From h332262@sirius.cab.u-szeged.hu Wed Oct 15 03:19:10 1997 Received: from sirius.cab.u-szeged.hu for h332262@sirius.cab.u-szeged.hu by www.ccl.net (8.8.3/950822.1) id CAA12837; Wed, 15 Oct 1997 02:30:25 -0400 (EDT) Received: (qmail 4314 invoked by uid 32262); 15 Oct 1997 06:29:30 -0000 Date: Wed, 15 Oct 1997 08:29:30 +0200 (MET DST) From: Kiss Gergo X-Sender: h332262@sirius To: chemistry@www.ccl.net Subject: Molucule sketcher under Linux ,Irix or DECUnix Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi everybody, I am looking for a FREE sketcher(drawer), which can create input files for quantum chemical software(mopac, gamess,...). It would be important, I need it bad, but my department can't afford it. Please Help!!!!! Kiss Gergo h332262@sirius.cab.u-szeged.hu From jochen@pc1.uni-duesseldorf.de Wed Oct 15 06:30:47 1997 Received: from sirene.rz.uni-duesseldorf.de for jochen@pc1.uni-duesseldorf.de by www.ccl.net (8.8.3/950822.1) id GAA13831; Wed, 15 Oct 1997 06:27:14 -0400 (EDT) Received: from bacchus.pc1.uni-duesseldorf.de by sirene.rz.uni-duesseldorf.de with SMTP (PP); Wed, 15 Oct 1997 12:26:39 +0200 Received: by bacchus.pc1.uni-duesseldorf.de (5.65v3.2/1.1.10.5/06Jan97-0309PM) id AA04111; Wed, 15 Oct 1997 12:26:39 +0200 Date: Wed, 15 Oct 1997 12:26:39 +0200 From: Jochen Kuepper Message-Id: <9710151026.AA04111@bacchus.pc1.uni-duesseldorf.de> To: h332262@sirius.cab.u-szeged.hu Subject: Re: CCL:M:Molucule sketcher under Linux ,Irix or DECUnix Cc: chemistry@www.ccl.net MIME-version: 1.0 Content-type: text/plain; charset="ISO-8859-1" Content-transfer-encoding: quoted-printable Content-Md5: hjiQw9Fl44bfCVMcL4oKmw== molden from http://www.caos.kun.nl/~schaft/molden/molden.html =20 Jochen ----------------------------------------------------------------------- Jochen K=FCpper Heinrich-Heine-Universit=E4t D=FCsseldorf = jochen@uni-duesseldorf.de Institut f=FCr Physikalische Chemie I Universit=E4tsstrasse 1, Geb 26.43.02.19 phone ++49-211-8113681 40225 D=FCsseldorf fax ++49-211-8115195 Germany http://www-public.rz.uni-duesseldorf.de/~jochen ----------------------------------------------------------------------- From rummey@chemie.uni-wuerzburg.de Wed Oct 15 07:30:49 1997 Received: from wrzx07.rz.uni-wuerzburg.de for rummey@chemie.uni-wuerzburg.de by www.ccl.net (8.8.3/950822.1) id HAA13988; Wed, 15 Oct 1997 07:20:30 -0400 (EDT) Received: from wocx04.chemie.uni-wuerzburg.de (wocx13.chemie.uni-wuerzburg.de [132.187.64.13]) by wrzx07.rz.uni-wuerzburg.de (8.8.5/8.8.5) with SMTP id NAA23393 for ; Wed, 15 Oct 1997 13:20:22 +0200 (MET DST) Received: by wocx04.chemie.uni-wuerzburg.de (940816.SGI.8.6.9/uniwue-C-3.0) id MAA02515; Wed, 15 Oct 1997 12:16:06 +0100 Date: Wed, 15 Oct 1997 12:16:06 +0100 (MET) From: Christian Rummey X-Sender: rummey@wocx13 To: chemistry@www.ccl.net Subject: Summary: g94 frequency-output Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi! About a week ago I posted a msg about visaulisation of the g94 frequency output. Thanks again to all who replied, and now for the people who asked about it: the summary - 1. Vibration Modes for Windows I didn't try it until now, possibly can only read gaussian92 output. available at ftp://ftp.ccl.net/pub/chemistry/software/MS-WIN3/Vibration_modes_for_Windows/ vibratio.zip - 2. Viewmol can only read g92 output (in this version) but Dr. Joerg-R. Hill sent me a 'patch' for g94 output. If one needs it, ask me for it. Sorry, but I'm very busy at the moment, so I didn't try to compile it yet. file://ftp.ask.uni-karlsruhe.de/pub/education/chemistry/viewmol.source-2.0.3.tar.gz - 3. AniMol (for Windows) but the poster didn't tell me where to get it. - 4. Molwin Avaikable at the CCL-Archive, needs the long frequency-output from gaussian94 (# freq=HPMode MP2/6-31G*) - 5. xvibs (version 4) ftp://www.ccl.net/pub/chemistry/software/SOURCES/C/xvibs/ Its output can be read eg by xmol. That's all. Sorry I did not have the time for testing yet. Cheers CR _________________________________________________________________ / \ | Christian Rummey | | Institut fuer Organische Chemie | | Universitaet Wuerzburg | | Computational Chemistry Group | | | | Am Hubland | email : rummey@chemie.uni-wuerzburg.de | | 97074 Wuerzburg | voice : +49-(0)931-888-4750 | | Germany | fax : +49-(0)931-888-4755 | \_________________________________________________________________/ From Marc.Prosenc@uni-konstanz.de Wed Oct 15 10:31:06 1997 Received: from nimbus.rz.uni-konstanz.de for Marc.Prosenc@uni-konstanz.de by www.ccl.net (8.8.3/950822.1) id JAA14652; Wed, 15 Oct 1997 09:32:28 -0400 (EDT) Received: from iris.rz.uni-konstanz.de by nimbus.rz.uni-konstanz.de with Intranet SMTP (PP); Wed, 15 Oct 1997 15:31:28 +0200 Received: by iris.rz.uni-konstanz.de (Smail3.1.29.1 #2) id m0xLTXq-002D7pC; Wed, 15 Oct 97 15:31 CDT Message-Id: From: Marc.Prosenc@uni-konstanz.de (Marc-Heinrich.Prosenc) Subject: vibration spectras from force-field calculations To: CHEMISTRY@www.ccl.net Date: Wed, 15 Oct 1997 15:31:26 +0200 (CDT) X-Mailer: ELM [version 2.4 PL24 PGP1] MIME-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit dear CCLers, it would be kind if anyone could tell me if there exist a program that calculates vibrational spectras from forcefields like MM2 or DISCOVER or HYPERCHEM .... for free ? do there any public domain routines exist, which are able to refine existing forcefields like mm2 or amber when the IR-spectrum is given ? thx in advance Marc Marc Heinrich Prosenc Universitaet Konstanz 78434 Konstanz Po 5560 M738 Prosenc@dg5.chemie.uni-konstanz.de From nbbienia@cyf-kr.edu.pl Wed Oct 15 10:39:33 1997 Received: from info.cyf-kr.edu.pl for nbbienia@cyf-kr.edu.pl by www.ccl.net (8.8.3/950822.1) id JAA14755; Wed, 15 Oct 1997 09:45:41 -0400 (EDT) Received: from kinga.cyf-kr.edu.pl (kinga.cyf-kr.edu.pl [149.156.4.10]) by info.cyf-kr.edu.pl (8.8.7/8.8.6) with ESMTP id PAA21892 for ; Wed, 15 Oct 1997 15:45:22 +0200 (METDST) Received: from kinga.cyf-kr.edu.pl (kinga.cyf-kr.edu.pl [149.156.4.10]) by kinga.cyf-kr.edu.pl (8.8.7/8.8.6) with SMTP id PAA10329 for ; Wed, 15 Oct 1997 15:45:21 +0200 (METDST) Date: Wed, 15 Oct 1997 15:45:21 +0200 (METDST) From: Leslaw Bieniasz To: chemistry@www.ccl.net Subject: cheminformatics Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Cracow, 15.10.97 Hello, I am looking for the (published) definition of "cheminformatics" and for the most recent review papers or other prominent references on this subject. I would appreciate any help. Sincerely, L. Bieniasz *-------------------------------------------------------------------* | Dr. Leslaw Bieniasz, | | Institute of Physical Chemistry of the Polish Academy of Sciences,| | Molten Salts Laboratory, ul. Zagrody 13, 30-318 Cracow, Poland. | | tel./fax: +48 (12) 266-03-41 | | E-mail: nbbienia@cyf-kr.edu.pl | | Web site: http://www.cyf-kr.edu.pl/~nbbienia | *-------------------------------------------------------------------* From elewars@alchemy.chem.utoronto.ca Wed Oct 15 10:44:01 1997 Received: from alchemy.chem.utoronto.ca for elewars@alchemy.chem.utoronto.ca by www.ccl.net (8.8.3/950822.1) id KAA14964; Wed, 15 Oct 1997 10:23:17 -0400 (EDT) Received: (from elewars@localhost) by alchemy.chem.utoronto.ca (8.7.4/8.7.3) id KAA10197 for chemistry@www.ccl.net; Wed, 15 Oct 1997 10:23:18 -0400 (EDT) Date: Wed, 15 Oct 1997 10:23:18 -0400 (EDT) From: "E. Lewars" Message-Id: <199710151423.KAA10197@alchemy.chem.utoronto.ca> To: chemistry@www.ccl.net Subject: EXTENDED HUECKEL AND ORTHOGONALIZATION Wed, 1997 Oct 15 >From E. Lewars To: CCL Subj: Extended Huckel Method Hello, Regarding the extended Hueckel method as implemented by Roald Hoffmann: I know that the overlap integrals are calculated and used to construct the Fock matrix elements (which are proportional to these integrals in the EHM). My question is: in Hoffmann's implementation are the overlap integrals used to calculate an orthogonalizing matrix to convert (e.g. by Loewdin orthogonalization) the matrix equation FC = SCe into standard eigenvalue form F'C' = C'e i.e F' = C'eC'^-1 as in ab initio calculations, OR is it simply pretended, as in simple Hueckel theory, that S=I ? I read Hoffmann's 1963 paper in J Chem Phys, but this point does not seem