From teomgs@theochem.uni-stuttgart.de Tue Jul 7 03:15:32 1998 Received: from indy2.theochem.uni-stuttgart.de (indy2.theochem.uni-stuttgart.de [129.69.55.32]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id DAA21386 Tue, 7 Jul 1998 03:15:18 -0400 (EDT) Received: from tc11.theochem.uni-stuttgart.de (teomgs@tc11.theochem.uni-stuttgart.de [129.69.55.131]) by indy2.theochem.uni-stuttgart.de (8.8.8/8.8.8) with ESMTP id JAA05045; Tue, 7 Jul 1998 09:15:05 +0200 (MDT) Received: from localhost (teomgs@localhost) by tc11.theochem.uni-stuttgart.de (8.8.8/8.8.8) with SMTP id JAA24996; Tue, 7 Jul 1998 09:15:04 +0200 (METDST) Date: Tue, 7 Jul 1998 09:15:03 +0200 (METDST) From: "Dr. Martin Schuetz" To: d3e102@emsl.pnl.gov cc: chemistry@www.ccl.net Subject: Re: CCL:BSSE and (H2O)2 In-Reply-To: <9807061258.ZM7636@ames.emsl.pnl.gov> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Here a remark to Note 3 of the list compiled by Dave Feller about BSSE studies on the water dimer: In the Abstract of paper by Feyereisen, Feller and Dixon (JPC 100, 2993 (1996), it is stated, that the core/valence correlation effects are found to increase the interaction energy by \approx 0.05 kcal/mol. On page 2996 however, they write (and I quote)" " core/valence correlation tends to increase the binding energy by 0.09 kcal/mol at the best level that we considered"... the authors performed RI-MP2 calculations using the aug-cc-pCVDZ* and aug-cc-pCVTZ* basis sets. For these two basis sets, the following core/valence correlation contributions were obtained (without and with CP correction): noCP CP aug-cc-pCVDZ* -0.09 -0.01 aug-cc-pCVTZ* -0.05 -0.03 it is evident, that the core/valence contributions are very sensitive to the application of the CP correction. the authors do not mention neither for the value of 0.05 kcal/mol in the abstract, nor for the value of 0.09 kcal/mol in the results section, how these were obtained (by some sort of basis set extrapolation ?), although it seems from that table, that a value below 0.05 kcal/mol would be more reasonable than the 0.09 kcal/mol they mentioned in their results section. In the calculations reported in JCP 107, 4597 (1997) on the other hand, a core polarization set as large as 4d3f2g1h was used, and a consistent value of 0.04 kcal/mol was obtained for the core/valence correlation contribution to the interaction energy, which no longer depends at all on the CP correction. ---------------------------------------------------------------------------- Dr. Martin G. Schuetz Phone: 0049 (0)711-685-4397 University of Stuttgart Fax: 0049 (0)711-685-4442 Institute for Theoretical Chemistry Pfaffenwaldring 55 Room Nr: 8.161 D-70569 Stuttgart Email: schuetz@theochem.uni-stuttgart.de WWW : http://www.theochem.uni-stuttgart.de/~teomgs/ ---------------------------------------------------------------------------- On Mon, 6 Jul 1998 d3e102@emsl.pnl.gov wrote: > Over the past several weeks there have been several messages posted to the > CCL concerning basis set superposition error and the water dimer. Here is > an admittedly selective list of just some of the calculations dealing with > the water dimer. This system has been examined by a large number of > researchers. > ----------------------------------------------------------------------------- > > Water Dimer Interaction Energies (kcal/mol) > > Basis Method DeltaE CP Reference > aug-cc-pVQZ MP2(FC) -5.05 N D. Feller, JCP 96, 6104 > MP2(FC) -4.81 Y (1992). (See Note 1) > Est. CBS MP2(FC) -4.95 +/- 0.05 NA > > R12-MP2 -4.94 NA W. Klopper, et al. JCP, > 103, 1085 (1995). > > aug-cc-pV5Z MP2(FC) -4.98 N M.W. Feyereisen et al. JPC > Est. CBS MP2(FC) -4.9 +/- 0.1 NA 100, 2993 (1996). > Est. CBS MP2 -4.95 +/- 0.1 NA > Est. CBS FCI -5.0 +/- 0.1 NA (see Note 2) > > 20s15p11d9f7g4h2i1k MP2(FC) -4.92 N M. Schutz et al. JCP, 107, > MP2(FC) -4.88 Y 4597 (1997). > Est. CBS MP2 -4.94 +/- 0.02 NA (see Note 3) > > aug-cc-pV5Z MP2(FC) -4.98 N A. Halkier, et al. TCA, > 97, > daug-cc-pVQZ MP2(FC) -5.10 N 150 (1997). > MP2(FC) -4.81 Y > Est. CBS MP2(FC) -4.91 +/- 0.07 NA > aug-cc-pVQZ CCSD(T)(FC) -5.05 N > Est. CBS CCSD(T)(FC) -4.96 +/- 0.07 NA > > CP: N=No, Y=Yes/ NA=Not Applicable > Note 1: The aug-cc-pVQZ binding energy was estimated by assuming the > contributions of the diffuse f and g functions on oxygen were > additive. > Note 2: The full CI estimate includes the effects of geometry relaxation, > core/valence corrections and higher order correlation recovery. > Note 3: The (20s15p11d9f7g4h2i1k) oxygen