charged system! > If some example about the charged system or the other calculation technique > exist, > it will be very helpful for me. Looks to me the multiplicity should be 1. Why the SUM OF THE ATOMIC NUMBERS IS 10? Hope this helps. Daquan Gao > > > > -------This is added Automatically by the Software-------- > -- Original Sender Envelope Address: tblee@camd.soongsil.ac.kr > -- Original Sender From: Address: tblee@camd.soongsil.ac.kr > CHEMISTRY@www.ccl.net: Everybody | CHEMISTRY-REQUEST@www.ccl.net: Coordinator > MAILSERV@www.ccl.net: HELP CHEMISTRY or HELP SEARCH | Gopher: www.ccl.net 73 > Anon. ftp: www.ccl.net | CHEMISTRY-SEARCH@www.ccl.net -- archive search > Web: http://www.ccl.net/chemistry.html > From gurp@pml.tno.nl Wed Aug 5 11:01:22 1998 Received: from frontier.tno.nl (frontier.tno.nl [134.221.1.2]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id LAA11675 Wed, 5 Aug 1998 11:01:21 -0400 (EDT) Received: from stevin.pml.tno.nl (stevin.pml.tno.nl [134.221.122.11]) by frontier.tno.nl (8.8.8/8.8.8) with SMTP id RAA19403 for ; Wed, 5 Aug 1998 17:00:51 +0200 (MET DST) Received: from mailrouter.pml.tno.nl (wnt-950140) by stevin.pml.tno.nl (4.1/1.53) id AA01581; Wed, 5 Aug 98 16:56:13 +0200 Received: from exchange.pml.tno.nl (EXCHANGE [134.203.134.74]) by mailrouter.pml.tno.nl with SMTP (Microsoft Exchange Internet Mail Service Version 5.5.1960.3) id 3D6QFJQA; Wed, 5 Aug 1998 16:58:28 +0200 Received: by postoffice.pml.tno.nl with Internet Mail Service (5.5.1960.3) id ; Wed, 5 Aug 1998 17:00:49 +0200 Message-Id: <97C27A97BB05D211B37100805FE2A63814A281@postoffice.pml.tno.nl> From: Gurp To: "'chemistry@www.ccl.net'" Cc: Linders Subject: Molecular area of adsorbates Date: Wed, 5 Aug 1998 17:00:48 +0200 Mime-Version: 1.0 X-Mailer: Internet Mail Service (5.5.1960.3) Content-Type: text/plain Dear Netters, We are looking for a program that calculates the area of a molecule, which is projected on a surface. The practical background is the following: consider molecules that are adsorbed on a surface. What is the average area they occupy on that surface ? This depends of course on how a particular molecule adsorbs on a surface, i.e. its orientation relative to the surface. As a first estimate one may take the average of a certain number of projections (or cross sectional areas). Does anyone know of a program that calculates such projected surfaces from a MOL, XYZ, PDB or QUANTA MSF file input, or, even better, a program which also takes into account the preferred orientations of a molecule on a surface ? I will summarize your reactions. Thanx, Ronald A. van Gurp Prins Maurits Laboratory TNO P.O. Box 45 2280 AA Rijswijk The Netherlands From asmellie@combichem.com Wed Aug 5 12:01:13 1998 Received: from hermes.combichem.com (hermes.combichem.com [207.158.48.4]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id MAA12171 Wed, 5 Aug 1998 12:01:13 -0400 (EDT) Received: from combichem.com ([207.158.46.99]) by hermes.combichem.com (Post.Office MTA v3.1.2 release (PO205-101c) ID# 0-49457U200L100S0) with ESMTP id AAA308; Wed, 5 Aug 1998 08:56:50 -0700 Message-ID: <35C8802F.EB4870ED@combichem.com> Date: Wed, 05 Aug 1998 08:54:23 -0700 From: asmellie@combichem.com (Andrew Smellie) X-Mailer: Mozilla 4.04 [en] (WinNT; I) MIME-Version: 1.0 To: ccl Subject: CCL: recommendations for an MM force field Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Deal CClers, I'm looking for recommendations for a molecular mechanics force field for use in a modelling package that measures relative energies of conformations of small biomolecules. Some desirable properties of such a force field are: (1) Parameterized widely (i.e. has parameters for all common organic element types (H,C,N,O,S,P,F,Cl,Br,I) and their internal coordinates (bonds, angles, torsions,vdw etc) (2) Has relatively few atom types. (3) Is publically available, or available at low cost (4) Has been validated on a large set of diverse compounds I will be happy to summarize the responses. Thank you for your help in this, Andrew Smellie -- Dr. Andrew Smellie, CombiChem Inc. 1804 Embarcadero Road, Palo Alto, CA 94303 Phone: (650)-842-0560 FAX: (650-842-0575 email: asmellie@combichem.com From lankau@blubber.chemie.uni-hamburg.de Wed Aug 5 13:24:14 1998 Received: from blubber.chemie.uni-hamburg.de (blubber.chemie.uni-hamburg.de [134.100.212.9]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with SMTP id NAA12750 Wed, 5 Aug 1998 13:24:11 -0400 (EDT) Received: by blubber.chemie.uni-hamburg.de (AIX 4.1/UCB 5.64/4.03) id AA03660; Wed, 5 Aug 1998 19:13:21 +0200 Date: Wed, 5 Aug 1998 19:13:20 +0200 (DFT) From: Timm Lankau To: chemistry@www.ccl.net Subject: G94 cube file to gnuplot (3D data) Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hello, I am looking for a simple program / shell script, which converts density data from a G94 cube file to a data file suitable for gnuplot to generate a 3D surface plotable with 'splot'. Thank you very much. Timm ========================================================================== Timm Lankau phone (+)40 4123 3686 Institut fuer Physikalische Chemie fax (+)40 4123 3452 Universitaet Hamburg e-mail lankau@chemie.uni-hamburg.de Bundesstr. 45 20146 Hamburg Germany From MARYJO@neu.edu Wed Aug 5 17:14:06 1998 Received: from NUHUB.DAC.NEU.EDU (nuhub.dac.neu.edu [129.10.1.6]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id RAA14248 Wed, 5 Aug 1998 17:14:06 -0400 (EDT) From: MARYJO@neu.edu Received: from neu.edu by neu.edu (PMDF V5.1-8 #24746) id <01J0935JK2OGADNPKZ@neu.edu> for chemistry@www.ccl.net; Wed, 5 Aug 1998 17:14:00 EST Date: Wed, 05 Aug 1998 17:13:59 -0500 (EST) Subject: point charges in GAMESS ? To: chemistry@www.ccl.net Message-id: <01J0935JM7UAADNPKZ@neu.edu> X-VMS-To: IN%"chemistry@www.ccl.net" MIME-version: 1.0 Hello. Does anybody know whether there is a version of GAMESS which will allow input of point charges? I want to represent the environment of my molecule as an array of point charges. Thanks very much, Mary j.o. From gustavo@hathi.chem.pitt.edu Wed Aug 5 17:19:23 1998 Received: from post-ofc06.srv.cis.pitt.edu (root@post-ofc06.srv.cis.pitt.edu [136.142.185.43]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id RAA14262 Wed, 5 Aug 1998 17:19:22 -0400 (EDT) Received: from hathi.chem.pitt.edu (hathi.chem.pitt.edu [136.142.109.10]) by post-ofc06.srv.cis.pitt.edu with SMTP (8.8.8/8.8.8/cispo-7.2.2.2) ID for <@smtp.pitt.edu:chemistry@www.ccl.net>; Wed, 5 Aug 1998 17:19:20 -0400 (EDT) Received: by hathi.chem.pitt.edu (940816.SGI.8.6.9/920502.SGI.AUTO) for chemistry@www.ccl.net id RAA19288; Wed, 5 Aug 1998 17:19:31 -0400 From: "Gustavo Moura" Message-Id: <9808051719.ZM19286@hathi.chem.pitt.edu> Date: Wed, 5 Aug 1998 17:19:28 -0400 X-Mailer: Z-Mail (3.2.0 26oct94 MediaMail) To: chemistry@www.ccl.net Subject: Off-diagonal elements of the CI matrix Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Dear CCL readers, I am writing a program to do CI calculations on some conjugated molecules using semiempirical (PPP) parameters. Unfortunately, I am having problems to calculate the off-diagonal elements of the CI matrix. In their book Szabo e Ostlund show (tables 2.3 and 2.4) how to calculate these elements when the determinants are in maximum coincidence. I am looking for references where I can find the answer to the following simple(?) question: HOW TO CALCULATE THE NUMBER OF PERMUTATIONS NECESSARY TO OBTAIN MAXIMUM COINCIDENCE BETWEEN THE DETERMINANTS? In other words: WHEN SHOULD I MULTIPLY THE EQUATIONS SHOWN IN THE BOOK BY -1? Thank you very much in advance. I will sumarize. Sincerely yours, Gustavo L.C. Moura gustavo@hathi.chem.pitt.edu From smithja@ucarb.com Wed Aug 5 17:20:57 1998 Received: from sctmg02.sct.ucarb.com ([140.170.101.20]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id RAA14274 Wed, 5 Aug 1998 17:20:56 -0400 (EDT) Received: by sctmg02.sct.ucarb.com with Internet Mail Service (5.0.1458.49) id ; Wed, 5 Aug 1998 17:21:45 -0400 Message-ID: From: "Smith JA (Jack)" To: "'chemistry@www.ccl.net'" , "'Gurp'" Subject: RE: Molecular area of adsorbates Date: Wed, 5 Aug 1998 16:44:20 -0400 X-Priority: 3 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.0.1458.49) Content-Type: text/plain Ronald A van Gurp wrote: > We are looking for a program that calculates the area of a molecule, > which is projected on a surface. The practical background is the > following: consider molecules that are adsorbed on a surface. What is > the average area they occupy on that surface ? This depends of course > on > how a particular molecule adsorbs on a surface, i.e. its orientation > relative to the surface. As a first estimate one