From chemistry-request@server.ccl.net Mon Nov 22 02:39:59 1999 Received: from uvaix7e1.comp.UVic.CA (root@uvaix7e1.comp.UVic.CA [142.104.5.107]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id CAA13492 for ; Mon, 22 Nov 1999 02:39:58 -0500 Received: from p17-126.dialup.UVic.CA (p17-126.dialup.UVic.CA [142.104.17.126]) by uvaix7e1.comp.UVic.CA (8.9.3/8.9.3) with SMTP id WAA193776; Sun, 21 Nov 1999 22:35:20 -0800 From: royj@uvic.ca (Roy Jensen) To: chemistry@ccl.net Subject: SUMMARY: Ionization of a molecule... Date: Mon, 22 Nov 1999 06:35:19 GMT Message-ID: <3838e423.2261170@pop.uvic.ca> X-Mailer: Forte Agent 1.5/32.451 MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id CAA13493 Thanks to those who responded. It appears that this field has not been heavily investigated. The trend of the respondents is that the electron cannot be localized making PES calculations difficult/currently impossible. Roy Jensen ORIGINAL MESSAGE ================= Is there a software package that will calculate the potential experienced by an electron as the parent molecule is ionized? I.e., calculate the energy as an electron is stepped further from the molecule (which is fixed in the optimized geometry). I am interested in determining the barrier as a polyanion is ionized. There is initially an attractive force holding the electron near the molecule. As the distance between the molecule (anion) and electron is increased, the dominant force becomes coulomb repulsion. Any references to published work would be appreciated. Roy Jensen REPLIES ======= "C.F. Matta" ====================================== > If I understand you correctly, you need something like the >potential-energy profile of say a diatomic molecule A-B as you stretch the >A-B separation, except that in your case B is an electron. > This sort of question is OK when A and B are atoms, i.e. >entities sufficiently massive to behave classically. However when B >is an electron, the question looses all meaning since the electron (B) can >no longer be localized to a sequence of points, as it flys away from the >molecule. This is a direct consequence of the Heizenberg's uncertainity >principle. > I hope this helps, but I think your question is interesting. chan@curl.gkcl.yorku.ca (Wai-To-Chan) ============================== > I am not sure about the nature of >the 'potential barrier' to the detachment >of an electron from an anion you refered to. >The only such quantity that can measure such >a barrier I know of is either the >potential term from the Hartree-Fock one-electron >equation or the one from the exact-one-electron >schrodinger equation. You may find the discussion from >Yang, Liu and Wang chem phys lett vol 258 pg 30 (1996) >which shows how the ionization potential of an electron is >related to the limit of the one-electron potential >at infinite distance from a molecule relevant. In principle you >can determine from visualization of distribution of the potential >where an electron is 'forbidden' or 'allowed' as >well as the barrier to removal of the electron in a molecule. >But I highly doubt such information will be useful for >spectroscopic measurement. > > If I am concerned with 'barrier' to ionization >of an anion I will evaluate the intensity of >the electron detachment spectrum (like calculating >the Frank-Condon factor for an electronic excitation >to determine how 'easy' a transition will take place) >instead. > > I recall seeing reports of calculation of intensity of >photo electron-detachment spectrum using some deconvolution >method long ago but don't have any references handy with me. >Email me if you are interested in any details. chan@curl.gkcl.yorku.ca (Wai-To-Chan) ============================== > Here are two clarifications for the sloppy wording >in my previous post: > >a) The asymptotic limit of > the one-electron