to be explicity made clear. Maybe I missed it. Thanks E. Lewars ============= From eldbjorg.sofie.heimstad@nilu.no Wed Oct 15 10:46:56 1997 Received: from samson.nilu.no for eldbjorg.sofie.heimstad@nilu.no by www.ccl.net (8.8.3/950822.1) id JAA14700; Wed, 15 Oct 1997 09:37:55 -0400 (EDT) Received: from afrodite.nilu.no (afrodite.nilu.no [128.39.66.2]) by samson.nilu.no (8.6.10/8.6.9) with ESMTP id PAA01135 for ; Wed, 15 Oct 1997 15:40:51 +0200 Received: from eshpc.nilu.no (eshpc.nilu.no [128.39.66.15]) by afrodite.nilu.no (8.6.12/8.6.12) with SMTP id PAA25098 for ; Wed, 15 Oct 1997 15:40:30 +0200 Received: by eshpc.nilu.no with Microsoft Mail id <01BCD980.056556E0@eshpc.nilu.no>; Wed, 15 Oct 1997 15:35:52 +-100 Message-ID: <01BCD980.056556E0@eshpc.nilu.no> From: =?iso-8859-1?Q?Eldbj=F8rg_Sofie_Heimstad?= To: "'chemistry@www.ccl.net'" Subject: Software for 3D-QSAR/QSTR Date: Wed, 15 Oct 1997 15:35:51 +-100 MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Dear members, I would be very happy if some of you could give me your opinions about = software packages which include the methods of SAR, CoMFA, QSAR, QSTR etc. I have some = information from the internet about the methods, but is more difficult = to evaluate the different software packages. For instance, is there a = need for several different software packages to get the most reliable = effect modelling. I have assumed that the molecular descriptors ( = electrostatic-, steric-,etc.) should be derived from 3D molecular = structures, do one separate between the definitions QSAR and 3D-QSAR ? My background are more or less within molecular mechanics and molecular = dynamics simulations of enzymes, but I am now looking into the = enviromental toxicology field.=20 All responses will be appreciated, Thanks in advance, ######################################### Eldbj=F8rg S. Heimstad, Dr.scient.=20 NILU Norwegian Institute for Air Research=20 P.O. Box 1245=20 N-9001 Troms=F8, Norway=20 Tel. +47-77 60 69 74 Fax. +47-77 60 69 71=20 E-mail: Eldbjorg.Sofie.Heimstad@nilu.no ######################################### From gmercier@mail.med.upenn.edu Wed Oct 15 10:48:19 1997 Received: from mail.med.upenn.edu for gmercier@mail.med.upenn.edu by www.ccl.net (8.8.3/950822.1) id JAA14807; Wed, 15 Oct 1997 09:57:04 -0400 (EDT) Received: (from gmercier@localhost) by mail.med.upenn.edu (8.8.6/8.8.6) id JAA31579 for chemistry@www.ccl.net; Wed, 15 Oct 1997 09:57:02 -0400 (EDT) From: "Gustavo A. Mercier Jr" Message-Id: <199710151357.JAA31579@mail.med.upenn.edu> Subject: moldy: quaternion constraint error To: chemistry@www.ccl.net Date: Wed, 15 Oct 1997 09:57:02 -0400 (EDT) X-Mailer: ELM [version 2.4 PL23-upenn3.1] MIME-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Hi! I am trying to perform some rigid body dynamic simulations using MOLDY 2.11b in an SGI box R4000 running IRIX5.3 The system is a manganese metalloporphyrins embeded in a water box (454 waters). This system was "equilibrated" using amber4.1 by letting the waters move around the fixed metalloporphyrin in a 22 ps simulation. Only the nonbonded interaction was kept. The water model is the TIP3P, a rigid water model available in amber4.1 I programmed a filter to get the amber output (XYZ) to the (COM, Rotation quaternion) used in moldy, but discarded the velocities! Below is the input to moldy (the control file). The system file contains the COM and quaternions, plus the parameters for a L-J potential, and atom-centered point charges. **** Problem: While heating the system up (starting at 300K gave the same error) doing 2ps runs at 0K, 50K, 100K, 150K I ran into the following error: *F* Quaternion (some #) constrain ... (another number) Looks like the magnitude of the quanternion is no longer 1.0 **** Question: What are possible causes...? Any help will be welcomed! I am already using a step size 0.001ps The scale interval is 0.005ps using Mx-Bz temperature scaling. I am only doing NVT dynamics. The box is 27.0488x26.8614x19.3569. This is the result of the amber4.1 NPT run at 300k using Baerends thermostat/pressure sink. The density is 