may take the average > of > a certain number of projections (or cross sectional areas). Does > anyone > know of a program that calculates such projected surfaces from a MOL, > XYZ, PDB or QUANTA MSF file input, or, even better, a program which > also > takes into account the preferred orientations of a molecule on a > surface > Look at Craig Taverner's steric program (ftp://hobbes.gh.wits.ac.za/pub/steric/) based on solid angles. The solid angle corresponds to a projection onto an enclosing sphere, but if you set the origin far enough away from the molecule (effectively increasing the radius of the enclosing sphere), the solid angle projection will approach an orthogonal projection. The projected area would be R*R*(Solid Angle), where R is the radius of the sphere (the distance between the origin and the furthest atom). The program will read PDB format, and it will generate a GnuPlot plot of the angular profile. The program should be easily modified to give the othogonal projection directly without resetting the origin. - Jack -=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=- Jack A. Smith || Union Carbide || Phone: (304) 747-5797 Catalyst Skill Center || FAX: (304) 747-4672 P.O. Box 8361 || S. Charleston, WV 25303 || smithja@ucarb.com -=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=- From qiang@tammy.harvard.edu Wed Aug 5 19:00:46 1998 Received: from karplus0.harvard.edu (tammy.harvard.edu [128.103.92.198]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id TAA14766 Wed, 5 Aug 1998 19:00:45 -0400 (EDT) Received: from topanga.harvard.edu (topanga [128.103.92.179]) by karplus0.harvard.edu (8.8.2/8.8.2) with ESMTP id TAA09339; Wed, 5 Aug 1998 19:10:49 -0400 (EDT) Received: from localhost (qiang@localhost) by topanga.harvard.edu (8.8.2/8.8.2) with SMTP id SAA01458; Wed, 5 Aug 1998 18:49:30 -0400 (EDT) Date: Wed, 5 Aug 1998 18:49:30 -0400 (EDT) From: Qiang Cui To: MARYJO@neu.edu cc: chemistry@www.ccl.net Subject: Re: CCL:point charges in GAMESS ? In-Reply-To: <01J0935JM7UAADNPKZ@neu.edu> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII On Wed, 5 Aug 1998 MARYJO@neu.edu wrote: > Hello. > > Does anybody know whether there is a version of GAMESS which will > allow input of point charges? > > I want to represent the environment of my molecule as an array of > point charges. As far as I know, CHARMM/GAMESS is the way to go if you want the MM enviroment. Otherwise, you can "cheat" the program by putting each point charge as an effective fragment with only the monopole part. If you have a lot of point charges, however, you have to re-compile the GAMESS package after changing the maximum # of allowed EF types. Good luck. > > Thanks very much, > > Mary j.o. > > -------This is added Automatically by the Software-------- > -- Original Sender Envelope Address: MARYJO@neu.edu > -- Original Sender From: Address: MARYJO@neu.edu > CHEMISTRY@www.ccl.net: Everybody | CHEMISTRY-REQUEST@www.ccl.net: Coordinator > MAILSERV@www.ccl.net: HELP CHEMISTRY or HELP SEARCH | Gopher: www.ccl.net 73 > Anon. ftp: www.ccl.net | CHEMISTRY-SEARCH@www.ccl.net -- archive search > Web: http://www.ccl.net/chemistry.html > > ___________________________________________________________________________ Qiang Cui Dept. of Chem. _ __..-;''`--/'/ /.',-`-. Harvard Univ. (`/' ` | \ \ \\ / / / / .-'/`,_ 12 Oxford St., /'`\ \ | \ | \| // // / -.,/_,'-, Cambridge, MA 02138 /<7' ; \ \ | ; ||/ /| | \/ |`-/,/-.,_,/') (617)-495-8997 / _.-, `,-\,__| _-| / \ \/|_/ | '-/.;.\' (617)-495-1775 `-` f/ ; / __/ \__ `/ |__/ | Fax: (617)-496-3204 `-' | -| =|\_ \ |-' | http://euch4m.chem.emory.edu/~qiang __/ /_..-' ` ),' // ((__.-'((___..-'' \__.' 65 Dane Street Somerville, MA 02143 (617)-623-5123 __________________________________________________________________________ From lemmen@gmd.de Tue Aug 4 07:25:36 1998 Received: from mail.gmd.de (mail.gmd.de [129.26.8.90]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id HAA22844 Tue, 4 Aug 1998 07:25:33 -0400 (EDT) Received: from escher (escher.gmd.de [129.26.8.103]) by mail.gmd.de (8.8.8/8.8.8) with SMTP id NAA07179 for ; Tue, 4 Aug 1998 13:25:10 +0200 (MET DST) Received: from gmd.de (localhost) by escher with SMTP id AA24504 (5.67b/IDA-1.5 for ); Tue, 4 Aug 1998 13:25:09 +0200 Sender: lemmen@gmd.de Message-Id: <35C6EF93.1C5521A1@gmd.de> Date: Tue, 04 Aug 