basis set of Schutz et al. was > uncontracted. It was used with an 11s5p4d3f2g1h hydrogen basis > set for a total of 1046 functions in the water dimer. These authors > state that their core/valence correction was only 0.04 kcal/mol, > whereas they claim that Feyereisen et al. recommended a value of > 0.09 kcal/mol. But in the abstract to the work of Feyereisen et al. > they clearly state that CV effects increase the binding energy by > ~0.05 kcal/mol. > > > > -- > > David Feller | Mail Stop K1-96 > Environmental Molecular Sciences Laboratory | 906 Battelle Blvd > Battelle Pacific Northwest National Lab | Richland, WA 99352 > | > e-mail:d3e102@emsl.pnl.gov | Fax: (509)-375-6631 > > -------This is added Automatically by the Software-------- > -- Original Sender Envelope Address: d3e102@emsl.pnl.gov > -- Original Sender From: Address: d3e102@emsl.pnl.gov > CHEMISTRY@www.ccl.net: Everybody | CHEMISTRY-REQUEST@www.ccl.net: Coordinator > MAILSERV@www.ccl.net: HELP CHEMISTRY or HELP SEARCH | Gopher: www.ccl.net 73 > Anon. ftp: www.ccl.net | CHEMISTRY-SEARCH@www.ccl.net -- archive search > Web: http://www.ccl.net/chemistry.html > > From tapas@risky3.thchem.siu.edu Tue Jul 7 10:50:28 1998 Received: from risky3.thchem.siu.edu (risky3.thchem.siu.edu [131.230.89.13]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id KAA28538 Tue, 7 Jul 1998 10:50:24 -0400 (EDT) Received: (from tapas@localhost) by risky3.thchem.siu.edu (AIX4.2/UCB 8.7/8.7) id JAA20920; Tue, 7 Jul 1998 09:54:28 -0500 (CDT) Date: Tue, 7 Jul 1998 09:54:28 -0500 (CDT) From: Tapas Kar To: "Dr. Martin Schuetz" cc: d3e102@emsl.pnl.gov, chemistry@www.ccl.net Subject: Re: CCL:BSSE and (H2O)2 In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Inclusion of core electrons in correlation also changes geometric parameters. I guess there is no comparetive study on core/valence correlation. On Tue, 7 Jul 1998, Dr. Martin Schuetz wrote: > Date: Tue, 7 Jul 1998 09:15:03 +0200 (METDST) > From: Dr. Martin Schuetz > To: d3e102@emsl.pnl.gov > Cc: chemistry@www.ccl.net > Subject: CCL:BSSE and (H2O)2 > > Here a remark to Note 3 of the list compiled by Dave Feller about BSSE > studies on the water dimer: > > In the Abstract of paper by Feyereisen, Feller and Dixon (JPC 100, 2993 > (1996), it is stated, that the core/valence correlation effects are found > to increase the interaction energy by \approx 0.05 kcal/mol. > On page 2996 however, they write (and I quote)" > " core/valence correlation tends to increase the binding energy by 0.09 > kcal/mol at the best level that we considered"... > the authors performed RI-MP2 calculations using the aug-cc-pCVDZ* and > aug-cc-pCVTZ* basis sets. For these two basis sets, the following > core/valence correlation contributions were obtained (without and with CP > correction): > noCP CP > aug-cc-pCVDZ* -0.09 -0.01 > aug-cc-pCVTZ* -0.05 -0.03 > > it is evident, that the core/valence contributions are very sensitive to > the application of the CP correction. > the authors do not mention neither for the value of 0.05 kcal/mol in the > abstract, nor for the value of 0.09 kcal/mol in the results section, > how these were obtained (by some sort of basis set extrapolation ?), > although it seems from that table, that a value below 0.05 kcal/mol > would be more reasonable than the 0.09 kcal/mol they mentioned in their > results section. > > In the calculations reported in JCP 107, 4597 (1997) on the other hand, > a core polarization set as large as 4d3f2g1h was used, and a consistent > value of 0.04 kcal/mol was obtained for the core/valence correlation > contribution to the interaction energy, which no longer depends at all > on the CP correction. > > ---------------------------------------------------------------------------- > Dr. Martin G. Schuetz Phone: 0049 (0)711-685-4397 > University of Stuttgart Fax: 0049 (0)711-685-4442 > Institute for Theoretical Chemistry > Pfaffenwaldring 55 Room Nr: 8.161 > D-70569 Stuttgart > Email: schuetz@theochem.uni-stuttgart.de > WWW : http://www.theochem.uni-stuttgart.de/~teomgs/ > ---------------------------------------------------------------------------- > > > > On Mon, 6 Jul 1998 d3e102@emsl.pnl.gov wrote: > > > Over the past several weeks there have been several messages posted to the > > CCL concerning basis set superposition error and the water dimer. Here is > > an admittedly selective list of just some of the calculations dealing with > > the water dimer. This system has been examined by a large number of > > researchers. > > ----------------------------------------------------------------------------- > > > > Water Dimer Interaction Energies (kcal/mol) > > > > Basis Method DeltaE CP Reference > > aug-cc-pVQZ MP2(FC) -5.05 N D. Feller, JCP 96, 6104 > > MP2(FC) -4.81 Y (1992). (See Note 1) > > Est. CBS MP2(FC) -4.95 +/- 0.05 NA > > > > R12-MP2 -4.94 NA W. Klopper, et al. JCP, > > 103, 1085 (1995). > > > > aug-cc-pV5Z MP2(FC) -4.98 N M.W. Feyereisen et al. JPC > > Est. CBS MP2(FC) -4.9 +/- 0.1 NA 100, 2993 (1996). > > Est. CBS MP2 -4.95 +/- 0.1 NA > > Est. CBS FCI -5.0 +/- 0.1 NA (see Note 2) > > > > 20s15p11d9f7g4h2i1k MP2(FC) -4.92 N M. Schutz et al. JCP, 107, > > MP2(FC) -4.88 Y 4597 (1997). > > Est. CBS MP2 -4.94 +/- 0.02 NA (see Note 3) > > > > aug-cc-pV5Z MP2(FC) -4.98 N A. Halkier, et al. TCA, > > 97, > > daug-cc-pVQZ MP2(FC) -5.10 N 150 (1997). > > MP2(FC) -4.81 Y > > Est. CBS MP2(FC) -4.91 +/- 0.07 NA > > aug-cc-pVQZ CCSD(T)(FC) -5.05 N > > Est. CBS CCSD(T)(FC) -4.96 +/- 0.07 NA > > > > CP: N=No, Y=Yes/ NA=Not Applicable > > Note 1: The aug-cc-pVQZ binding energy was estimated by assuming the > > contributions of the diffuse f and g functions on oxygen were > > additive. > > Note 2: The full CI estimate includes the effects of geometry relaxation, > > core/valence corrections and higher order correlation recovery. > > Note 3: The (20s15p11d9f7g4h2i1k) oxygen basis set of Schutz et al. was > > uncontracted. It was used with an 11s5p4d3f2g1h hydrogen basis > > set for a total of 1046 functions in the water dimer. These authors > > state that their core/valence correction was only 0.04 kcal/mol, > > whereas they claim that Feyereisen et al. recommended a value of > > 0.09 kcal/mol. But in the abstract to the work of Feyereisen et al. > > they clearly state that CV effects increase the binding energy by > > ~0.05 kcal/mol. > > > > > > > > -- > > > > David Feller | Mail Stop K1-96 > > Environmental Molecular Sciences Laboratory | 906 Battelle Blvd > > Battelle Pacific Northwest National Lab | Richland, WA 99352 > > | > > e-mail:d3e102@emsl.pnl.gov | Fax: (509)-375-6631 > > > > -------This is added Automatically by the Software-------- > > -- Original Sender Envelope Address: d3e102@emsl.pnl.gov > > -- Original Sender From: Address: d3e102@emsl.pnl.gov > > CHEMISTRY@www.ccl.net: Everybody | CHEMISTRY-REQUEST@www.ccl.net: Coordinator > > MAILSERV@www.ccl.net: HELP CHEMISTRY or HELP SEARCH | Gopher: www.ccl.net 73 > > Anon. ftp: www.ccl.net | CHEMISTRY-SEARCH@www.ccl.net -- archive search > > Web: http://www.ccl.net/chemistry.html > > > > > > > -------This is added Automatically by the Software-------- > -- Original Sender Envelope Address: teomgs@theochem.uni-stuttgart.de > -- Original Sender From: Address: teomgs@theochem.uni-stuttgart.de > CHEMISTRY@www.ccl.net: Everybody | CHEMISTRY-REQUEST@www.ccl.net: Coordinator > MAILSERV@www.ccl.net: HELP CHEMISTRY or HELP SEARCH | Gopher: www.ccl.net 73 > Anon. ftp: www.ccl.net | CHEMISTRY-SEARCH@www.ccl.net -- archive search > Web: http://www.ccl.net/chemistry.html > > -------------------------------------------- Tapas Kar, Ph. D Asst. Scientist Forestry Bldg 118 Department of Chemistry Southern Illinois University at Carbondale Illinois 62901-4409 Fax: (618) 453 6408 Tel: (618) 453 6433(Lab) 6485(Office) -------------------------------------------- From elewars@alchemy.chem.utoronto.ca Tue Jul 7 11:42:12 1998 Received: from alchemy.chem.utoronto.ca (alchemy.chem.utoronto.ca [142.150.224.224]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id LAA29556 Tue, 7 Jul 1998 11:42:12 -0400 (EDT) Received: (from elewars@localhost) by alchemy.chem.utoronto.ca (8.7.4/8.7.3) id LAA20023 for chemistry@www.ccl.net; Tue, 7 Jul 1998 11:42:07 -0400 (EDT) Date: Tue, 7 Jul 1998 11:42:07 -0400 (EDT) From: "E. Lewars" Message-Id: <199807071542.LAA20023@alchemy.chem.utoronto.ca> To: chemistry@www.ccl.net Subject: QUESTIONS:ELECTRON CORRELATION Tues, 1998 July 7 SOME QUESTIONS ABOUT ELECTRON CORRELATION AND THE HARTREE-FOCK METHOD Hello, The HF method (HFM), even at the basis set limit, gives an energy which is higher than the exact expectation value of the Hamiltonian, the energy difference being the correlation energy. The higher value of the HF energy is said to be due to overestimation of *potential* energy ("the HF method always underestimates the kinetic energies of the electrons"--Pilar, 2nd ed, p 286), specifically electron-electron repulsion. The HFM is also said to underestimate the coulomb hole ("the coulomb hole is neglected almost completely" -- Pilar, p 296/297) and to overestimate the fermi hole (Pilar 296). So the HFM gives an energy that is too high, because it overestimates el-el potential E ; as far as *kinetic* energy goes, the HFM would give an energy that is too *low*. QUESTIONS: 1) Does anyone question any of the above statements? 