potential (defined as > del^2 sqrt(rho)/2 * sqrt(rho)) is related > to the 1st ionization potential of > a molecule not the IP of an electron. > >b) "Barrier to removal of an electron" should be changed to > "the force an electron is subjected > to locally in a molecule". One-electron potential is > the quantum potential and its gradient measures the > quantum mechanical force on an electron. "Nguyen N. Anh" ============================== >Your question seems very interesting, though I'm not sure that I understand >you correctly. Presently I'm doing quantum chemical calculations on H2 system >in an intense field. That is, the coulomb potential of H2 is distorted by a >linear potential, and electrons can tunnel out, i.e. get ionized. > >Since you cannot discribe the electron's plan wave by L2 localized basis, >standard quantum chemical methods cannot be used in conventional ways . Myself >I'm using Gaussian but with floatting basis to describe continiuum wave >funtions as the electrons get ionized. > >Unfortunately little work has been done in this topic. Mine is not yet >published. However take a look at the following, hope it's of any use: > >JCP 93, 1125 (1990) From chemistry-request@server.ccl.net Mon Nov 22 05:45:05 1999 Received: from mail.jadeinc.com (mail.jadeinc.com [209.57.24.15]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id FAA14373 for ; Mon, 22 Nov 1999 05:45:05 -0500 Received: from igor [209.57.24.225] by mail.jadeinc.com with ESMTP (SMTPD32-5.05) id AF911B8B014C; Mon, 22 Nov 1999 04:40:33 -0500 Message-Id: <4.2.0.58.19991122043836.00a04e40@mail.jadeinc.com> X-Sender: smolnar@mail.jadeinc.com X-Mailer: QUALCOMM Windows Eudora Pro Version 4.2.0.58 X-Priority: 1 (Highest) Date: Mon, 22 Nov 1999 04:43:23 -0500 To: gamess-users@Glue.umd.edu, Chemistry@ccl.net From: "Stephen P. Molnar, Ph.D." Subject: Problem Linking GAMESS Object Files Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii"; format=flowed Due to an abortive attempt to upgrade from the Mandrake v6.0 distribution of Linux to v6.1, and the subsequent reversion to 6.0, I lost the version of GAMESS with which I had been happily working. Subsequently, I received the 6 Jun 1999 distribution. I'm using the distribution default installation of g77 on a K6-2/300 with 128MB of RAM. Compiling went smoothly, without any error messages. However, when I attempted to link the object files to generate the executable I got the following messages: Sun Nov 21 11:09:09 EST 1999 GAMESS will be linked into the executable image gamess.06.x.chdir objectgcc -o ../gamess.06.x gamess.o unport.o blas.o zunix.o ddi.o ddisoc.o aldeci.o basecp.o basext.o bashuz.o bashz2.o basn21.o basn31.o bassto.o cphf.o cprohf.o delocl.o dftstb.o drc.o ecp.o ecpder.o ecphw.o ecplib.o ecpsbk.o efdrvr.o efgrda.o efgrdb.o efgrdc.o efgrd2.o efinp.o efinta.o efintb.o efelec.o efpaul.o eigen.o ffield.o frfmt.o guess.o gradex.o grd1.o grd2a.o grd2b.o grd2c.o gugdga.o gugdgb.o gugdm.o gugdm2.o gugdrt.o gugem.o gugsrt.o gvb.o hess.o hss1a.o hss1b.o hss2a.o hss2b.o inputa.o inputb.o inputc.o int1.o int2a.o int2b.o iolib.o lagran.o local.o loccd.o locpol.o mccas.o mcqdpt.o mcqud.o mcscf.o mctwo.o morokm.o mp2.o mp2ddi.o mp2grd.o mpcdat.o mpcgrd.o mpcint.o mpcmol.o mpcmsc.o mthlib.o nameio.o ordint.o parley.o pcm.o pcmcav.o pcmder.o pcmdis.o pcmpol.o pcmvch.o prpel.o prplib.o prppop.o rhfuhf.o rxncrd.o ryspol.o scflib.o scfmi.o scrf.o sobrt.o soffac.o sozeff.o statpt.o surf.o symorb.o symslc.o tdhf.o trans.o trfdm2.o trnstn.o trudge.o vibanl.o zheev.o zmatrx.o qmmm.o -lf2c -lmunport.o: In function `abrt_':unport.o(.text+0xc8): undefined reference to `G77_abort_0'unport.o: In function `flshbf_':unport.o(.text+0x1e1): undefined reference to `G77_flush1_0'unport.o: In function `tmdate_':unport.o(.text+0xa22): undefined reference to `G77_fdate_0'iolib.o: In