From chemistry-request@server.ccl.net Tue Oct 9 00:33:03 2001 Received: from sesosn01.astrazeneca.com ([212.209.42.131]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id f994X2B28927 for ; Tue, 9 Oct 2001 00:33:03 -0400 Received: from sesosn11.seso.astrazeneca.net (sesosn11.seso.astrazeneca.net [192.168.199.18]) by sesosn01.astrazeneca.com (8.9.3/8.9.3.DEF) with ESMTP id GAA17224 for ; Tue, 9 Oct 2001 06:33:01 +0200 (MET DST) From: parthiban.srinivasan@astrazeneca.com Received: from sesosn21.seso.astrazeneca.net (sesosn21.seso.astrazeneca.net [192.71.145.181]) by sesosn11.seso.astrazeneca.net (8.9.3/8.9.3) with ESMTP id GAA03752 for ; Tue, 9 Oct 2001 06:31:57 +0200 (MET DST) Received: from astra-cdc-x03.seso.astrazeneca.net (astra-cdc-x03.seso.astrazeneca.net [192.71.145.48]) by sesosn21.seso.astrazeneca.net (8.10.1/8.10.1) with ESMTP id f994VuQ20506 for ; Tue, 9 Oct 2001 06:31:56 +0200 (MET DST) Received: by astra-cdc-x03.seso.astrazeneca.net with Internet Mail Service (5.5.2650.21) id ; Tue, 9 Oct 2001 06:31:56 +0200 Message-ID: To: CHEMISTRY@ccl.net Subject: CCL: ADSORPTIVE INTERACTION Date: Tue, 9 Oct 2001 06:45:10 +0200 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2650.21) Content-Type: text/plain; charset="iso-8859-1" Dear CCLers: I am writing this mail on behalf of my collegue. She needs to perform calculations on ADSORPTIVE INTERACTIONS by Frontier Orbital Theory. She needs to perform HOMO and LUMO energy and orbital coefficients. Using MOPAC interfaced in InsightII, she gets the HOMO and LUMO energies but not the orbital coefficients. Could you please tell us how to get the orbital coefficients in the calculation. Thanks in advance. -parthi From chemistry-request@server.ccl.net Tue Oct 9 08:26:10 2001 Received: from smtp1.dti.ne.jp ([202.216.228.36]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id f99CQ9B11048 for ; Tue, 9 Oct 2001 08:26:10 -0400 Received: from b159504364 (PPP58.fukuoka-ip.dti.ne.jp [211.132.92.58]) by smtp1.dti.ne.jp (8.9.3/3.7W) with SMTP id VAA11526 for ; Tue, 9 Oct 2001 21:26:08 +0900 (JST) Message-ID: <00a901c150bc$8cbaa340$3a5c84d3@b159504364> From: "TELKUNI" To: Subject: PW91 calculation trouble of Gaussian98W Date: Tue, 9 Oct 2001 21:18:47 +0900 MIME-Version: 1.0 Content-Type: text/plain; charset="Windows-1252" Content-Transfer-Encoding: 7bit X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 5.50.4133.2400 X-MimeOLE: Produced By Microsoft MimeOLE V5.50.4133.2400 Hello! CCLers, I'm trying to do DFT calculation with Gaussian98W (Version-5.2, Rev-A.7). I have serious problems. My purpose is to optimize the SiH4 structure (It is similar to methane.) with PW91 (Pardew and Wang 91) using my PC (Memory=256MB, OS=Win98SE, CPU=Celeron 400MHz). When I set the Job File as follows ( "***... " means the input form): --- --- Job File --- --- % " %chk=SiH4.chk " Route " # PW91PW91/6-31G Opt " Title Section " SiH4 " Charge , " 0 1 " - Molecule (Structure) - Si H 1 r21 H 1 r31 2 a312 H 1 r41 2 a412 3 d4123 0 H 1 r51 2 a512 3 d5123 0 r21 1.460856 r31 1.460848 r41 1.460839 r51 1.460818 a312 109.476160 a412 109.474287 a512 109.469184 d4123 -120.012518 d5123 119.993483 --- --- --- --- --- --- --- I always get following message: Run Progress: Link died! "Severe Error Message # 2070 The processing of the last link ended abnormally. All processing has been aborted." And it always ends with: Default route: MaxDisk=2000MB ------------------------------------ #T SVWN/6-31G(d) Test SCF=(Tight,QC) ------------------------------------ I can't understand what the message means and don't know the clue of the solution. If anyone know the reason or solution, please teach me. All responses, I will appreciate. And I will summarize them for novice Gaussian98 user, just like me! Thanks in advance, ---------------------------------------------- Telkuni Tsuru Kyushyu Electronic Technology and Research telkuni@venus.dti.ne.jp ---------------------------------------------- From chemistry-request@server.ccl.net Mon Oct 8 21:40:16 2001 Received: from mail.tsinghua.edu.cn ([166.111.8.18]) by server.ccl.net (8.11.6/8.11.0) with SMTP id f991e2B22579 for ; Mon, 8 Oct 2001 21:40:02 -0400 Message-Id: <200110090140.f991e2B22579@server.ccl.net> Received: (qmail 11116 invoked by alias); 9 Oct 2001 09:36:07 +0800 Received: from unknown (HELO denny) (166.111.27.50) by mail.tsinghua.edu.cn with SMTP; 9 Oct 2001 09:36:07 +0800 Date: Tue, 9 Oct 2001 9:41:49 +0800 From: Denny To: Zhenhua Li CC: "chemistry@ccl.net" Subject: Re: CCL:exact energy of atoms or