1.0087gm/cc Using defaults the e-walds parameters yields the following: Interaction cut-off = 10.394 A Alpha parameter for Ewald sum = 0.326263 A(-1) Reciprocal space cut-off = 2.21282 A(-1) *I* Distant potential correction = -76.180287, Pressure correction = -17.982072 *I* MD cell divided into 1521 subcells (13x13x9) *I* Neighbour list contains 488 cells *W* System has net electric charge of 1 - correction of 1.45791 kJmol(-1) added to self energy *I* Ewald self-energy = 2168.232620 Kj/mol *I* 1298 K-vectors included in reciprocal-space sum -------- Input file --------------------- title=MnPm/TIPS3 after 22.5 ps; Q's tweaked; d=1.0087 sys-spec-file=mnpmW.sys lattice-start=1 nsteps=2000 # 2.0 ps step=0.001 save-file=mnpmW4.rst restart-file=mnpmW3.rst # run at 100K text-mode-save=0 scale-interval=5 const-temp=0 scale-options=8 # Mx-Bz distribution temperature=150.0 const-pressure=0 strain-mask=238 # all off diagonals fixed strict-cutoff=0 # only cell to cell interaction otherwise tooo slow! surface-dipole=0 average-interval=100 rdf-interval=10 # every 0.05 ps dump-file=mWdmp time-unit=4.8888213e-14 # reading kcal/mol; not kJ/mol end -- ("`-/")_.-'"``-._ Gustavo A. Mercier,Jr.,MD,PhD (. . `) -._ )-;-,_() Division of Nuclear Medicine (v_,)' _ )`-.\ ``- Dept. of Radiology _;- _,-_/ / ((,' University of Pennsylvania ((,.-' ((,/ 3400 Spruce St. gmercier@mail.med.upenn.edu Philadelphia, PA 19104 215-662-3069/3091 fax: 215-349-5843 From daizadeh@indigo.ucdavis.edu Wed Oct 15 11:31:02 1997 Received: from indigo.ucdavis.edu for daizadeh@indigo.ucdavis.edu by www.ccl.net (8.8.3/950822.1) id LAA15518; Wed, 15 Oct 1997 11:10:08 -0400 (EDT) Received: by indigo.ucdavis.edu (940816.SGI.8.6.9/940406.SGI.AUTO) id IAA20692; Wed, 15 Oct 1997 08:11:47 -0700 From: "Iraj Daizadeh" Message-Id: <9710150811.ZM20690@indigo.ucdavis.edu> Date: Wed, 15 Oct 1997 08:11:33 -0700 X-Mailer: Z-Mail (3.2.0 26oct94 MediaMail) To: chemistry@www.ccl.net, daizadeh@indigo.ucdavis.edu Subject: Molecular Dynamics on Biological Molecules. Cc: molecular-dynamics-news@mailbase.ac.uk Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Hello. Our group has just bought 2 DEC 500 au (low-end workstations) running DEC UNIX 4.0c and we are trying to find computational chemistry software packages that can calculate classical dynamics of motion for large (circa. 2000+atoms) biological molecules. It would be nice if the programs could implement a Nose/Hoover thermostat and equipped with a variety of force fields such as amber, ESFF, cff91, etc... Futhermore, the programs (which may be free or commercial) must be able to write out trajectories to some sort of archive file in ascii form for our own calculations. I will summarize the results as is customary. Thanks in advance for all contributions. Iraj. -- Iraj Daizadeh Department of Chemistry University of California One Shields Ave. Davis, CA 95616-5295 Phone: 916.754.8695 Fax: 916.752.8995 email: daizadeh@indigo.ucdavis.edu From yliu@mail.wesleyan.edu Wed Oct 15 12:30:57 1997 Received: from mail.wesleyan.edu for yliu@mail.wesleyan.edu by www.ccl.net (8.8.3/950822.1) id LAA15776; Wed, 15 Oct 1997 11:44:50 -0400 (EDT) Received: from violet.chem.wesleyan.edu (violet.chem.wesleyan.edu [129.133.20.94]) by mail.wesleyan.edu (8.8.6/8.7.3) with SMTP id LAA18657; Wed, 15 Oct 1997 11:43:38 -0400 (EDT) Message-Id: <2.2.32.19971015154139.006893a8@mail.wesleyan.edu> X-Sender: yliu@mail.wesleyan.edu X-Mailer: Windows Eudora Pro Version 2.2 (32) Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Wed, 15 Oct 1997 11:41:39 -0400 To: chemistry@www.ccl.net From: Yongxing Liu Subject: Summary: Assign Atomic Types for Small Molecules. Cc: dbeveridge@mail.wesleyan.edu Dear CCLers, Thanks again for all who answered my questions. This a summary. **** The Original Question**** I am looking for rules based on SMILES to assign molecular mechanic atomic types( e.g. for OPLS all atom model) to a variety kinds of small organic molecules and molecular ions(total about 300 molecules). By doing that I can assign atomic charges and VDW radii for each molecule atom. Would any one