function `openda_':iolib.o(.text+0x45c): undefined reference to `G77_getenv_0'iolib.o: In function `mqopda_':iolib.o(.text+0x962): undefined reference to `G77_getenv_0'iolib.o: In function `raopen_':iolib.o(.text+0x208b): undefined reference to `G77_getenv_0'iolib.o: In function `seqopn_':iolib.o(.text+0x263e): undefined reference to `G77_getenv_0'collect2: ld returned 1 exit statusunset echo1.340u 0.960s 0:02.51 91.6% 0+0k 0+0io 4484pf+0w I suspect that I failed to install a critical application when I reinstalled Mandrake v6.0, but I don't have a clue as to what it may be. I would greatly appreciate any assistance which may be forthcoming to resolve thiw problem. Thanks in advance. --------------------------------------------------------------- Stephen P. Molnar, Ph.D. Life is a fuzzy set Foundation for Chemistry Stochastic and multivariant 614.486.4076 From chemistry-request@server.ccl.net Mon Nov 22 10:20:11 1999 Received: from theory.tc.cornell.edu (THEORY.TC.CORNELL.EDU [128.84.30.174]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id KAA16203 for ; Mon, 22 Nov 1999 10:20:10 -0500 Received: from tc.cornell.edu (REN.TC.CORNELL.EDU [128.84.20.129]) by theory.tc.cornell.edu (8.8.4/8.8.3/CTC-1.0) with ESMTP id JAA16260; Mon, 22 Nov 1999 09:15:36 -0500 Sender: richard@tc.cornell.edu Message-ID: <38395008.345C5D9A@tc.cornell.edu> Date: Mon, 22 Nov 1999 09:15:36 -0500 From: Richard Gillilan X-Mailer: Mozilla 4.5 [en] (X11; I; IRIX 6.2 IP22) X-Accept-Language: en MIME-Version: 1.0 To: Deepak Singh CC: Computational Chemistry List Subject: Re: CCL:Open Visualization Data Explorer References: <38388CCA.79919B77@syr.edu> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Deepak Singh wrote: > > Hi, > > I have been looking into software (for IRIX) that will allow me to > visualize MO's, charge densities etc. I heard a lot about AVS but that > seems to have disappeared. I ran into IBM's 'Open Visualization Data > Explorer' today and it seems to be similar to AVS. I would like to know > if people have used this a lot with G98/94, GAMESS and MOPAC? Is the > performance similar to AVS? I have used DX and OpenDX to visualize both output of MOPAC and experimental density files (XPLOR format) from time-resolved xtallography. You'll probably want the m2dx filter written by Tom Jackman (IBM). The current IRIX 6.5 executable for OpenDX that can be downloaded from www.OpenDX.org seems to be stable enough for most routine use, although there has been a lot of activity among developers trying to track down some aparent memory access violation problems. My chemistry module suite gives DX the ability to combine conventional ball-and-stick, ribbon, solvent surface, etc. with density files sliced and diced in creative ways if you are willing to work at it. When in graphics hardware mode, it takes advantage of SGI graphics engines and can even do hardware (Crystal-Eyes) stereo now. Richard Cornell Theory Center From chemistry-request@server.ccl.net Mon Nov 22 11:40:57 1999 Received: from darkwing.uoregon.edu (genghis@darkwing.uoregon.edu [128.223.142.13]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id LAA16650 for ; Mon, 22 Nov 1999 11:40:57 -0500 Received: from localhost (genghis@localhost) by darkwing.uoregon.edu (8.9.3/8.9.3) with SMTP id HAA19244 for ; Mon, 22 Nov 1999 07:36:23 -0800 (PST) Date: Mon, 22 Nov 1999 07:36:23 -0800 (PST) From: "Dale A. Braden" Reply-To: "Dale A. Braden" To: cclpost Subject: Summary: G98 TS optimizations Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear CCL, Two weeks ago I posted a request for help in getting Gaussian98 to do a transition state optimization when two modes had negative hessian eigenvalues (original question below). Thank you to all respondents. There isn't really a proper solution, although there is a workaround. There seems to be no general