small poly-atoms X-mailer: FoxMail 3.0 beta 1 [cn] Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: 7bit aug-cc-pv6z **************************** * Denny Chen * * Center for Astrophysics * * Tsinghua University * * Beijing, P.R.China * * 8610-62792126(phone) * * 8610-62792125(fax) * **************************** Email:dilys98@mails.tsinghua.edu.cn ********You wrote********* >Dear listers, >Have you any idea how to find energies of exact or close to exact (either >SCF or correlation level) one-particle basis set limit for atoms or small >poly-atoms? >Are there any exact energies of atoms or small poly-atoms (exact solution of >Schrodinger equation)? > >Li Zhenhua > > > > >-= This is automatically added to each message by mailing script =- >CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins >MAILSERV@ccl.net -- HELP CHEMISTRY or HELP SEARCH >CHEMISTRY-SEARCH@ccl.net -- archive search | Gopher: gopher.ccl.net 70 >Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net From chemistry-request@server.ccl.net Tue Oct 9 06:02:14 2001 Received: from nenuphar.saclay.cea.fr ([132.166.192.7]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id f99A2DB08283 for ; Tue, 9 Oct 2001 06:02:13 -0400 Received: from muguet.saclay.cea.fr (muguet.saclay.cea.fr [132.166.192.6]) by nenuphar.saclay.cea.fr (8.9.1a/8.9.1/CEAnet-relay-5.0.D20+Y2K) with ESMTP id MAA21381 for ; Tue, 9 Oct 2001 12:02:11 +0200 (MET DST) Received: from lycose.saclay.cea.fr (lycose.saclay.cea.fr [132.166.192.104]) by muguet.saclay.cea.fr (8.9.1a/8.9.1/CEAnet-relay-5.2.D20+Y2K) with ESMTP id MAA18010 for ; Tue, 9 Oct 2001 12:02:10 +0200 (MET DST) Received: from penelope.saclay.cea.fr (unverified) by lycose.saclay.cea.fr (Content Technologies SMTPRS 4.2.5) with ESMTP id ; Tue, 9 Oct 2001 12:02:10 +0200 Received: by penelope.saclay.cea.fr with Internet Mail Service (5.5.2653.19) id <4KB4PQY0>; Tue, 9 Oct 2001 12:02:27 +0200 Message-ID: From: VITORGE Pierre 094605 To: "'elewars'" , chemistry@ccl.net Subject: RE: charges on sphere, summary Date: Tue, 9 Oct 2001 11:46:51 +0200 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2653.19) Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by muguet.saclay.cea.fr id MAA18010 Content-Transfer-Encoding: 8bit I am only a chemist; but most of the answers do not convince me from a mathematical point of view: show the answer to math specialists before writting on the list! I am not convince when you (explicitly or implicitly) add the last charge to the n-1 previous ones, just because geometries can be very different in the n and n-1 cases. It is neither a simple mathematical problem to put small spheres on a big one. Pierre Vitorge CEA Saclay DEN/DPC/SCPA/LCRE Bat.450 pce 157D UMR 8587 (Universite d'Evry-CNRS-CEA) 91191 Gif sur Yvette cedex France pierre.vitorge@cea.fr phone +33 169-08-32-65, secretary: +33 169-08-32-50, fax: +33 169-08-32-42 http://perso.club-internet.fr/vitorgen/pierre/pierre.html pierre.vitorge@laposte.net -----Message d'origine----- De: elewars [mailto:elewars@trentu.ca] Date: lundi 8 octobre 2001 16:06 À: chemistry@ccl.net Objet: CCL:charges on sphere, summary 2001 Oct 8 Hello, Here is the summary of replies I got to the question about the energy of a set of charges confined on/in a sphere. I thank all who responded, and hope I have not overlooked any reply. All the answers were intereresting and helpful. E. Lewars === The question: 2001 Oct 3 Hello, A colleague posed this question. Suppose you have two like point charges (e.g. two protons, considered dimensionless), which must be on or inside a sphere. The minimum energy geometry (MEG) is that they be on the surface, at the ends of a diameter of the sphere. For three charges, the MEG is on the surface, at the corners of an equilateral triangle. And so on for 4, 5, ...? charges, the MEG having all of them on the surface. Question: is there a number or numbers _n_ of charges for which migration of one or more charges _into_ the sphere would lower the energy? Is there some theorem in math or physics that deals with this? Thanks E. Lewars ============= #1 Prof. Lewars, I enjoy this type of problem. I know it is a theorem that there is no arrangement of (pos and neg) charges in space that is a local minimum. I suspect that the same is true of charges in an environment where there are some fixed charges about, which would mean that the charges in the interior can always move in some direction so as to lower the total energy. Then the MEG would have to have all charges on the surface. David