1998 13:25:07 +0200 From: Christian Lemmen X-Mailer: Mozilla 4.05 [en] (X11; I; SunOS 5.6 sun4u) Mime-Version: 1.0 To: chemistry@www.ccl.net Subject: Free flexible superposition software Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear Colleague! FlexS is a program for automatic, flexible structural alignment of small organic molecules. We are offering a free Demo-License for the FlexS-Software package. This License covers the full functionality of FlexS including the visualization program FlexV and the FlexS static data package. The license will be valid for approximately eight weeks. After that time period, you can obtain a perpetual license for FlexS. You can download FlexS for Sun Solaris, SGI IRIX, and LINUX operation systems free of charge from our web-page http://cartan.gmd.de/FlexS Sincerely, Christian Lemmen -- SSSSSSS CCCCCCC A IIIIIIII Christian Lemmen SSS CCCC AAA II SS CC AA AA II GMD (SCAI) SSS CC A A II Schloss Birlinghoven SSSSS CC AA AA II D - 53754 St. Augustin SSS CC AAAAAAAAA II Germany SS CC AA AA II Tel.: +49 2241 14 2481 SSS CCCC AA AA II Sec.: +49 2241 14 2776 SSSSSSS CCCCCCC AA AA IIIIIIII Fax.: +49 2241 14 2656 From dons@hamilton.math.missouri.edu Tue Aug 4 15:01:30 1998 Received: from math.missouri.edu (math.missouri.edu [128.206.72.13]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with SMTP id PAA06090 Tue, 4 Aug 1998 15:01:29 -0400 (EDT) Received: from hamilton.math.missouri.edu by math.missouri.edu via ESMTP (940816.SGI.8.6.9/940406.SGI) for <@math.missouri.edu:chemistry@www.ccl.net> id OAA05238; Tue, 4 Aug 1998 14:01:31 -0500 Received: by hamilton.math.missouri.edu (940816.SGI.8.6.9/940406.SGI) for chemistry@www.ccl.net id NAA27849; Tue, 4 Aug 1998 13:28:37 -0500 From: "Don Steiger" Message-Id: <9808041328.ZM27847@hamilton.math.missouri.edu> Date: Tue, 4 Aug 1998 13:28:35 -0500 X-Mailer: Z-Mail (3.2.0 26oct94 MediaMail) To: chemistry@www.ccl.net Subject: Drug design - summary. Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Below is a summary of the replies to a question I recently posted. I would like to thank everybody who replied to the question. First the question. > I am a math graduate student and working with one of the theoretical chemist at > the university here I developed a multipole algorithm for calculating coulomb > interactions. With some modifications, this method can be used as a rapid > screening procedure for the electrostatic version of the docking problem. > The chemist that I am working with feels that this is a very important problem > in the area of drug design and that I should pursue it further. In helping me > to decide if I should pursue this, I was wondering if someone could briefly > summarize the state of the art in this field. The reply summary follows. > Hierarchical multpole methods are very usefull mathematical > tools in chemsitry. See my page for papers with bibliography > on this topic. > > On the other hand, attempting to fit or parameterize chemical > interactions with multipoles (or other functions) is an art, not a > science, as there are an infinite number of posibilities. My two > cents is to focous on mathematical tools, and to avoid at all > costs anything that looks like a parameterization. > > Cheers, Matt > > +-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ > Matt Challacombe > Los Alamos National Laboratory http://www.t12.lanl.gov/~mchalla/ > Theoretical Division email: mchalla@t12.lanl.gov > Group T-12, Mail Stop B268 phone: (505) 665-5905 > Los Alamos, New Mexico 87545 fax: (505) 665-3909 ______________________________________________________________________________ I am somewhat familiar with the work of the above individual. Two very interesting and novel papers of his are the following. 1) Fast assembly of the Coulomb matrix: A quantum chemical tree code. J. Chem. Phys. 104(12) pages 4685-4698. 