From chemistry-request@server.ccl.net Mon Mar 13 04:02:11 2000 Received: from xena.oai.co.uk (xena.oai.co.uk [195.172.92.249]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id EAA11202 for ; Mon, 13 Mar 2000 04:02:11 -0500 Received: by XENA with Internet Mail Service (5.5.2448.0) id <1X2B4HC5>; Mon, 13 Mar 2000 09:02:01 -0000 Message-ID: <73FCD39B2473D211A43E00A0C9EA66A60140ECD6@XENA> From: "Charlton, Michael" To: "'chemistry@ccl.net'" Subject: DFT on mips processors Date: Mon, 13 Mar 2000 09:02:00 -0000 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2448.0) Content-Type: text/plain; charset="iso-8859-1" Hi, does anyone have any idea of the relative performance of R10k (180MHz) vs R12k (300MHz) for DFT calculations ? Thanks, Michael Charlton. mcharlton@oai.co.uk From chemistry-request@server.ccl.net Mon Mar 13 06:35:49 2000 Received: from qorws1.uab.es (qorws1.uab.es [158.109.12.1]) by server.ccl.net (8.8.7/8.8.7) with SMTP id GAA11776 for ; Mon, 13 Mar 2000 06:35:36 -0500 Received: by qorws1.uab.es (940816.SGI.8.6.9/930416.SGI) for chemistry@ccl.net id MAA14427; Mon, 13 Mar 2000 12:35:43 -0800 From: "Pascal Bonnet" Message-Id: <10003131235.ZM14425@qorws1.uab.es> Date: Mon, 13 Mar 2000 12:35:42 -0800 X-Mailer: Z-Mail (3.2.2 10apr95 MediaMail) To: chemistry@ccl.net Subject: Pd parameters Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Hi, Could anyone give me the Pd parameters for a Molecular Mechanics study (MM3) or/and for a Semi empirical study (AM1)? or where can I find them in the web? The molecule has two N-R2 coordinated to PdCl2. Thanks in advance. -- ******************************************************************************** Pascal Bonnet pascal@qorws1.uab.es Unitat Quimica Organica and Institut de Chimie Organique et Analytique Facultat de Ciences UFR Sciences - UPRES-A 6005 Universitat Autonoma de Barcelona Rue de Chartres - BP 6759 08193 Bellaterra (SPAIN) 45067 ORLEANS CEDEX 2 - France Tel: 34935811266 Tel: 0238494577 Fax: 34935811265 ******************************************************************************** From chemistry-request@server.ccl.net Mon Mar 13 07:30:54 2000 Received: from mailrelay2.lrz-muenchen.de (mailrelay2.lrz-muenchen.de [129.187.254.102]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id HAA12889 for ; Mon, 13 Mar 2000 07:30:53 -0500 Received: from ruppert.phys.chemie.tu-muenchen.de by mailrelay2.lrz-muenchen.de for @mailout.lrz-muenchen.de:chemistry@ccl.net; Mon, 13 Mar 2000 13:30:42 +0100 Received: from physik.tu-muenchen.de by ruppert.phys.chemie.tu-muenchen.de via ESMTP (940816.SGI.8.6.9/930416.SGI) for id NAA04725; Mon, 13 Mar 2000 13:30:28 +0100 Sender: tmehnert@physik.tu-muenchen.de Message-Id: <38CCDF5E.59C4C462@physik.tu-muenchen.de> Date: Mon, 13 Mar 2000 13:30:23 +0100 From: Mehnert Thomas X-Mailer: Mozilla 4.04 [en] (X11; I; IRIX 5.3 IP22) MIME-Version: 1.0 To: "'chemistry@ccl.net'" Subject: Resign from CCL Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi, I would like to resign from the CCL. Please arrange that I will not get any longer any kind of e-mails from the CCL. Thanks in advance Thomas Mehnert From chemistry-request@server.ccl.net Mon Mar 13 09:30:27 2000 Received: from ucidoor.unitedcatalysts.com ([208.23.162.2]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id JAA13397 for ; Mon, 13 Mar 2000 09:30:26 -0500 Received: by ucidoor.unitedcatalysts.com; (8.8.8/1.3/10May95) id JAA07928; Mon, 13 Mar 2000 09:33:36 -0500 (EST) Received: from 10.1.0.50 by ucismtp02.unitedcatalysts.com (InterScan E-Mail VirusWall NT); Mon, 13 Mar 2000 