Anick MD PhD David.Anick@gte.net Dear Prof. Lewars, Ignore previous response. The proof is easy. Suppose you have n point charges in fixed positions and you want to add the (n+1)st. Let F be the electric field generated by the original n. Then div(F) = 0 (Gauss's law). The divergence theorem says that the surface integral of Fn^ over a small bubble enclosing the new charge, equals the volume integral of div(F), which we know is zero. Make the bubble very small. Fn^ is positive in some direction(s) and negative in others. If the position of the new charge were a local min, F would point inward everywhere on the bubble, i.e. Fn^ would be negative on the entire bubble surface. This contradiction shows that there cannot be any local min for the energy as a function of the position of the new charge (with the other n positions fixed), except on the boundary. Once that charge moves to the boundary, the others may lower the energy further by moving around on the boundary, but that's not your question. NOTE: there can be saddle points for the potential energy in the interior, i.e. an interior charge might experience a force of zero, but they would be unstable stationary points. In the limit where there are thousands of charges spread out on the surface in a uniform distribution, as you know, the potential inside becomes constant. David Anick MD PhD David.Anick@gte,net ============== #2 Use the variational procedure to maximize the distance between points with the constraint that they lie on a sphere of radius R. The constraint is a lagrange multiplier and you simply work though the Ritz variational method. Alternatively, argue from simple geometry. In two dimensions, if you have a n-point polygon with all points on a circle of radius R, then the configuration which maximizes the distance (and hence minimizes the energy or cost function) between all points is a regular polygon. So, again, it's a result of the variational theorem. ERB -- Prof. Eric R. Bittner Department of Chemistry Univ. of Houston ph: 713-743-2775 fax: 713-743-2709 bittner@uh.edu http://k2.chem.uh.edu/bittner/ Actually, I didn't read your question carefully enough, but you could still use the variational method followed by classical perturbation theory to check this. But, geometry seems to argue that if you have n points distributed evenly over a sphere at the vertices of a regular polyhedron, the lowest energy configuration for the addition of one charge *inside* the sphere is at the center. The issue of whether perturbing one vertex of the polyhedron keeping the rest fixed is simple as well. From the point of view of the one charge being deflected, moving closer to any of the (n-1) charges must increase its potential energy. So the minimal energy configuration for the deflected charge is at r-> + infinity. This must be true for all n> 1. -- Prof. Eric R. Bittner Department of Chemistry Univ. of Houston ph: 713-743-2775 fax: 713-743-2709 bittner@uh.edu http://k2.chem.uh.edu/bittner/ ---------------------------------------------------------------------------- --------------- The sun, with all those planets revolving around it and dependent upon it, can still ripen a bunch of grapes as if it had nothing else in the universe to do. -Galileo Galilei, physicist and astronomer (1564-1642) ================= #3 Dear Prof. Lewars, I can't cite any theorems with respect to your colleague's question. However, since same-charge repulsion diminishes with the square of the distance, a good rule of thumb would be to make the smallest distance between charges as large as possible. This is related to the question of how many spheres of a given radius can be fitted into a sphere of unit- radius. The topic of densest packing might be a good starting point for searching the mathematical literature. Borane or metal clusters might also provide examples. Since the boundary conditions are different (no penetration of packed spheres vs. minimum repulsive energy), the packing problem is probably not the definitive answer but still a good starting point. >From a more practical point of view, I think that charges inside the sphere become competitive when the smallest distance d between charges on the surface of the sphere is smaller than the radius of the sphere. In a regular octahedron, d=sqrt(2)*r. In a cube, d=2r/sqrt(3). In a 4-sided antiprism the ratio d/r would be somewhat smaller (but still larger than 1, I believe). Therefore my guess is that with 8 charges one should be inside the sphere. The other 7 charges might