2) If the fermi hole is overestimated, should this decrease el-el repulsion, since the fermi hole means a region around each el. unfriendly to other electrons of the same spin--if any two electrons avoid one another they repel one another less; in which case: 3) Shouldn't the neglect of the *coulomb hole* be the real cause of the over- estimation of el-el repulsion? In other words, shold not most of the el-el repulsion in the HFM be between electrons of *opposite* spin (electrons of the same spin avoiding one another because of the Pauli effect (i.e. because of the fermi hole)? 4) Overestimation of the fermi hole is simply a result of using a one- determinant wavefunction--right? 5) Is there a way to see *intuitively* that the HFM must overestimate electron-electron repulsion and underestimate electron kinetic energy? Thanks E. Lewars ======================== From rkrocha@dedalus.lcc.ufmg.br Tue Jul 7 12:20:09 1998 Received: from dedalus.lcc.ufmg.br (dedalus.lcc.ufmg.br [150.164.65.10]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with SMTP id MAA00286 Tue, 7 Jul 1998 12:20:06 -0400 (EDT) Received: from localhost by dedalus.lcc.ufmg.br (AIX 3.2/UCB 5.64/4.03) id AA39060; Tue, 7 Jul 1998 13:20:13 -0300 Organization: Universidade Federal de Minas Gerais - LCC - Brasil Date: Tue, 7 Jul 1998 13:20:13 -0300 (BSC) From: ramon kleber da rocha To: Computational Chemistry Mailing List Subject: Parameterization for organometalic compounds Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Could anybody send me references about or parameters or parameterization for MM1 and AMBER forcefield for organotin and organoplatinum compounds? I will sumarize. Best regards. ________________________________________________________________________________ Ramon Kleber da Rocha VOICE +55-31-499-5765 e-mail rkrocha@dedalus.lcc.ufmg.br FAX +55-31-499-5700 Laboratorio de QSAR e Modelagem Molecular Nucleo de Estudos em Quimica Medicinal - NEQUIM - http://www.qui.ufmg.br/~nequim Departamento de Quimica - Instituto de Ciencias Exatas Universidade Federal de Minas Gerais Av. Presidente Antonio Carlos, 6627 Campus Pampulha CEP 31-270-901 - Belo Horizonte - Minas Gerais - Brasil ________________________________________________________________________________ From nowak@chemie.uni-halle.de Mon Jul 6 11:18:04 1998 Received: from mailserv.rz.fh-merseburg.de (mailserv.rz.fh-merseburg.de [149.205.18.1]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id LAA08617 Mon, 6 Jul 1998 11:17:56 -0400 (EDT) Received: from localhost (nowak@localhost) by mailserv.rz.fh-merseburg.de (8.8.8/8.8.7) with SMTP id RAA13287 for ; Mon, 6 Jul 1998 17:20:11 +0200 (METDST) X-Authentication-Warning: mailserv.rz.fh-merseburg.de: nowak owned process doing -bs Date: Mon, 6 Jul 1998 17:20:11 +0200 (METDST) From: Thomas Nowak X-Sender: nowak@mailserv.rz.fh-merseburg.de Reply-To: Thomas Nowak To: chemistry@www.ccl.net Subject: CCL: Energy analysis? Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi, I am looking for program for the analysis of the bond energy. I know there is one implementation of the Morokuma algorithm in ADF, so i looking for other implementations of this or similar algorithm which can be used with other quantum chemistry programs. It would be great, if we can do such analysis on DFT level. Regards, Thomas Nowak Martin-Luther Universitaet Halle FB Chemie (Merseburg) IPC 06099 Halle email: nowak@chemie.uni-halle.de From khoroshun@terra.chem.emory.edu Tue Jul 7 21:49:54 1998 Received: from terra.chem.emory.edu (khoroshun@terra.chem.emory.edu [170.140.39.242]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id VAA09441 Tue, 7 Jul 1998 21:49:54 -0400 (EDT) Received: (from khoroshun@localhost) by terra.chem.emory.edu (8.7.5+2.6Wbeta6/3.4W3) id VAA11560; Tue, 7 Jul 1998 21:49:51 -0400 From: Dmitry Khoroshun Message-Id: <199807080149.VAA11560@terra.chem.emory.edu> Subject: Re: CCL:SUMMARY: DFT B3LYP/6-31+G(d,p) Convergence Problem To: mn1@helix.nih.gov (M. Nicklaus) Date: Tue, 7 Jul 1998 21:49:51 -0400 (EDT) Cc: chemistry@www.ccl.net In-Reply-To: <199806270019.UAA25588@helix.nih.gov> from "M. Nicklaus" at Jun 26, 98 08:19:48 pm Content-Type: text Hello! I am sorry