09:30:36 -0500 (Eastern Standard Time) Received: from lvlxch01.unitedcatalysts.com ([10.1.0.88]) by lvlmail.unitedcatalysts.com (PMDF V5.2-32 #33820) with ESMTP id <0FRD00AD572IHZ@lvlmail.unitedcatalysts.com> for chemistry@ccl.net; Mon, 13 Mar 2000 09:32:42 -0500 (EST) Received: by lvlxch01.unitedcatalysts.com with Internet Mail Service (5.5.2650.21) id ; Mon, 13 Mar 2000 09:29:18 -0500 Content-return: allowed Date: Mon, 13 Mar 2000 09:29:09 -0500 From: "Shobe, Dave" Subject: Re: CCL:pgplot for Salford FTN95 To: "'CCL'" Message-id: <157A51F55AAAD3119CD70008C7B1629D03E421@lvlxch01.unitedcatalysts.com> MIME-version: 1.0 X-Mailer: Internet Mail Service (5.5.2650.21) Content-type: text/plain; charset="iso-8859-1" More on my problems with pgplot and Salford FTN95: The two files that give errors are grdos.f and w9driv.f. According to the comments in the program, MSFLIB is a graphics library. Salford has a "run-time library" but there don't seem to be any graphics routines in it. --David Shobe From chemistry-request@server.ccl.net Mon Mar 13 10:57:27 2000 Received: from kasei.materials.ox.ac.uk (kasei.materials.ox.ac.uk [163.1.64.46]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id KAA13848 for ; Mon, 13 Mar 2000 10:57:27 -0500 Received: from localhost (hfield@localhost) by kasei.materials.ox.ac.uk (8.9.3/8.9.3) with ESMTP id PAA15974 for ; Mon, 13 Mar 2000 15:59:38 GMT X-Authentication-Warning: kasei.materials.ox.ac.uk: hfield owned process doing -bs Date: Mon, 13 Mar 2000 15:59:38 +0000 (GMT) From: Andrew Horsfield X-Sender: hfield@kasei.materials.ox.ac.uk Reply-To: Andrew Horsfield To: Computational Chemistry List Subject: Gradient Corrections Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi, I am thinking about adding gradient corrections to a density functional code that works with numerical atomic type orbitals. Given that there are a number of functionals in the literature, I would welcome suggestions of where to start. Note that I cannot include any exact exchange since it is too expensive to evaluate the integrals with numerical orbitals. In particular, questions that come to mind are: 1) Is exchange better described by gradient corrections than correlation (i.e. would implementing just Becke exchange be a worthwhile move)? 2) Is the correct choice of functional very problem dependent? Is there one choice that gives better *overall* results than the others? 3) Are there other methodologies for improving on LDA besides gradient corrections? If so, what (dis)advantages do they have? Cheers, Andrew +----------------------------------------------------+ Andrew Horsfield e-mail: horsfield@fecit.co.uk FECIT, 2 Longwalk Road, Stockley Park, Uxbridge, Middlesex UB11 1AB, United Kingdom. phone: +44-(0)181-606-4653 FAX: +44-(0)181-606-4422 +----------------------------------------------------+ From chemistry-request@server.ccl.net Mon Mar 13 11:02:37 2000 Received: from deliverator.sgi.com (deliverator.sgi.com [204.94.214.10]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id LAA13888 for ; Mon, 13 Mar 2000 11:02:37 -0500 Received: from nodin.corp.sgi.com (fddi-nodin.corp.sgi.com [198.29.75.193]) by deliverator.sgi.com (980309.SGI.8.8.8-aspam-6.2/980310.SGI-aspam) via ESMTP id HAA24519; Mon, 13 Mar 2000 07:57:15 -0800 (PST) mail_from (omar@sgi.com) Received: from arkham.hudson.sgi.com (arkham.hudson.sgi.com [169.238.41.21]) by nodin.corp.sgi.com (980427.SGI.8.8.8/980728.SGI.AUTOCF) via ESMTP id IAA41776; Mon, 13 Mar 2000 08:01:20 -0800 (PST) Received: from localhost (omar@localhost) by arkham.hudson.sgi.com (SGI-SGI-8.9.3/8.9.3) with SMTP id LAA55077; Mon, 13 Mar 2000 11:01:09 -0500 (EST) X-Authentication-Warning: arkham.hudson.sgi.com: omar owned process doing -bs Date: Mon, 13 Mar 2000 11:01:08 -0500 (EST) From: Omar Stradella X-Sender: omar@arkham.hudson.sgi.com Reply-To: Omar Stradella To: Wang Xiaogang cc: ccl , Omar Stradella Subject: Re: CCL:large array, fortran 90, SGI compiler In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII On Fri, 10 Mar 2000, Wang Xiaogang wrote: > Dear CCLers, > > The question is about how to handle large array in fortran 90. > > An example: > > program > real*8 a(10000,10000) ! an 800MB array > common /test/a > end > > However on one SGI origin2000, MIPSpro Fortran 90 Version 7.3, > the compiling fails. > > On another SGI origin2000, Ragnarok Compilers: Version 6.2, > the compiling passes. > It also passes on DEC Alpha with Digital f90 compiler. > > It seems that the SGI f90 compiler (version 7.3) puts the common block > data to the stack segment instead of data segment. The error message > is 'exceeds 268,435,455 bytes, the maximum storage size available' > > Any hints? Thanks. > > Xiaogang Xiaogang, This is not related to stack vs data segment allocation. All common blocks are allocated in the data segment. The problem here is a limitation in the current f90 to statically allocate any array that exceeds 256 MB when you compile with -n32. The workarounds are to compile with -64 if possible (i.e. you are not planning to run on 32-bit kernels) or to use dynamic allocation. The 6.2 f90 didn't have that problem because it was a different compiler. Omar. +---------------------------------------------------------------------+ Omar G. Stradella, Ph.D. SGI / Chemistry and Biology Applications Group 1 Cabot Rd, Suite 250, Hudson, MA 01749, USA N 42 22'40" W 71 33'44" E-mail: omar@sgi.com Phone: +1-781-839-2258 FAX: +1-978-562-7450 http://www.sgi.com/chembio http://reality.sgi.com/omar +-------- Ph-nglui mglw'nafh Cthulhu R'lyeh wgah'nagl fhtagn -------+ From chemistry-request@server.ccl.net Mon Mar 13 11:10:37 2000 Received: from mtiwmhc27.worldnet.att.net (mtiwmhc27.worldnet.att.net [204.127.131.52]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id LAA14018 for ; Mon, 13 Mar 2000 11:10:37 -0500 Received: from dell ([12.73.134.68]) by mtiwmhc27.worldnet.att.net (InterMail vM.4.01.02.31a 201-229-119-114) with SMTP id <20000313161019.TGJR24363.mtiwmhc27.worldnet.att.net@dell>; Mon, 13 Mar 2000 16:10:19 +0000 Message-Id: <3.0.6.32.20000313080654.00987240@postoffice.worldnet.att.net> X-Sender: davidgallagher@postoffice.worldnet.att.net (Unverified) X-Mailer: QUALCOMM Windows Eudora Light Version 3.0.6 (32) Date: Mon, 13 Mar 2000 08:06:54 -0800 To: "Risser, Steven M" From: David Gallagher Subject: Re: Solid state themodynamics Cc: "'CHEMISTRY@ccl.net'" In-Reply-To: <8D6D98F05334D1118BE600A0C96E9612023AEFA6@ns-bco-mse4.im.ba ttelle.org> Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Steve, The latest version of MOPAC 2000 has 3D periodic boundary conditions for handling solids. The author, Jimmy Stewart, has reported comparable accuracies to PM3 in the gas phase when calculating thermodynamic properties of solids during his limited testing to date. MOPAC 2000 also has d-orbital parameters for some transition metals. There is more information in the MOPAC 2000 User manual on-line at http://www.schrodinger.com/mopac2.html Hope this helps, David Gallagher Fujitsu At 08:15 AM 1/5/00 -0500, Risser, Steven M wrote: >Hi all, > >I am interested in calculating the tyhermodynamic properties (particularly >heat capacity) of a solid. I would appreciate any suggestions on methods, >useful software, etc... I am already familiar with the standard methods of >deriving the molecular thermo properties from molecules, and was hoping for >a similar approach for solids. > >Thanks in advance >Steve > > >****************************************************** >Dr. Steven M. Risser >Principal Research Scientist >Core Technology >Battelle Memorial Institute >rissers@battelle.org >614-424-3715 614-424-7479 (FAX) >****************************************************** > > >-= 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 Mon Mar 13 11:26:36 2000 Received: from wavefun.com ([216.217.70.2]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id LAA14265 for ; Mon, 13 Mar 2000 11:26:36 -0500 From: yu@wavefun.com Date: Mon, 13 Mar 2000 08:33:22 -0800 Message-Id: <10003130833.ZM1937@wavefun.com > In-Reply-To: "Pascal Bonnet" "CCL:Pd parameters" (Mar 13, 12:35pm) References: <10003131235.ZM14425@qorws1.uab.es> X-Mailer: Z-Mail-SGI (3.2S.3 08feb96 MediaMail) To: "Pascal Bonnet" Subject: Re: CCL:Pd parameters Cc: CHEMISTRY@ccl.net Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii On Mar 13, 12:35pm, Pascal Bonnet wrote: > Subject: CCL:Pd parameters > Hi, > > Could anyone give me the Pd parameters for a Molecular Mechanics study (MM3) > or/and for a Semi empirical study (AM1)? or where can I find them in the web? > > The molecule has two N-R2 coordinated to PdCl2. > Wavefunction has developed the PM3 parameters of Pd (and other 20 transition metals). To just get the parameters, you can visit our FTP site. If you like to use SPARTAN, Wavefunction's chemical modeling package, please contact sales@wavefun.com Jianguo Yu -- +-----------------------+------------------+-------------------------+ |Jianguo Yu, Ph.D. | ______________ | E-Mail: yu@wavefun.com | |Computational Chemist | \ _________ / | Phone: (949)955-2120 | |Wavefunction Inc. | \ \\\\\\\\/ | Fax: (949)955-2118 | |18401 Von Karman | \ \\\\\/ | "The doctrines observe | |Suite 370 | \ \\/ | nature" | |Irvine, CA 92612 | \/ | Lao-tzu (604-531 B.C.)| +----------------------http://www.wavefun.com------------------------+ From chemistry-request@server.ccl.net Mon Mar 13 12:15:11 2000 Received: from mailhost.msi.com (fire.msi.com [146.202.0.242]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id MAA14568 for ; Mon, 13 Mar 2000 12:15:10 -0500 Received: (from daemon@localhost) by mailhost.msi.com (980427.SGI.8.8.8/970903.SGI.AUTOCF) id JAA07989; Mon, 13 Mar 2000 09:12:50 -0800 (PST) Message-Id: <200003131712.JAA07989@mailhost.msi.com> Received: from osman-pc.msi.com(146.202.7.202) by mailhost via smap (V2.0) id xma007985; Mon, 13 Mar 00 09:12:27 -0800 X-Sender: osman@146.202.6.217 X-Mailer: QUALCOMM Windows Eudora Pro Version 4.0.1 Date: Mon, 13 Mar 2000 09:12:19 -0800 To: CHEMISTRY@ccl.net, CHMINF-L@LISTSERV.INDIANA.EDU, owner-qsar_society@unil.ch From: "Osman F. Guner" Subject: First book on Pharmacophores is out Mime-Version: 1.0 Content-Type: multipart/alternative; types="text/plain,text/html"; boundary="=====================_8604898==_.ALT" --=====================_8604898==_.ALT Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable The book entitiled "Pharmacophore Perception, Development, and Use in Drug Design" has been released . It should appear in Barnes & Noble and Amazon sites shortly. Meanwhile you can contact the publisher for a copy at info@iul-press.com=20 Below is the Table of Contents... Preface O.F.G=FCner Part I: The Origins of Pharmacophore Research 1. Evolution