be in an arrangement derived from a capped octahedron. Yours, Stefan Fau ______________________________________________________________________ Dr. Stefan Fau | fau@qtp.ufl.edu Quantum Theory Project | (352) 392-6714 University of Florida Gainesville, FL 32611-8435 =============== #4 Just a quick comment which I think shows that at some point you will want to put charge inside the sphere: if you consider a uniform charge density smeared over the sphere surface (approximating the situation where there are already many protons), the energy to add a new charge q on the surface comes out (in my hands) as 8 pi q sigma while the energy to put it at the center of the sphere is 4 pi q sigma, ie it is smaller. If you find a sophisticated exact result I'd be interested to hear about it... Cheers,simonson@schlitz.u-strasbg.fr Organization: CNRS Tom Simonson ========== #5 Dear Dr. Lewars ! If the charges are mobile within the sphere they will always accumulate on the surface - that's just Faraday's principle. If you have a charged piece of metal (i.e. "real life" equivalent of a system in which charges are freely mobile within a certain volume) any addiditonal charges will always accumulate on the surface (that's actually independent of the shape of the piece of metal. regards, egbert Egbert Zojer =================== ============= -= This is automatically added to each message by mailing script =- CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins MAILSERV@ccl.net -- HELP CHEMISTRY or HELP SEARCH CHEMISTRY-SEARCH@ccl.net -- archive search | Gopher: gopher.ccl.net 70 Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net From chemistry-request@server.ccl.net Tue Oct 9 10:14:48 2001 Received: from bayer2.bayer-ag.de ([194.120.191.2]) by server.ccl.net (8.11.6/8.11.0) with SMTP id f99EElB13717 for ; Tue, 9 Oct 2001 10:14:47 -0400 Received: from by17v3.bayer-ag.com (by-inetin.bayer-ag.com) by bayer2.bayer-ag.de with SMTP id QAA13937 (SMTP Gateway 4.2 for ); Tue, 9 Oct 2001 16:14:46 +0200 Subject: TDDFT - MO's To: CHEMISTRY@ccl.net X-Mailer: Lotus Notes Release 5.0.3 (Intl) 21 March 2000 Message-Id: From: andreas.goeller.ag@bayer-ag.de Date: Tue, 9 Oct 2001 16:19:12 +0200 X-Mimetrack: Serialize by Router on BY-INET1/Central/LEV/DE/BAYER(Release 5.0.8 |June 18, 2001) at 10/09/2001 04:14:47 PM Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Dear CCLers, TDDFT (at least Gaussian outputs) give information on transition energy, oscillator strengths, and the MO's envolved in the respective transition. Excitation energies and oscillator strengths: Excited State 1: Singlet-B1 8.0068 eV 154.85 nm f=0.0142 3 -> 14 -0.01126 5 -> 6 0.69120 5 -> 11 0.01351 with the coefficients defining only the alpha electron. The question now is: There is a lot of discussion if the basis set (which even in HF theory is only a model for the real AO's), which represents the real electron density of the whole state, can be used for interpretation as MO's. It seems to be accepted, that these auxiliary functions usually are able to represent the frontier orbitals reasonably well. But can we then really interpret these orbitals as the ones from and to which electrons are excited? Is this model stable and can it be interpreted photochemically? I am not aware of any publication dealing with this. Best regards Andreas Goeller P.S.: I will summarize the results. From chemistry-request@server.ccl.net Tue Oct 9 11:48:01 2001 Received: from hschipaa.hsc.usf.edu ([131.247.16.97]) by server.ccl.net (8.11.6/8.11.0) with SMTP id f99Fm1B15917 for ; Tue, 9 Oct 2001 11:48:01 -0400 Received: from hschipaa.hsc.usf.edu ([131.247.16.105]) by hsc.usf.edu (8.9.3+Sun/8.9.3) with SMTP id LAA28010 for ; Tue, 9 Oct 2001 11:47:59 -0400 (EDT) Message-ID: <3BC31C33.935C7012@mindless.com> Date: Tue, 09 Oct 2001 11:48:03 -0400 From: David Smith X-Mailer: Mozilla 4.78 [en] (Win95; U) X-Accept-Language: en MIME-Version: 1.0 To: CCL Subject: Running Autodock3 under linux2 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hello all, I have recently compiled Autodock under redhat6.0 and the compilation went well except for a few warnings which didn't seem to be to bad. I followed the instruction according to an online instruction document on compiling this software on redhat and everything went good, and most of the programs work in the suit. However, the primary program autodock3 when run, after 5-10 seconds I get back an error: "Segmentation fault (core dump)" with no output or further error messages. So I don't even