2) Linear scaling computation of the Fock matrix. J. Chem. Phys. 106(13) pages 5526-5536. Don _____________________________________________________________________________________________________________________________ > The difficulty here, as I understand it, is that multipole methods > are useful only in the "far field" case, while it is nearby interactions > that predominate in protein/ligand interactions. I looked into > multipole methods for a slightly different, but related, purpose > some years back and decided that it wasn't worth it. But don't let > my decision for a somewhat different problem and a less-than-perfect > understanding of multipole expansions discourage you from looking into > the problem more deeply yourself. Just make sure that the part of the total > calculation that you want to speed up is a sufficiently large part of > the total calculation that it makes a difference. Remember that a > 90% speed-up of 10% of the calculation is only a 9% improvement overall. > > > regards, > > Ethan A Merritt > > ----------------------------------------------------------------- > Dept of Biological Structure K428b Health Sciences > University of Washington SM-20 (206)543-1421 > Seattle, WA 98195-7742 merritt@u.washington.edu Comment. Multipole expansions have decent convergence only in the far field case. However, I think this problem can be ameliorated with a couple of tricks. The first is to fragment the molecules and compute the multipole moments for each of the fragments. The second trick would be to use non-linear convergence acceleration methods on the multipole expansion. This idea has been tried on a spherical harmonic multipole expansion by H.H.H. Homeier in a paper recently published in the Internet Journal of Chemistry; http://www.ijc.com/articles/1998v1/28. What I suspect to be the most difficult problem to work around are the induced effects. Don ________________________________________________________________________________ > Greengard-Rokhlin algorithm. Leslie Greengard is at Yale. > I don't know who has implemented this for finding molecular > energies. Use Science Citation Index to find out. Can > you treat molecular models in solution, with one > dielectric constant inside the molecule, and a second, > in general different, dielectric constant outside the > molecule? I have a fast diffusion method for solving these problems. > We are using it to calculate solvation energies of macromolecules. > > > Best, > > Jim Given > > Center for Advanced Research in Biotechnology _______________________________________________________________________________ > While purely electrostatic interaction potentials were developed and > tried a few decades ago, they remain a very important part of > computational chemistry. At present, most people do not use multipolar > representations for electrostatic interations (they stick with monomers > alone or use bond dipoles) since the computational time for multipolar > interaction calculations is significantly greater. Don Williams > (Kentucky, I think) has some code which will fit electrostatic > potentials to a set of multipoles, of both atom and bond centered > character. I believe that this code can also be used to compute and > export potentials using the derived multipoles. There are a number of > other groups who have worked in this area, so please do not assume that > this posting is comprehensive. Price, Stone and our own group > (Breneman) have also worked in this area. Earlier workers are Ritchie > and Hirschfeld. There is a rich literature in this area, but there is > always room for good ideas. > > Prof Curt Breneman > RPI Chemistry Department ________________________________________________________________________________ > That work sounds very interesting and I would like to hear about any useful > replies you get please. My colleague, Frank Burden (Chemistry Department > Monash University) have been working on molecular multipoles for screening > applications for some time. We are basically improving the methods > developed by Silverman and Platt (Platt, D.E.; Silverman, B.D. J. > Computat. Chem. (1996), 17, 358-66; > Silverman, B.D; Platt, D.R. J. Med. Chem. (1996) 39, 2129-40). The > critical question for drug design is how you define your axis system for > the electric multipoles with respect to the inertial axes. If this can be > done correctly, the so-called 'alignment problem' (the need to superimpose > molecules which at act at the same receptor in a consistent way) can be > eliminated. We do not agree with how S&P have defined theirs by feel they > were on the right track. We have also added steric/inertial multipoles and > , in collaboration with Glen Kellogg at Virginia Commonwealth University, > have included 'hydropoles' (essentially