I have a stupid question: > ================= Original Question (Tue, 9 Jun 1998) ================= > > After optimizing a structure (60 atoms, 37 non-H) at the HF/3-21G* level, > I'm trying to calculate a DFT single point energy at the B3LYP/6-31+G(d,p) > level, reading geometry and initial wave function from the checkpoint file. > > After nearly seven days (!) of CPU time on a very fast machine, the job > aborts without having converged, with the following end of the output file: > > [snip] > >>>>>>>>>> Convergence criterion not met. > SCF Done: E(RB+HF-LYP) = -34352969.2846 A.U. after 65 cycles Which molecule is that? I mean, for each non-H atom you have *million* Hartree? It very well may be a convergence, grid, cutoff, or computational strategy problem, but I would bet in any of this cases you will never get such an energy in any calculation no matter what and how. > Convg = 0.1924D-03 -V/T = ******* Considering the V/T ratio, I would guess your calculation has just crashed or something like that. Or you should immediately contact DOE for a huge grant waiting there for you. It is awesome many people get similar energies and fight them -- it must be a pleasure! Sincerely, Dmitry Khoroshun From greene@info.combichem.com Tue Jul 7 22:42:54 1998 Received: from info.combichem.com (leonardo.info.combichem.com [207.158.46.72]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with SMTP id WAA10080 Tue, 7 Jul 1998 22:42:52 -0400 (EDT) Received: from info.combichem.com by info.combichem.com via ESMTP (940816.SGI.8.6.9/940406.SGI) id TAA06345; Tue, 7 Jul 1998 19:52:58 -0700 Message-ID: <35A2DC15.EC2498DD@info.combichem.com> Date: Tue, 07 Jul 1998 19:40:21 -0700 From: Jonathan Greene X-Mailer: Mozilla 4.04 [en] (WinNT; I) MIME-Version: 1.0 To: chemistry@www.ccl.net Subject: Summary: Visualization of molecules and arbitrary geometric objects Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Below is the original posting, followed by (lightly edited) responses grouped by program. === Original posting ================================== We (and probably others!) are interested in a visualization tool as described below: 1. 3D graphics of quality similar to RasMol with interactive rotation, zoom, pan, etc. 2. Import and display multiple small molecules in various styles (tube, wireframe, etc.). 3. Import and display multiple geometric objects, such as triangulated meshes, iso-surfaces of a field, spheres of arbitrary radius, lines. These should be arbitrary data specified by the user, not something computed from the molecule by the tool itself. 4. Interactive selection of objects to control their color and turn their visibility on or off. 5. Interactive measurements, e.g. select two atoms and report distance between them. 6. Runs on PC under Windows. 7. Could be a stand-alone program that gets its input via files, or better yet a toolkit with an API to which we could pass the data. If you know of anything like this, please e-mail me. I will summarize responses for the list. Some of the things we've considered: WebLab, Rasmol: don't import arbitrary geometry. Chime 2.0: doesn't support interactive measurements, limited ability to import geometry. Insight, Midas, C2-SDK: limited to UNIX. Catalyst: cannot maintain alignment of multiple molecules when imported, geometry limited to spheres in hypotheses. Jonathan Greene, CombiChem, Inc. jgreene@combichem.com === CAChe =================================================== Date: Thu, 28 May 1998 15:14:38 -0800 From: Daniel Poole In response to your recent email, the product that fits your 3-D molecular visualation needs is a software package entitled CAChe: >1. 3D graphics of quality similar to RasMol with interactive rotation, >zoom, pan, etc. After building or importing a molecule, end-users can select, zoom in or out, rotate, translate, and scale any organic or inorganic chemical structure imagineable, containing any element. >2. Import and display multiple small molecules in various styles (tube, >wireframe, etc.). CAChe supports viewing and editing of structures from experimental crystallographic data or from standard databases such as MDL, Brookhaven Protein Databank, Cambridge Crystallographic, as well as SD and MOL files. CAChe has the ability to display molecules as simple line drawing, space filling CPK (Corey-Pauling-Kolton model), wire frame, ball & stick, ball & cylinder, and as partial charge and calculated bond order (atoms displayed as dotted or shaded spheres) in addition to choices for