know were to start with this problem. I've repeated the process with the software included examples and I get the same error, so I believe this may be do to a faulty compilation. Has anyone out there experience this kind of problem (under linux 2) or does any one have any info that might be helpful to solving this problem? Thanks for everyone's comments. David Smith From chemistry-request@server.ccl.net Tue Oct 9 11:25:25 2001 Received: from quantix.u-strasbg.fr ([130.79.34.133]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id f99FPPB15522 for ; Tue, 9 Oct 2001 11:25:25 -0400 Received: from quantix.u-strasbg.fr (loopback [127.0.0.1]) by quantix.u-strasbg.fr (AIX4.3/8.9.3/8.9.3) with ESMTP id RAA11956 for ; Tue, 9 Oct 2001 17:27:48 +0200 Sender: saue@quantix.u-strasbg.fr Message-ID: <3BC31773.3A07792B@quantix.u-strasbg.fr> Date: Tue, 09 Oct 2001 17:27:47 +0200 From: SAUE Trond X-Mailer: Mozilla 4.07 [fr_FR] (X11; I; AIX 4.3) MIME-Version: 1.0 To: chemistry@ccl.net Subject: Minimal coupling Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit External fields are introduced into the Hamiltonian by the substitutions p --> p-qA ; H -> H +q(phi) This is referred to as minimal coupling or, more formally, as the principle of minimal electromagnetic coupling and ensures gauge invariance of the resulting Hamiltonian. My questions is: Who introduced this principle ? I have been looking in a number of standard books ranging from classical electromagnetic theory to QED without finding such historical references and a general discussion of the principle. All the best, Trond Saue -- Trond SAUE (DIRAC: http://dirac.chem.sdu.dk/) Laboratoire de Chimie Quantique et Modélisation Moléculaire Université Louis Pasteur ; 4, rue Blaise Pascal ; F-67000 STRASBOURG tél: 03 90 24 13 01 fax: 03 90 24 15 89 email: saue@quantix.u-strasbg.fr From chemistry-request@server.ccl.net Tue Oct 9 11:23:18 2001 Received: from alcides.host4u.net ([216.71.64.98]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id f99FNIB15480 for ; Tue, 9 Oct 2001 11:23:18 -0400 Received: from saturn.simbiosys.ca (cr808583-b.shprd1.on.wave.home.com [24.43.18.40]) by alcides.host4u.net (8.11.6/8.11.6) with ESMTP id f99FG2a27224 for ; Tue, 9 Oct 2001 10:16:03 -0500 Received: from simbiosys.ca (jupiter.simbiosys.ca [192.168.213.6]) by saturn.simbiosys.ca (Postfix) with ESMTP id F392D1901 for ; Tue, 9 Oct 2001 11:23:11 -0400 (EDT) Sender: aniko@simbiosys.ca Message-ID: <3BC31660.48C84483@simbiosys.ca> Date: Tue, 09 Oct 2001 11:23:12 -0400 From: Aniko Simon Organization: SimBioSys Inc. X-Mailer: Mozilla 4.77 [en] (X11; U; Linux 2.4.3-20mdk i686) X-Accept-Language: en MIME-Version: 1.0 To: "chemistry@ccl.net" Subject: CCL: New software CLiDE for Chemical Literature Data Extraction Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit SimBioSys Inc. is pleased to announce CLiDE and CLiDE Lite v 2.0 CLiDE, an acronym for Chemical Literature Data Extraction, is a document image processing software, which extracts content of printed chemistry documents. The aim of CLiDE is to process whole pages from scanned chemical documents and to extract the maximum amount of information from both the text and the graphic regions. CLiDE is a chemistry intelligent equivalent of an OCR software. Just as an OCR can recognize characters from a scanned images of a printed text, CLiDE can recognize structures, reactions and text from scanned images of printed chemistry literature. FEATURES & BENEFITS - Extracts chemical structure and text information from printed/scanned pages and stores the information in various forms (e.g. MOL file, ChemDraw). - CLiDE also extracts reaction information. Reaction information can be entered into databases automatically. Saves hours of redrawing. - Extracts generic structure information from graphics and text. CLiDE will expand condensed generic structures so they can be entered into your DB either expanded or condensed. - CLiDE recognizes and extracts page layout information. Bibliographical information (e.g. title, author etc.) is conveniently extracted automatically thus saving time cataloging and organizing your DB. AVAILABILITY CLiDE v2.0 is primarily available on MS Windows 2000/NT 4.0/Me/98/95 platforms. CLiDE Lite is also available from: SciStore: http://chemstore.cambridgesoft.com/software/product.cfm?pid=269 Further information regarding CLiDE and CLiDE Lite can be found at http://www.simbiosys.ca/ -- Aniko Simon Ph.D. aniko@simbiosys.ca From chemistry-request@server.ccl.net Tue Oct 9 