please give me any information about where can I find these rules and programs(free source code) to do this ? Or are there any alternative ways to assign MM atomic charges and VDW radii for small organic molecules automatically? **** Comments to the question **** My goal is to assign OPLS-AA/AMBER charges and VDW radius to each atom for my 300 molecules training set. I tried HyperChem and Insight-Buider. HyperChem can assign AMBER types to all my moelcules, but AMBER do not have charge parameters for all my small molecules(Unless you do the ab initio calculation which I can not afford for all my 300 molecules). I also do not want to write OPLS rules for InsightII Builder. *** Answers from Professor DOUGH **** BABEL does conversion of simple SMILES to MM2/MM3 file formats - you should search for it to find the places it can be obtained. *** Answers From Professor TJ O'Donnell *** We published a paper on a method to assign atom types using SMARTS, an extension of SMILES to define molecular substrucutres, which of course include atoms. I believe this is what you were looking for. We have sets of SMARTS for a variety of atom-type sets, e.g. AMBER, GRIN/GRID, etc., but not for OPLS. The actual implementation uses an old (no longer supported) Daylight program GCL and we have not modified the program to work with newer Daylight versions. However, the SMARTS strings defining the atomic environments are entirely compatible with recent versions of Daylight SMARTS. A General Approach for Atom-Type Assignment and the Interconversion of Molecular Structure Files, TJ O'Donnell, et. al., J. Comput. Chem., 12, 209-213 (1991). *** Answers From Professor Richard Gillilan *** Although FFAssign is not yet available for general use, I am interested in any intrepid early users who would be willing put the code to a good test (not too many please). Currently the code should reproduce all the charge assignments in Halgren's papers and supplementary material except two or three cases documented in the README (soon to be fixed). Many of the exotic chemical types have not been tested yet. The assignments are being tested against available published results and should agree with all values in Halgren's papers (please notify me if you find exceptions). I have not yet compaired absolute energy values against those in commercial implementations (soon, maybe). Interested persons should contact me (Richard Gillilan) richard@tc.cornell.edu --------------- >>>> FFAssign Version 0.0 <<<< Copyright (C) 1997 Cornell Theory Center FFAssign is an independent implementation of the MMFF94 force field written at the Cornell Theory Center. The Theory Center's Parallel Processing Resource for Biomedical Scientists is supported by the National Center for Research Resources of the NIH under grant # P41 RR04293. What does FFAssign do? FFAssign reads in a molecular coordinate file (in either of two formats) and assigns empirical forcefield parameters based on the chemical types encountered and supplies efficient basic simulation functionality suitable for inclusion in user-written (C++) applications. Output files generated are also compatible with Trevor Hart's RESEARCH docking program. FFAssign is a FULL implementation of the Merck Molecular Force Field (MMFF94) based on the published work of T.A. Halgren: T.A. Halgren. "Merck Molecular Force Field. I. Basis, Form, Scope, Parameterization, and Performance of MMFF94 Journal of Computational Chemistry", Vol 17 Nos 5,6 pp 490-519 (1996) (See also parts II-V in the same Journal and supplementary material) *** Conclusion *** The above answers are very helpful to me. Based on the answers, I will write a program suitable for my purpose. Yongxing Liu Department of Chemistry Wesleyan University Middletown CT 06459 E-mail yliu@wesleyan.edu Telephone: 860-685-2777(Office) 860-343-7330(Home) 860-685-7467(Home) Fax: 860-685-2211 Http://linus.chem.wesleyan.edu/yliu/ From sichelj@UMoncton.ca Wed Oct 15 14:30:51 1997 Received: from bosoleil.ci.umoncton.ca for sichelj@UMoncton.ca by www.ccl.net (8.8.3/950822.1) id OAA16694; Wed, 15 Oct 1997 14:02:47 -0400 (EDT) Received: by bosoleil.ci.umoncton.ca (1.37.109.20/16.2) id AA239408666; Wed, 15 Oct 1997 15:04:26 -0300 Date: Wed, 15 Oct 1997 15:04:26 -0300 (ADT) From: "J. Sichel" Subject: Re: CCL:EXTENDED HUECKEL AND ORTHOGONALIZATION To: "E. Lewars" Cc: chemistry@www.ccl.net In-Reply-To: <199710151423.KAA10197@alchemy.chem.utoronto.ca> Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Yes, Hoffmann's EH method uses explicit Lowdin orthogonalization; I remember working through a copy of his computer code as a graduate student in 1964! As for his 1963 JCP paper, he does say (p.1399) that "the complete set of Eq.(2) [the secular equations] is solved with _two_ matrix diagonalizations." If S = 1 were assumed, only one diagonalization would be required. John Sichel Dept de chimie et biochimie Universite de Moncton, NB, Canada On Wed, 15 Oct 1997, E. Lewars wrote: > Regarding the extended Hueckel method as implemented by Roald Hoffmann: > I know that the overlap integrals are calculated and used to construct > the Fock matrix elements (which are proportional to these integrals in > the EHM). My question is: > in Hoffmann's implementation are the overlap integrals used to calculate an > orthogonalizing matrix to convert (e.g. by Loewdin orthogonalization) the > matrix equation > FC = SCe > into standard eigenvalue form > F'C' = C'e i.e F' = C'eC'^-1 > > as in ab initio calculations, > OR is it simply pretended, as in simple Hueckel theory, that > S=I ? > > I read Hoffmann's 1963 paper in J Chem Phys, but this point does not > seem to be explicity made clear. Maybe I missed it. > > Thanks > E. Lewars From bruno@antas.agraria.uniss.it Wed Oct 15 14:35:53 1997 Received: from ICINECA.CINECA.IT for bruno@antas.agraria.uniss.it by www.ccl.net (8.8.3/950822.1) id OAA16691; Wed, 15 Oct 1997 14:01:56 -0400 (EDT) Received: from cinymp.cineca.it by ICINECA.CINECA.IT (IBM VM SMTP V2R2) with TCP; Wed, 15 Oct 97 20:03:02 ITA Received: from antas.agraria.uniss.it by cinymp.cineca.it with SMTP (5.61/CRI-80.1) id AA50076; Wed, 15 Oct 97 20:02:12 +0200 Date: Wed, 15 Oct 1997 20:00:22 +0100 (NFT) From: "Dr. Bruno Manunza" To: Iraj Daizadeh Cc: chemistry@www.ccl.net, daizadeh@indigo.ucdavis.edu, molecular-dynamics-news@mailbase.ac.uk Subject: Re: Molecular Dynamics on Biological Molecules. In-Reply-To: <9710150811.ZM20690@indigo.ucdavis.edu> Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII On Wed, 15 Oct 1997, Iraj Daizadeh wrote: > Hello. > > Our group has just bought 2 DEC 500 au (low-end workstations) running DEC UNIX > 4.0c and we are trying to find computational chemistry software packages that > can calculate classical dynamics of motion for large (circa. 2000+atoms) > biological molecules. It would be nice if the programs could implement a > Nose/Hoover thermostat and equipped with a variety of force fields such as > amber, ESFF, cff91, etc... Futhermore, the programs (which may be free or > commercial) must be able to write out trajectories to some sort of archive file > in ascii form for our own calculations. I will summarize the results as is > customary. > > Thanks in advance for all contributions. > > Iraj. Dear Iraj, there are several programs doing the things you want. I just recall DLPOLY from Daresbury (free after signing a licence), and Amber (commercial). You'll find links to the above and several others looking throught our software page at http://antas.agraria.uniss.it go there an then click the Computational Chemistry Software link. You'll find some info also in the molmod page Hope it helps regards Bruno Dr Bruno Manunza DISAABA (Dept. of Agricultural Environm. Sci) University of Sassari V.le Italia 39 07100 Sassari, ITALY phone: 39 79 229215 fax: 39 79 229276 e-mail: bruno@antas.agraria.uniss.it e-mail: bruno@tharros.dipchim.uniss.it e-mail: gx6bot81@cray.cineca.it web: http://antas.agraria.uniss.it From schrecke@t12.lanl.gov Wed Oct 15 16:31:01 1997 Received: from mailhost.lanl.gov for schrecke@t12.lanl.gov by www.ccl.net (8.8.3/950822.1) id PAA17412; Wed, 15 Oct 1997 15:40:50 -0400 (EDT) Received: from [128.165.22.209] (machgs.lanl.gov [128.165.22.209]) by mailhost.lanl.gov (8.8.7/8.8.7) with SMTP id NAA14786 for ; Wed, 15 Oct 1997 13:40:46 -0600 (MDT) Message-Id: Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: quoted-printable Date: Wed, 15 Oct 1997 13:43:50 -0700 To: CHEMISTRY@www.ccl.net (CCL) From: schrecke@t12.lanl.gov (Georg Schreckenbach) Subject: summary: DFT MO energies Dear CCL readers, last week, I posted a question about DFT MO energies, and how they are different in hybrid methods vs. GGA or LDA. I got a few interesting replies -- thanx to those who took the time to write! If anybody wants to comment further, please do so, either to me, or to the CCL. I have posted this summary also at my webpages, cf. http://www.t12.lanl.gov/~schrecke/research.DIR/CCL_DFTMOEnergies.html ----------------------------------------------- Original question: Date: Fri, 10 Oct 1997 10:59:01 -0700 Subject:DFT MO energies Dear CCL readers, is anybody aware of papers that study DFT orbital energies? More precisely, I would like to learn how those orbital energies (Kohn-Sham eigenvalues) are different in hybrid methods like B3LYP as compared to GGAs like BP86 or PW91, or also as compared to the LDA. If there are systematic differences (which I am sure is the case) then I would like to know how they can be understood. There was recently some discussion on the list about the possible physical meaning of the Kohn-Sham eigenvalues. While this is an interesting subject in itself, it is, this time, *not* my question. ----------------------------------------------- Reply by Jon Rienstra In general, the hybrid methods are to some degree sucessful in incorporating some of the HF electron self-interaction cancellation, and in many cases succeed in giving negative HOMO energies, even in anions. GGA's on the other hand often give positive HOMO energies (esp in anions), and much recent debate has focused on whether or not this is problematic. =46or more details see: See Galbraith and Schaefer, J. Chem. Phys. 105, 1996 p. 862 and Rosch and Trickey, J. Chem. Phys. 106, 1997 p. 8940 ----------------------------------------------- Reply by P. A. Politzer Dear Dr. Schreckenbach, We have recently finished a comparison of Hartree-Fock and various DFT Kohn-Sham orbital energies. There are indeed some interesting patters. The paper has been submitted to Theoretical Chemical Accounts. I will be glad to send you a preprint. Best regards, Peter Politzer ----------------------------------------------- Reply by Ulrike Salzner (this one was also posted to the CCL) Dear Georg, I have testet DFT orbital energies for some small and medium sized organic systems with pi-bonds (acetylene oligomers, thiophene monomer through trimer, pyrrole and similar systems). There are significant differences between LSDA and hybrid methods. The paper will soon appear in the Journal of Computational Chemistry. To summarize: The IPs (negative HOMO energies) are closer to experiment with hybrid functionals than at LSDA. The P86 correlation functional seems to work better than the LYP correlation functional. All IPs with DFT are smaller than experimental values (about 0.5 - 1 eV) and smaller than at HF with the same basis set which are quite close to experiment. In my limited data set it looks like there is little depenedence of the quality of IP on the size of the system. The negative LUMO energies used as EAs are by far superior with all DFT methods than with HF. LSDA works slightly better than hybrid functionals. Again the P86 correlation functional works better than LYP. I obtained the "experimental EAs" using experimental IPs and excitation energies. So they have to be treated with some caution. It looks like the agreement improves as the systems get larger. But the data are more than insecure. According to this, DFT corrects for the main deficiency of HF theory and brings the LUMO down. I reasoned that this must have to do with the error in the Coulomb terms in HF which seems to be absent in DFT. I was pleased to see that Baerends et al. came to a similar conclusion in their feature article in J. Phys. Chem. The