mode-following algorithm in G98, because opt=ef is limited to 50 active variables and opt(tvector=n) isn't recognized, even though it's in the manual. The workaround works only when the mode with the lowest eigenvalue is the one of interest, which is probably the case most often. So one can just use opt(ts,calcfc,noeigentest). The "noeigentest" option prevents the program from stopping if two or more negative eigenvalues are encountered. This happens all the time when there are internal rotors. A few people suggested using the QST2 or QST3 methods, but I think these also follow only the mode with the lowest eigenvalue, so they won't work when a different mode is of interest. (I did actually give QST2 a try, but it could not generate coordinates for the TS structure.) Best wishes to all, Dale Dale Braden Department of Chemistry University of Oregon Eugene, OR 97403-1253 genghis@darkwing.uoregon.edu ---original post--- I am trying to use Gaussian98 to locate a transition state. Using opt=(calcfc,ts) results in two negative hessian eigenvalues, and the job fails. Thus I need a way to specify which mode should be followed. According to the manual, this can be done by specifying tvector=N where N is the mode number. In fact, this keyword is not even recognized. An alternative is to use opt=ef to select the eigenvalue following algorithm. Unfortunately, this is limited to 50 variables, which is too small for the molecule I'm looking at. This leaves opt=noeigentest, in which case I assume that the mode with the lowest eigenvalue is followed, but what if one wants the other one? G98 prints out one eigenvector, in internal coordinates, which is required to have a negative eigenvalue, even when there are two or more negative eigenvalues. What is needed is the eigenvectors for ALL negative eigenvalues, in cartesian coordinates, so that they can be visualized (animated) and the wrong modes identified. Then, at least, the geometry could be manually displaced downhill along the modes that are not to be followed. How does one handle this situation in G98? From chemistry-request@server.ccl.net Mon Nov 22 12:14:06 1999 Received: from ysbl.york.ac.uk (batman.chem.york.ac.uk [144.32.72.190]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id MAA16824 for ; Mon, 22 Nov 1999 12:13:56 -0500 Received: from yorvic.york.ac.uk (pingu [144.32.72.76]) by ysbl.york.ac.uk (8.9.3/8.8.7) with ESMTP id QAA113912 for ; Mon, 22 Nov 1999 16:09:20 GMT Sender: caves@ysbl.york.ac.uk Message-ID: <38396AB0.4CF88B3C@yorvic.york.ac.uk> Date: Mon, 22 Nov 1999 16:09:20 +0000 From: Leo Caves Organization: University of York X-Mailer: Mozilla 4.5C-SGI [en] (X11; I; IRIX 6.5 IP22) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net Subject: MGMS Meeting Announcement Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit http://www.mgms.org/york2000 ----- 18th International Meeting of the Molecular Graphics and Modelling Society. Modelling Biomolecular Mechanism: From States to Processes at the Atomic Level April 5-8, 2000 at the University of York, UK * Further Details & Information Conference Web Site now open at http://www.mgms.org/york2000 Information on the Scientific Programme, Contributions, Registration and Travel available on the Web site * Meeting Agenda The meeting focuses on the study of biomolecular processes incuding chemical reactions, protein folding, transport & diffusion and energy transduction. The meeting showcases advances in theoretical and computational approaches to studying biomolecular processes as well as powerful single molecule and time-resolved experimental techniques. With contributions from leading international researchers, the meeting provides an important and timely opportunity to review and stimulate discussion across the many disciplines addressing the mechanistic aspects of structure-function