of the Pharmacophore Concept in Pharmaceutical Research P.Gund Part II: Analog-Based Pharmacophores 2. Manual Pharmacophore Generation: Visual Pattern Recognition O.F.G=FCner 3. Pharmacophore Definition Using the Active Analog Approach D.D.Beusen, G.R.Marshall Automated Pharmacophore Development Systems 4. DISCO: What We Did Right and What We Missed Y.C.Martin 5. HipHop: Pharmacophores Based on Multiple Common-Feature Alignments O.A.Clement, A.T.Mehl 6. GASP: Genetic Algorithm Superposition Program G.Jones, P.Willett,= R.C.Glen 7. Exploring Pharmacophores with Chem-X S.J.Cato Predictive Model Development - 3D QSAR 8. Apex-3D: Activity Prediction Expert System with 3D QSAR E.R.Vorpagel, V.E.Golander 9. Pharmacophore Models and Comparative Molecular Field Analysis (CoMFA) R.D.Clark, J.M.Leonard, A.Strizhev=20 10. HypoGen: An Automated System for Generating Predictive 3D Pharmacophore Models H.Li, J.M.Sutter, R.Hoffmann Applications in Drug Design 11. Metric for Analyzing Hit Lists and Pharmacophores O.F.G=FCner, D.R.Henry 12. Strategies in Database Mining and Pharmacophore Development O.F.G=FCner, M.Waldman, R.Hoffmann, J-H.Kim 13. Pharmacophore Modeling by Automated Methods: Possibilities and= Limitations M.Langg=E5rd, B.Bj=F8rnholm, K.Gundertofte 14. Database Mining Using Pharmacophore Models to Discover Novel Structural Prototypes J.J.Kaminski, D.F.Rane, M.L.Rothofsky 15. Predicting Drug-Drug Interactions in Silico using Pharmacophores: A Paradigm for the Next Millenium S.Ekins, B.J.Ring, G.Bravi, J.H.Wikel, S.A.Wrighton= =20 16. Feature-Based Pharmacophores: Applications to Some Biological Systems R.Hoffmann, H.Li, T.Langer 17. The Design and Pharmacophore Definition of Retinoid-X-Receptor Specific Ligands S.K.White Part III: Receptor-Based Pharmacophores 18. Receptor-based Pharmacophore Perception and Modeling C.M.Venkatachalam, P.Kirchhoff, M.Waldman 19. Pharmacophore-Based Molecular Docking B.E.ThomasIV, D.Joseph-McCarthy, J.C.Alvarez Applications in Drug Design 20. The Use of Multiple Excluded Volumes Derived from X-Ray Crystallographic Structures in 3D Database Searching and 3D-QSAR M.Gillner, P.Greenidge 21. Docking-Derived Pharmacophores from Models of Receptor-Ligand Complexes R.Griffith, J.B.Bremner, B.Coban 22. Technique for Developing a Pharmacophore Model That Accommodates= Inherent Protein Flexibility: An Application to HIV-1 Integrase K.M.Masukawa, H.A.Carlson, J.A.McCammon Part IV: New Algorithms in Pharmacophore Development 23. Pharmacophores Derived from the 3D Substructure Perception S.Handshuh, J.Gasteiger 24. The Electron-Conformational Method of Identification of Pharmacophore= and Anti-Pharmacophore Shielding I.B.Bersuker, S.Bahceci, J.E.Boggs 25. Development and Optimization of Property-Based Pharmacophores= A.G.Ozkabak, M.A.Miller, D.R.Henry, O.F.G=FCner 26. Effect of Variable Weights and Tolerances on Predictive Model Generation J.M.Sutter, O.F.G=FCner, R.Hoffmann, M.Waldman Part V: The Future of Pharmacophore Research 27. Future Directions in Pharmacophore Discovery J.H.VanDrie --- Osman F. G=FCner, Ph.D. Director, Lead Identification & Optimization Molecular Simulations Inc. (858) 799-5341 osman@msi.com http://www.msi.com=20 --=====================_8604898==_.ALT Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable The book entitiled "Pharmacophore Perception, Development, and Use in Drug Design" has been released .  It should appear in Barnes & Noble and Amazon sites shortly.  Meanwhile you can contact the publisher for a copy at info@iul-press.com

Below is the Table of Contents...