main error in DFT seems to be due to the IP and not to the EA. Taking t= he difference between the two, I got very nice excitation energies. These improve as the systems get larger. The agreement is pretty poor for monomers but with trimers of purrole and thiophene the excitation energies become good. I also tried what happens when the weight of the HF exchange is increased. I got the best HOMO-LUMO gaps with 30% HF exchange instead of 20%. Geometries were not changed by this. For ethylene I increased the HF exchange stepwise up to 100%. There is no convergence. With 100% HF exchange the gap is as bad as with HF but the orbital levels are shifted compared to those at HF. So all this fudging is empirical and can - at least for now - not be put on solid theoretical ground. As for my personel interest in the band gaps of conducting polymers this is good enough. Needless to say that I had major problems to publish this. It took 1 1/2 years and one reviewer said it was not interesting enough for rapid publication. But the first paper is in press now as mentioned above. There will be two more papers extending these findings to band gaps of polymers by extrapolation. These are submitted to J. Phys. Chem. and Synth. Met. Maybe in two years you can read them. By the way. You're right I am German. I keep writing in English so more people can read it. Cheers, Dr. Ulrike Salzner ----------------------------------------------- Reply by Heinz Schiffer Hi George, see table III in : Garnet K.-L. Chan, David J. Tozer, and Nicholas C. Handy, Correlation potentials and functionals in Hartree-Fock-Kohn-Sham theory, J. Chem. Phys. 107(5) (1997) 1536-1543 Ciao Heinz ----------------------------------------------- (End of summary) Best regards, Georg -- Dr. Georg Schreckenbach Tel: (USA)-505-667 7605 Theoretical Chemistry T-12 FAX: (USA)-505-665 3909 M.S. B268, Los Alamos National E-mail: schrecke@t12.lanl.gov Laboratory, Los Alamos, New Mexico, 87545, USA Internet: http://www.t12.lanl.gov/~schrecke/ From rvenable@deimos.cber.nih.gov Wed Oct 15 18:34:15 1997 Received: from deimos.cber.nih.gov for rvenable@deimos.cber.nih.gov by www.ccl.net (8.8.3/950822.1) id RAA18672; Wed, 15 Oct 1997 17:57:36 -0400 (EDT) Received: from localhost by deimos.cber.nih.gov with SMTP (1.37.109.14/16.2) id AA172412449; Wed, 15 Oct 1997 17:54:09 -0400 Date: Wed, 15 Oct 1997 17:54:09 -0400 (EDT) From: Rick Venable To: Iraj Daizadeh Cc: chemistry@www.ccl.net, molecular-dynamics-news@mailbase.ac.uk Subject: Re: CCL:Molecular Dynamics on Biological Molecules. In-Reply-To: <9710150811.ZM20690@indigo.ucdavis.edu> Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII On Wed, 15 Oct 1997, Iraj Daizadeh wrote: > Our group has just bought 2 DEC 500 au (low-end workstations) running DEC UNIX > 4.0c and we are trying to find computational chemistry software packages that > can calculate classical dynamics of motion for large (circa. 2000+atoms) > biological molecules. It would be nice if the programs could implement a > Nose/Hoover thermostat and equipped with a variety of force fields such as > amber, ESFF, cff91, etc... Futhermore, the programs (which may be free or > commercial) must be able to write out trajectories to some sort of archive file > in ascii form for our own calculations. I will summarize the results as is > customary. I know that the DEC Alpha is one of the platforms supported by the academic version of CHARMM; it does have Nose/Hoover, can easily handle 30,000 atoms or more, and individual coordinate frames from a trajectory can be easily written in the CHARMM ASCII format, or in PDB format. It's not so great at supporting other force fields, for a variety of reasons (some technical). The academic version is available for a modest fee via the Karplus group at Harvard; for more info see http://yuri.harvard.edu -- Rick Venable =====\ |=| "Eschew Obfuscation" FDA/CBER Biophysics Lab |____/ |=| Bethesda, MD U.S.A. | \ / |=| ( Not an official statement or rvenable@deimos.cber.nih.gov | \ / |=| position of the FDA; for that, http://nmr1.cber.nih.gov/ \/ |=| see http://www.fda.gov )