expansions of the lipophilic > properties of drug molecules). > > We would be interested in hearing more about your work. Can you send us > any papers, reports, theses etc on what you have achieved? > > Cheers, > > Dave > > Dr. David A. Winkler Email: dave.winkler@molsci.csiro.au > Senior Principal Research Scientist Voice: 61-3-9545-2477 > CSIRO Molecular Science Fax: 61-3-9545-2446 > Private Bag 10,Clayton South MDC 3169 http://www.csiro.au > Australia http://www.molsci.csiro.au > > _______________________________________________________________________________ > Check out papers by > Greengard and Rokhlin, > S.Lustig and N.J.Wagner et.al. > sorry don't have them handy, > these are all quite recent publications, last maybe 4-5 years, > I am sure you'll find it in the database, > > Hope this helps, > Mike > > ------------------------------------------------------------------------------- > Michael J. Kotelyanskii Phone (814) 863 43 81 > Polymer Science Program FAX (814) 865 29 17 > Department of Materials Science and > Engineering kotelyan@plmsc.psu.edu > Pennsylvania State University http://www.plmsc.psu.edu/~kotelyan > University Park, PA 16802, USA ________________________________________________________________________________ > Yes, treating correctly Coulomb interactions in molecular simulations > (without using a cutoff in the list of interacting centers) is indeed an > important topic. The contest seems to have been won by smooth particle > mesh Ewald sums (SPME), which scales as O(N) like the fast multipole > technique, but with a much smaller costant factor, as I am said: see > T.A. Darden, D.M. York, L.G. Pedersen, J. Chem. Phys., 98, 10089 (1993); > U. Essmann, L. Perera, M. Berkowitz, T. Darden, H. Lee, L.G. Pedersen, > J. Chem. Phys., 103, 8577 (1995); P. Procacci and M. Marchi, J. Chem. > Phys., 104, 3003-3012 (1996); P. Procacci, T. Darden, M. Marchi, > J. Phys. Chem., 100, 10464-10468 (1996). > > Two references for the fast multipole method, which I admit to have > never read though, are K.E. Schmidt, M.A. Lee, J.Stat.Phys. 1223-1235 > (1991) and J. Shimada, H. Kaneko, T. Takada, J. Comp. Chem. 15, 28 > (1994). See also the book D.Frenkel, B.Smit, Understanding Molecular > Simulation, Academic Press (1996). > > It's not clear to me, however, if high accuracy and periodic boundary > conditions are needed in docking problems as well as in molecular > dynamics simulations. If they aren't, maybe the fast multipole method > which was originally devised for a cluster of ions is indeed a better > choice than SPME. > > Regards > > Dr. Guido Germano > > Research Assistant in Theoretical Physics, University of Bristol, England > Tel. +44-117-928 8755, http://www.phy.bris.ac.uk/staff/germano_g.html > ________________________________________________________________________________ > There is an abundance of reviews on drug design. Look at the book series, > Reviews in Computational Chemistry, edited by Lipkowitz and myself. > Particularly Vol. 5 (1994) and Vol. 11 (1997). These books will probably be > in your chemistry department library. Also, take a look at the May 1998 issue > of CHEMTECH magazine, p.19. Again it should be in your chemistry department > library. > > Don > Donald B. Boyd, Ph.D. > Editor, Journal of Molecular Graphics and Modelling > Department of Chemistry > Indiana University-Purdue University at Indianapolis > 402 North Blackford Street > Indianapolis, Indiana 46202-3274, U.S.A. > E-mail boyd@chem.iupui.edu ________________________________________________________________________________ > I suggest that you look at papers by S L Price (University College > London) to see applications of multipole calculations in molecular > modelling. However her work may not be directly applicable to > docking calculations: I think she is mainly interested in small- > molecule crystallographic modelling issues. Certainly multipole > calculations are an important technique in that area (although > they are rarely used in practice because the major modelling > software packages cannot handle them at present). I don't know > anything about docking myself so I cannot comment on how useful > they would be in docking calculations. > > -- > John Osborn > University of Bradford, UK. > Email j.c.osborn@bradford.ac.uk -- Don Steiger dons@hamilton.math.missouri.edu