10:07:38 2001 Received: from hotmail.com ([64.4.37.188]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id f99E7bB13530 for ; Tue, 9 Oct 2001 10:07:38 -0400 Received: from mail pickup service by hotmail.com with Microsoft SMTPSVC; Tue, 9 Oct 2001 07:07:32 -0700 Received: from 133.11.92.210 by pv2fd.pav2.hotmail.msn.com with HTTP; Tue, 09 Oct 2001 14:07:32 GMT X-Originating-IP: [133.11.92.210] From: "tianxiao young" To: chemistry@ccl.net Cc: chemistry-request@server.ccl.net Subject: potential developement Date: Tue, 09 Oct 2001 14:07:32 +0000 Mime-Version: 1.0 Content-Type: text/plain; format=flowed Message-ID: X-OriginalArrivalTime: 09 Oct 2001 14:07:32.0575 (UTC) FILETIME=[BD30A6F0:01C150CB] Hello, I am using AMBER to calculate the hydration of thorium. Firstly I calculate the potential of Th(IV)-H2O using quantum mechanical method. My question is how to use this potential line to get the force field of AMBER, such as the bond constant, the angle constant and the dihedral angle constant? I can not find my answer in the AMBER manaul. I am new to AMBER, would you please help me out? Do you know any good references on force field developement? Your kind help is most appreciated. Best wishes, young _________________________________________________________________ Get your FREE download of MSN Explorer at http://explorer.msn.com/intl.asp From chemistry-request@server.ccl.net Tue Oct 9 12:36:58 2001 Received: from ribotargets.com ([194.129.39.11]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id f99GawB17372 for ; Tue, 9 Oct 2001 12:36:58 -0400 Received: from szilva (helo=localhost) by echo.ribotargets.com with local-esmtp (Exim 3.13 #1) id 15qzpv-0001H5-00; Tue, 09 Oct 2001 16:34:31 +0000 Date: Tue, 9 Oct 2001 16:34:30 +0000 (GMT) From: Szilveszter Juhos To: David Smith cc: CCL Subject: Re: CCL:Running Autodock3 under linux2 In-Reply-To: <3BC31C33.935C7012@mindless.com> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII On Tue, 9 Oct 2001, David Smith wrote: > "Segmentation fault (core dump)" You can find strace/ltrace useful or if you have a debugger like gdb (that is always comes with Linux) you can try: gdb core [ ..lot of info written... ] (gdb) where [ ..this will give you a backtrace.. ] If you are lucky that can give a clue what went wrong. In the strace output you can check for permission/open errors first. Szilva From chemistry-request@server.ccl.net Tue Oct 9 12:57:27 2001 Received: from mail.iitk.ac.in ([203.200.95.130]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id f99GvPB17959 for ; Tue, 9 Oct 2001 12:57:26 -0400 Received: from qasid.cc.iitk.ac.in (qasid.cc.iitk.ac.in [172.31.1.16]) by mail.iitk.ac.in (8.9.3+Sun/8.9.3) with ESMTP id WAA10522; Tue, 9 Oct 2001 22:26:41 +0530 (IST) Received: from Debug (IDENT:nobody@www.iitk.ac.in [203.200.95.132]) by qasid.cc.iitk.ac.in (8.9.2/8.9.2) with SMTP id WAA12474; Tue, 9 Oct 2001 22:13:16 +0530 (IST) Message-Id: <200110091643.WAA12474@qasid.cc.iitk.ac.in> To: David Smith Cc: CHEMISTRY@ccl.net From: ranjan@iitk.ac.in Subject: Re: CCL:Running Autodock3 under linux2 Date: Tue, 9 Oct 2001 16:32:26 GMT X-Mailer: Endymion MailMan Standard Edition v3.0.35 Hi David, It seems to be a general problem for linux users. Actually the problem is with smaller stack size in linux.So set the stack size to a larger size. type in the shell: ulimit -s 66666 the value is essentially any thing you like ( i.e of the order of 60 MB here) Thr default for linux is 8MB. Keep increasing the stack size till it does not give core dump. It should help.. Chinmoy Ranjan, I.I.T Kanpur India. Hello all, > > I have recently compiled Autodock under redhat6.0 and the compilation > went well except for a few warnings which didn't seem to be to bad. I > followed the instruction according to an online instruction document on > compiling this software on redhat and everything went good, and most of > the programs work in the suit. > > However, the primary program autodock3 when run, after 5-10 seconds I > get back an error: > > "Segmentation fault (core dump)" > > with no output or further error messages. So I don't even know were to > start with this problem. I've repeated the process with the software > included examples and I get the same error, so I believe this may be do > to a faulty compilation. > > Has anyone out there experience this kind of problem (under linux 2) or > does any one have any info that might be helpful to solving this > problem? > > Thanks for everyone's comments. > > David Smith > > -= This is automatically