atom labeling, atom shape, atome color, etc. >3. Import and display multiple geometric objects, such as triangulated >meshes, iso-surfaces of a field, spheres of arbitrary radius, lines. >These should be arbitrary data specified by the user, not something >computed from the molecule by the tool itself. Choices such as size, shape, shading, ability to hide or show atoms, bonds & electrons of a cetain type, color palettes, labeling, isplay to text, lines, etc are just a sampling of the settings that can be adjusted and defined by the end-user. >4. Interactive selection of objects to control their color and turn >their visibility on or off. Yes, absolutely a feature. >5. Interactive measurements, e.g. select two atoms and report distance >between them. Yes, absolutely. >6. Runs on PC under Windows. Yes, Windows 95 or NT versions are available. Specs: 486-66 but Pentium recommended Windows 95 or NT 4.0 16 MB RAM but 32 MB recommended 100 MB HD space SVGA monitor WinSock compliant TCP/IP stack >7. Could be a stand-alone program that gets its input via files, or >better yet a toolkit with an API to which we could pass the data. CAChe is available as stand-alone, desktop tool, but can also be configured as a client-server, able to send out experimental calcuations to a server. Additional information, demo CDs, or a trial-use are all available to get a closer look at the CAChe software. >> We wish to display arbitrary geometry that we can specify superimposed on >> the molecules. You can draw "dummy" atoms, not part of your molecule, and set these up as specific shapes like squares or triangles etc. of defined sizes and shapes using geometry labels, to see if your molecule fits inside it. But I get the nagging feeling this is not what you're asking me. Dan Poole Oxford Molecular === ChemSymphony =============================================== Date: Fri, 22 May 1998 11:13:31 +0100 From: Adam Hodgkin ChemSymphony can do pretty much all that you are asking for and ChemSymphony Beans gives you access to the toolkit and the API's. Using the Beans you can do a LOT MORE than you are asking for. Check out our www site: http://www.cherwell.com/chemsymphony/index.html Note that we offer both (1) a free LITE applet; (2) a suite of applets -- ChemSymphony Pro (JDK 1.0); and (3) ChemSymphony Beans which will be of primary interest if you are willing to do your own software development for an intranet etc (requires JDK 1.1). Below I give some url's which take you straight to examples of the functions you seek. Our support of geometric objects is via the chemistry file formats which ChemSymphony takes as input (Sneddon edited some PDB files); but we note the suggestion that direct support of geometric objects would be a nice feature. >1. 3D graphics of quality similar to RasMol with interactive rotation, >zoom, pan, etc. lots of examples eg http://www.cherwell.com/chemsymphony/example8.html >2. Import and display multiple small molecules in various styles (tube, >wireframe, etc.). http://www.cherwell.com/chemsymphony/example3.html >3. Import and display multiple geometric objects, such as triangulated >meshes, iso-surfaces of a field, spheres of arbitrary radius, lines. >These should be arbitrary data specified by the user, not something >computed from the molecule by the tool itself. http://www.sas.upenn.edu/~carrollp/sneddon.html >4. Interactive selection of objects to control their color and turn >their visibility on or off. This is more customisable with ChemSymphony Beans >5. Interactive measurements, e.g. select two atoms and report distance >between them. See (select angles, bond lengths etc and collect a list): http://www.sas.upenn.edu/~carrollp/jo.html or http://www.cherwell.com/chemsymphony/sulfanil2.html >6. Runs on PC under Windows. And Unix and Mac and any system with suitable Java. >7. Could be a stand-alone program that gets its input via files, or >better yet a toolkit with an API to which we could pass the data. http://www.cherwell.com/chemsymphony/ChemSymphonyBeans/CSBeansUse/CSBeansIntro.html Our white paper gives explanations and examples of how the Beans can be used to construct intranet solutions Adam Hodgkin | e-mail: adam@cherwell.com Chairman | Phone: +44 (0)1865 784810 Cherwell Scientific Publishing | Fax: +44 (0)1865 784801 Oxford OX4 4GA, UK | URL: http://www.cherwell.com === DataExplorer ================================================ Date: Thu, 21 May 1998 17:07:16 -0500 (CDT) From: "Fred P. Arnold" If you're willing to massage your data a bit (such as recast it into HDF format), the obvious answer would seem to be DataExplorer from IBM. www.almaden.ibm.com/dx. I used it in conjunction with a solid-state band code to visualize unit-cells, atoms, and electron densities in a variety of formats. -fred Frederick P. Arnold, Jr. "...But if you give theorists enough Advanced Research Systems time, they can predict anything." 