relationships in biological processes at the atomic level. * Scientific Programme -- Sessions Include: Pathway Methods; Enzyme Reactions; Transport & Diffusion; Folding; Manipulation; Energy Transfer & Transduction; Solution Dynamics -- Confirmed Invited Speakers and Titles: HJC Berendsen, Univ. of Groningen "Diffusion-limited enzyme catalysis: Lecithin into phospholipase A2" Bernie Brooks, NIH (Title TBA) Charlie Brooks, TSRI "Protein Folding Landscapes, Mechanism and Kinetics: Insights from Theory and Simulation" Leonor Cruzeiro-Hansson, Herriot-Watt Univ. "Vibrational energy transfer as the first step in protein function" Ron Elber, Cornell "Long time dynamics of biomolecules using the stochastic path approach" Stefan Fischer, Univ. of Heidelberg "Molecular kinematics: essential motion and energetics of slow (>1us) processes in proteins." Hans Frauenfelder, Los Alamos Natl Laboratory "Complexity in protein dynamics and protein reactions." Hermann Gaub, Univ. of Munich (Title TBA; topic on AFM-related work) Ian Hillier, Univ. of Manchester "What can QM/MM calculations tell us about enzyme reactions?" Martin Karplus, Univ. of Strasbourg/Harvard (Title TBA) Peter Kollman, UCSF (Title TBA - topic on folding) Andy McCammon, UCSD "Dynamics of Molecular Recognition" Justin Molloy, Univ. of York "Use of optical techniques to probe the mechanism of energy transduction of single molecular motors" David Perahia, CNRS Orsay "Study of conformational pathways in proteins: methods and applications" Simon Phillips, Univ. of Leeds "Towards a movie of catalysis in copper amine oxidases" Rudolf Rigler, Karolinska Institute "Spectroscopy of Single Biomolecules: The fluctuating enzyme" Benoit Roux, Univ. of Montreal "Simulating the Flow of Ions across Membrane Channels" Klaus Schulten, Univ. of Illinois "Steered Molecular Dynamics to Study Biopolymer Association and Stretching" Lorna Smith, Univ. of Oxford "Characterisation of denatured and partially folded protein conformations" John Straub, Boston Univ. "Direct computation of long time processes in peptides and proteins" Michael Schaefer, Univ. of Strasbourg "Structural and thermodynamic characterization of polypeptides by computer simulation: Helices, beta-hairpins, and chameleons." Wilfred van Gunsteren, ETH Zurich (Title TBA) RJP Williams, Univ of Oxford "Coupling between electron and proton energies in Proteins" Peter Wolynes, Univ. of Illinois "Pure and Applied Protein Folding Kinetics." ----- http://www.mgms.org/york2000 -- Leo Caves Structural Biology Laboratory, Dept. of Chemistry, University of York York, YO10 5DD, UK tel:(+44)1904 434521 fax:(+44)1904 410519 From chemistry-request@server.ccl.net Mon Nov 22 14:09:37 1999 Received: from oc30.uni-paderborn.de (oc30.uni-paderborn.de [131.234.240.90]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id OAA17427 for ; Mon, 22 Nov 1999 14:09:37 -0500 Received: from localhost (cpilger@localhost) by oc30.uni-paderborn.de (980427.SGI.8.8.8/980728.SGI.AUTOCF) via ESMTP id TAA05212 for ; Mon, 22 Nov 1999 19:13:19 +0100 (CET) Date: Mon, 22 Nov 1999 19:13:19 +0100 From: Christian Pilger To: Computational Chemistry List Subject: 3D-QSAR In-Reply-To: <38388CCA.79919B77@syr.edu> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear CCLers, we plan to perform a Comparative Molecular Field Analysis (CoMFA) on a dataset of compounds with known activities. As the X-ray structure of the receptor is known, we used an automated docking procedure to generate a reasonable alignment. I have the following questions: - Field geometry: does anyone have experience with different field geometries, i.e. cubic arrangement of interaction points vs. spherical arrangement ? - Would it be better to use an energetic cutoff value for the interaction energies (as in SYBYL) or should those grid points, that are located within