added to each message by mailing script =- > CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins > MAILSERV@ccl.net -- HELP CHEMISTRY or HELP SEARCH > CHEMISTRY-SEARCH@ccl.net -- archive search | Gopher: gopher.ccl.net 70 > Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net > > > > From chemistry-request@server.ccl.net Tue Oct 9 13:49:56 2001 Received: from m1.dbb.su.se (IDENT:root@[130.237.190.131]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id f99HntB19399 for ; Tue, 9 Oct 2001 13:49:55 -0400 Received: from chaperone.dbb.su.se (chaperone.dbb.su.se [130.237.179.120]) by m1.dbb.su.se (8.11.2/8.11.2) with ESMTP id f99Hp1x06055; Tue, 9 Oct 2001 19:51:01 +0200 Message-Id: <5.0.1.4.2.20011009194110.022ccec0@mail.dbb.su.se> X-Sender: zhang@mail.dbb.su.se X-Mailer: QUALCOMM Windows Eudora Version 5.0.1 Date: Tue, 09 Oct 2001 19:44:53 +0200 To: David Smith From: Xiao-Ping Zhang Subject: Re: CCL:Running Autodock3 under linux2 Cc: chemistry@ccl.net In-Reply-To: <3BC31C33.935C7012@mindless.com> Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii"; format=flowed Hi, David, You may check the stack size of your machine. Try to set it as unlimited. Good luck! Xiao-Ping Zhang At 11:48 AM 10/9/01 -0400, you wrote: >Hello all, > >I have recently compiled Autodock under redhat6.0 and the compilation >went well except for a few warnings which didn't seem to be to bad. I >followed the instruction according to an online instruction document on >compiling this software on redhat and everything went good, and most of >the programs work in the suit. > >However, the primary program autodock3 when run, after 5-10 seconds I >get back an error: > >"Segmentation fault (core dump)" > >with no output or further error messages. So I don't even know were to >start with this problem. I've repeated the process with the software >included examples and I get the same error, so I believe this may be do >to a faulty compilation. > >Has anyone out there experience this kind of problem (under linux 2) or >does any one have any info that might be helpful to solving this >problem? > >Thanks for everyone's comments. > >David Smith > >-= This is automatically added to each message by mailing script =- >CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins >MAILSERV@ccl.net -- HELP CHEMISTRY or HELP SEARCH >CHEMISTRY-SEARCH@ccl.net -- archive search | Gopher: gopher.ccl.net 70 >Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net ------------------------------------------------ Xiao-Ping Zhang Department of Biochemistry and Biophysics Arrhenius Laboratories of Natural Sciences Stockholm University 106 91 Stockholm Sweden Phone: +46-(0)8-162472 (O); +46-(0)8-6121936 (H) Fax: 46-08-153679 e-mail: zhang@dbb.su.se From chemistry-request@server.ccl.net Tue Oct 9 16:05:38 2001 Received: from web14707.mail.yahoo.com ([216.136.224.124]) by server.ccl.net (8.11.6/8.11.0) with SMTP id f99K5bB23787 for ; Tue, 9 Oct 2001 16:05:38 -0400 Message-ID: <20011009200537.92799.qmail@web14707.mail.yahoo.com> Received: from [129.13.107.105] by web14707.mail.yahoo.com via HTTP; Tue, 09 Oct 2001 22:05:37 CEST Date: Tue, 9 Oct 2001 22:05:37 +0200 (CEST) From: =?iso-8859-1?q?y=20tantirungrotechai?= Subject: Visualize NMR tensors with gaussview? To: chemistry@ccl.net MIME-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit Dear All, I have tried to repeat the calculation given at the http://www.gaussian.com/show/nmrvisgv001.htm but not succeeded. Basically it's a gaussian run with nmr keyword on ethane, ethylene and ethyne. Everything runs smoothly (I have accessed to Gaussian 98 Rev.A7) until I tried to format the checkpoint. In contrast to the example file given at the URL address, there is no information on the current density in my formatted checkpoint. So I wonder how one could view NMR tensors according to that webpage? Or is it just happen that there's something wrong in that part of Rev A7 (the example output file is produced by the development version)? Any suggestions would be appreciated. Best regards, Yuthana Tantirungrotechai __________________________________________________________________ Es ist soweit: das Nokia Game beginnt. Sei bereit für das multimediale Abenteuer. Melde dich bis zum 3. November bei http://de.promotions.yahoo.com/info/nokiagame an! From chemistry-request@server.ccl.net Tue Oct 9 20:48:02 2001 Received: from carbon.chem.ucla.edu ([128.97.35.55]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id f9A0m1B03578 for ; Tue, 9 Oct 2001 20:48:01 -0400 Received: from Laurence.mbi.ucla.edu (pc-ll.chem.ucla.edu [128.97.35.245]) by carbon.chem.ucla.edu (8.11.4/8.11.4) with ESMTP id f9A0m0r28682 for ; Tue, 9 Oct 2001 17:48:00 -0700 (PDT) Message-Id: <5.1.0.14.2.20011009174934.047c38f8@127.0.0.1> X-Sender: lavelle/mbi.ucla.edu@127.0.0.1 X-Mailer: QUALCOMM Windows Eudora Version 5.1 Date: Tue, 09 Oct 2001 17:51:07 -0700 To: CCL From: Laurence Lavelle Subject: Summary: Average DNA-Protein binding (free) energy Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii"; format=flowed Here is the summary. Two responses. >Sender: chandra@ysbl.york.ac.uk >Date: Thu, 04 Oct 2001 09:58:13 +0100 >From: Chandra Verma >Organization: York Structural Biology Laboratory >X-Mailer: Mozilla 4.7C-SGI [en] (X11; I; IRIX 6.5 IP22) >X-Accept-Language: en >To: Laurence Lavelle >Subject: Re: CCL:Average DNA-Protein binding (free) energy > >Hi > >Look up the work of L. Nilsson >Date: Tue, 9 Oct 2001 13:07:53 -0400 (EDT) >From: Nai-Yuan Chang >To: >Subject: Re: Average DNA-Protein binding (free) energy > > >Hi, > > You may find these 2 references helpful: >1. Acc. Chem. Res. 2000, 33, 889-897 >2. Curr. Opin. in Struct. Bio. 2000, 10, 311-317 > >Regards, >Nai-yuan > >========================================================================= >Date: Wed, 03 Oct 2001 15:40:34 -0700 >To: CCL >From: Laurence Lavelle >Subject: Average DNA-Protein binding (free) energy >Mime-Version: 1.0 >Content-Type: text/plain; charset="us-ascii"; format=flowed > >I am looking for a (review ?) paper discussing DNA-protein binding >energies. > >That is, experimental and calculated average delta G values (per DNA base >pair) for: > > DNA + Protein <-----> DNA-Protein > > >Comments and/or literature pointers. Appreciated. > >Laurence Lavelle From chemistry-request@server.ccl.net Tue Oct 9 22:51:27 2001 Received: from hschipaa.hsc.usf.edu ([131.247.16.97]) by server.ccl.net (8.11.6/8.11.0) with SMTP id f9A2pQB08576 for ; Tue, 9 Oct 2001 22:51:27 -0400 Received: from hschipaa.hsc.usf.edu ([131.247.16.105]) by hsc.usf.edu (8.9.3+Sun/8.9.3) with SMTP id WAA22617; Tue, 9 Oct 2001 22:51:20 -0400 (EDT) Message-ID: <3BC3B767.652AFCAD@mindless.com> Date: Tue, 09 Oct 2001 22:50:15 -0400 From: David Smith X-Mailer: Mozilla 4.78 [en] (Win95; U) X-Accept-Language: en MIME-Version: 1.0 To: ranjan@iitk.ac.in CC: CHEMISTRY@ccl.net Subject: Re: CCL:Running Autodock3 under linux2 References: <200110091643.WAA12474@qasid.cc.iitk.ac.in> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hey there, Thanks for your suggestion, setting my stack size to unlimited got me past the segmentation fault problem but I ended up with another. Now I'm getting another error: "Floating Point exception (core dumped)" Any Ideas??? Thanks to all, David Smith ranjan@iitk.ac.in wrote: > > Hi David, > It seems to be a general problem for linux users. > Actually the problem is with smaller stack size in linux.So set the stack size > to a larger size. > type in the shell: > ulimit -s 66666 > the value is essentially any thing you like ( i.e of the order of 60 MB here) > Thr default for linux is 8MB. Keep increasing the stack size till it does not > give core dump. > It should help.. > > Chinmoy Ranjan, > I.I.T Kanpur > India. > > Hello all, > > > > I have recently compiled Autodock under redhat6.0 and the compilation > > went well except for a few warnings which didn't seem to be to bad. I > > followed the instruction according to an online instruction document on > > compiling this software on redhat and everything went good, and most of > > the programs work in the suit. > > > > However, the primary program autodock3 when run, after 5-10 seconds I > > get back an error: > > > > "Segmentation fault (core dump)" > > > > with no output or further error messages. So I don't even know were to > > start with this problem. I've repeated the process with the software > > included examples and I get the same error, so I believe this may be do > > to a faulty compilation. > > > > Has anyone out there experience this kind of problem (under linux 2) or > > does any one have any info that might be helpful to solving this > > problem? > > > > Thanks for everyone's comments. > > > > David Smith > > > > > > > > > > > > -= This is automatically added to each message by mailing script =- > CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins > MAILSERV@ccl.net -- HELP CHEMISTRY or HELP SEARCH > CHEMISTRY-SEARCH@ccl.net -- archive search | Gopher: gopher.ccl.net 70 > Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net