5640 S. Ellis Ave Dr. M. S. Turner, U. Chicago. Chicago, IL 60637 === ICM ===================================================== Date: Fri, 22 May 1998 10:43:51 -0500 From: Info We have a program which satisfies to all your criteria and is used in pharmaceutical companies and academia now for 6 years. The program is ICM and is distributed by Molsoft, LLC. >1. 3D graphics of quality similar to RasMol with interactive rotation, >zoom, pan, etc. High quality, representations include wire (+chemical representations), ball, stick, surface, molecular surface (both solid and mesh), cpk, depth queing, side by side and hardware stereo, clipping planes. >2. Import and display multiple small molecules in various styles (tube, >wireframe, etc.). Import of pdb, mol, mol2, csd >3. Import and display multiple geometric objects, such as triangulated >meshes, iso-surfaces of a field, spheres of arbitrary radius, lines. >These should be arbitrary data specified by the user, not something >computed from the molecule by the tool itself. Import any geometrical object of dots and/or lines and/or triangles in the wavefront format or the ICM easy text format Functions in ICM to create such objects, interactive editing of these objects >4. Interactive selection of objects to control their color and turn >their visibility on or off. Flexible selections, display, undisplay, color etc. command Interactive selections. >5. Interactive measurements, e.g. select two atoms and report distance >between them. Yes >6. Runs on PC under Windows. Runs on PC under Windows (as well as under LINUX, DEC, SGI) >7. Could be a stand-alone program that gets its input via files, or >better yet a toolkit with an API to which we could pass the data. Can be a stand alone program or read from a pipe and quit Molsoft L.L.C. P.O.Box 113 Metuchen NJ 08840 fax 732-321-4180 tel 732-321-8690 e-mail info@molsoft.com http://www.molsoft.com === MacroModel ================================================= Date: Thu, 21 May 1998 16:40:33 -0400 From: "Peter Shenkin" Our new MacroModel interface will do all these things, I think, but won't be ready for some months. Date: Fri, 22 May 1998 13:46:22 -0400 From: "Peter Shenkin" I spoke too soon. Arbitrary geometric objects will be included in a later revision, not in our first release, sorry. Also, it will run on NT, but probably not vanilla Windows. * Peter S. Shenkin; Chemistry, Columbia U.; 3000 Broadway, Mail Code 3153 * ** NY, NY 10027; shenkin@columbia.edu; (212)854-5143; FAX: 678-9039 *** *MacroModel WWW page: http://www.columbia.edu/cu/chemistry/mmod/mmod.html * === Sculpt ======================================================= Date: Thu, 21 May 1998 14:25:22 -0700 From: Dan Haun Allow me to add one more variability. You're interested in an interactive visualization tool and you had tried Chime 2.0 with limitations on not having the capabilities to measure between atoms as well as limitations in geometries. I'd like to introduce you to SCULPT which has the capabilities of hot linking with Chime 2.0 and does allow you to measure distances and torsion angles. It won't however pass the test for all of the geometry requirements; it does allow you exhibit mutiple small molecules, it does allow you to have rendering options such as tubes, wire frames, and CPK spheres; it does not allow one to alter colors of atoms o nor does it highlight. It also runs on the PC for Windows95/NT, PowermAcs and SGIs', and allows one to copy and paste from ISIS draw, ChemBuilder3D, Chem3D and ChemWindows. It also allows one to overlay mutiple structures for confirmational analyses. If you are interested or know others who are working with organic structures, I would invite you to try SCULPT http://www.intsim.com. Daniel P. Haun Tel: (619) 658-9462 Interactive Simulations Inc. Toll Free: (888) 272-8578 5330 Carroll Canyon Rd. Email: haun@intsim.com San Diego, CA 92121 Fax: (619) 658-9463 Web site http://www.intsim.com === Tinker ====================================================== Date: Thu, 21 May 1998 14:59:54 -0700 From: guo here it is: http://dasher.wustl.edu/tinker/ === VMD ======================================================= Date: Fri, 22 May 1998 17:59:00 +0400 (MSD) From: Eugene Leitl > 1. 