the common volume of the aligned structures be omitted at all ? I can imagine a program that compares the distance of each grid point to each atom of the aligned structures. If this distance is smaller than the van-der-Waals radius of one of the considered atoms, the specified grid point is excluded. Would such an approach be resonable ? - Which type of probes should be used/avoided ? I want to employ the program GRID by Peter Goodford. I appreciate any comments. Furthermoe I'm interested in different 3D-methods, which might be suitable for my problem. Regards, Christan ----------------------------------------------------------------- Dipl.-Chem. Christian Pilger Uni-GH Paderborn FB 13 - Organische Chemie Warburger Str. 100 D-33098 Paderborn/Germany Tel.: 05251-60279/-602183 Fax : 05251-603245 email: cpilger@oc30.uni-paderborn.de Word Wide Web: http://oc30.uni-paderborn.de/~cpilger ----------------------------------------------------------------- From chemistry-request@server.ccl.net Mon Nov 22 22:53:05 1999 Received: from mailbox.syr.edu (root@mailbox.syr.edu [128.230.18.5]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id WAA20042 for ; Mon, 22 Nov 1999 22:53:05 -0500 Received: from syr.edu (curie.syr.edu [128.230.187.116]) by mailbox.syr.edu (8.9.2/8.9.2) with ESMTP id VAA25266 for ; Mon, 22 Nov 1999 21:48:22 -0500 (EST) Sender: desingh@mailbox.syr.edu Message-ID: <383A0193.6E70DA22@syr.edu> Date: Mon, 22 Nov 1999 21:53:08 -0500 From: Deepak Singh Organization: Dept. of Chemistry, Syracuse University X-Mailer: Mozilla 4.61C-SGI [en] (X11; I; IRIX64 6.5 IP30) X-Accept-Language: en MIME-Version: 1.0 To: Computational Chemistry List Subject: AVS/IBM explorer followup Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Thank you to everyone who replied to the following post ----------------------- Hi, I have been looking into software (for IRIX) that will allow me to visualize MO's, charge densities etc. I heard a lot about AVS but that seems to have disappeared. I ran into IBM's 'Open Visualization Data Explorer' today and it seems to be similar to AVS. I would like to know if people have used this a lot with G98/94, GAMESS and MOPAC? Is the performance similar to AVS? ------------------------ I think I should clarify a few things. When I say AVS has disappeared, I mean the "Application Visualization System"produced by produced by Advanced Visual Systems which used to have a "chemistry" viewer. I found this at the following site http://www.arl.hpc.mil/PET/cta/ccm/training/courses/scivis/AVS/AVS-schedule.html I might be wrong but as someone did point out to me, AVS express does not have the chemistryu module per se. Some people wrote to me about MOLDEN, which is what I use now, but molden cannot give me the quality of graphics which I require. It is great as a reference and research tool, but we have always used something like "mathematica" to get better graphics . The IBM explorer seems to be a similar product to AV, and it is FREE. I tried getting it running today but had a bunch of compilation trouble. I would not like to spend too much time on it, if people have had trouble with it. In short, I guess what I need to know is that, on a SGI, which product would give me the best quality graphics for G98, MOPAC and GAMESS output, without unnecessary headaches. I have no personal bias. Just a note gopenmol is good, but seems better for MD analysis. Deepak. -- ********************************************************************** Deepak Singh Tel : (315)443 1739 (w) Graduate Student (315)472 9659 (h) Dept. of Chemistry Fax : (315)443 4070 Syracuse University email : desingh@syr.edu 1-014 CST, Syracuse URL : http://web.syr.edu/~desingh NY 13244 "Violence is the last refuge of the incompetent." --- Salvor Hardin **********************************************************************