3D graphics of quality similar to RasMol with interactive rotation, > zoom, pan, etc. VMD does nicely. > 2. Import and display multiple small molecules in various styles (tube, > wireframe, etc.). VMD does that also. > 3. Import and display multiple geometric objects, such as triangulated > meshes, iso-surfaces of a field, spheres of arbitrary radius, lines. > These should be arbitrary data specified by the user, not something > computed from the molecule by the tool itself. Err, you would have to tweak the sources to do that. Tcl scripts may suffice, but I doubt that. > 4. Interactive selection of objects to control their color and turn > their visibility on or off. Tcl scripts. > 5. Interactive measurements, e.g. select two atoms and report distance > between them. Should do. > 6. Runs on PC under Windows. Why would one cripple himself deliberately? Windows as a computational/viz platform is doomed anyway. Have you considered installing Linux/Win95 as a dual-boot on that PC? Date: Thu, 21 May 1998 19:45:18 -0500 From: "Sergei Izrailev" I guess, running on Windows is one of your main requirements, and it is not met yet. The Windows port is under way, but it'll take several months to complete. VMD thus falls into the same category as Insight, Midas, C2-SDK: limited to UNIX. I would like to emphasize that VMD is a free program distributed with the source code written in C++, so you can adapt it for your needs. Please take a look at VMD web page http://www.ks.uiuic.edu/Research/vmd/ I'll go through the rest of the list. > 1. 3D graphics of quality similar to RasMol with interactive rotation, > zoom, pan, etc. Yes. > 2. Import and display multiple small molecules in various styles (tube, > wireframe, etc.). Yes. Actually, VMD can also display large molecules (such as proteins and DNA). > 3. Import and display multiple geometric objects, such as triangulated > meshes, iso-surfaces of a field, spheres of arbitrary radius, lines. > These should be arbitrary data specified by the user, not something > computed from the molecule by the tool itself. First of all, yes, VMD can draw user-provided geometrical objects through its powerful and easy to learn Tcl based scripting language. Importing of triangulated meshes and iso-surfaces can be added with relatively little effort through the Tcl interface. For the import to be fast, of course, some source code modifications may be needed. > 4. Interactive selection of objects to control their color and turn > their visibility on or off. Yes, through very easy to use interface. > 5. Interactive measurements, e.g. select two atoms and report distance > between them. Yes. > 6. Runs on PC under Windows. As I mentioned earlier, we are working on porting VMD to Windows, but it'll take some time. > 7. Could be a stand-alone program that gets its input via files, or > better yet a toolkit with an API to which we could pass the data. It's a stand-alone program, which uses several external programs for various purposes, including import/export of files and calculation of surfaces. Adding another interface should not be a problem with the source code provided. Please write to vmd@ks.uiuc.edu if you have further questions. Sincerely, Sergei Izrailev === gOpenMol =================================================== Date: Sat, 23 May 1998 18:39:08 +0300 (EET DST) From: Leif Laaksonen Please have a look at gOpenMol (http://laaksonen.csc.fi/gopenmol/). It's a very flexible program you can extend by writing more Tcl/Tk code or you can write extensions using the dynamic loading feature. Yes you can import arbitrary spheres and you can tilt them (like eggs), lines, cylinders, arrows. However, you can not import triangulated meshes or iso-surfaces. I'm currently implementing that. Later there will be a Tcl command to save or load the triangulated meshes. If you mean by interactive the possibility to "pick" atoms the answer is no. However, you can measure lenghts, angles, torsions by writing in the atom name or number. You can also follow the variation of the property through a trajectory. The picking is a bit tricky because the GUI is pure Tcl/Tk that talks to gOpenMol and not the other way around. Center for Scientific Computing | Phone: 358 9 4572378 P.O. Box 405 | Mobile: 358 400425203 FIN-02101 Espoo | Telefax: 358 9 4572302 FINLAND | Mail: Leif.Laaksonen@csc.fi URL: http://laaksonen.csc.fi/leif.laaksonen.html