Preface O.F.G=FCner
Part I: The Origins of Pharmacophore Research
1. Evolution of the Pharmacophore Concept in Pharmaceutical Research P.Gund
Part II: Analog-Based Pharmacophores
2. Manual Pharmacophore Generation: Visual Pattern Recognition=20 O.F.G=FCner
3. Pharmacophore Definition Using the Active Analog Approach D.D.Beusen, G.R.Marshall
Automated Pharmacophore Development Systems
4. DISCO: What We Did Right and Wha= t We Missed Y.C.Martin
5. HipHop: Pharmacophores Based on Multiple Common-Feature Alignments O.A.Clement, A.T.Mehl
6. GASP: Genetic Algorithm Superpositio= n Program G.Jones, P.Willett,=20 R.C.Glen
7. Exploring Pharmacophores with Chem-X S.J.Cato
Predictive Model Development - 3D QSAR
8. Apex-3D: Activity Prediction Expert System with 3D QSAR E.R.Vorpagel, V.E.Golander
9. Pharmacophore Models and Comparative Molecular Field Analysis (CoMFA) R.D.Clark, J.M.Leonard, A.Strizhev
10. HypoGen: An Automated System for Generating Predictive 3D  Pharmacophore Models H.Li, J.M.Sutter, R.Hoffmann
Applications in Drug Design
11. Metric for Analyzing Hit Lists and Pharmacophores O.F.G=FCner, D.R.Henry
12. Strategies in Database Mining and Pharmacophore Development O.F.G=FCner, M.Waldman, R.Hoffmann, J-H.Kim
13. Pharmacophore Modeling by Automated Methods: Possibilities and Limitations M.Langg=E5rd, B.Bj=F8rnholm, K.Gundertofte
= 14. Database Mining Using Pharmacophore Models to Discover Novel Structural Prototypes J.J.Kaminski, D.F.Rane, M.L.Rothofsky
15. Predictin= g Drug-Drug Interactions in Silico using Pharmacophores: A Paradigm for the Next Millenium S.Ekins, B.J.Ring= , G.Bravi, J.H.Wikel, S.A.Wrighton
16. Feature-Based Pharmacophores: Applications to Some Biological Systems R.Hoffmann, H.Li, T.Langer
17. The Design and Pharmacophore Definition of Retinoid-X-Receptor Specific Ligands S.K.White
Part III: Receptor-Based Pharmacophores
18. Receptor-based Pharmacophore Perception and Modeling C.M.Venkatachalam, P.Kirchhoff, M.Waldman
19. Pharmacophore-Based Molecular Docking B.E.ThomasIV, D.Joseph-McCarthy, J.C.Alvarez
Applications in Drug Design
20. The Use of Multiple Excluded Volumes Derived from X-Ray Crystallographic Structures in 3D Database Searching and 3D-QSAR M.Gillner, P.Greenidge
21. Docking-Derived Pharmacophores from Models of Receptor-Ligand Complexes R.Griffith, J.B.Bremner, B.Coban
22. Technique for Developing a Pharmacophore Model That Accommodates Inherent Protein Flexibility: An Application to HIV-1 Integrase K.M.Masukawa, H.A.Carlson, J.A.McCammon
Part IV: New Algorithms in Pharmacophore Development
23. Pharmacophores Derived from the 3D Substructure Perception S.Handshuh, J.Gasteiger
24. The Electron-Conformational Method of Identification of Pharmacophore and Anti-Pharmacophore Shielding I.B.Bersuker, S.Bahceci,  J.E.Boggs
25. Development and Optimization of Property-Based Pharmacophores A.G.Ozkabak, M.A.Miller, D.R.Henry, O.F.G=FCner
26. Effect of Variable Weights and Tolerances on Predictive Model Generation J.M.Sutter, O.F.G=FCner, R.Hoffmann, M.Waldman
Part V: The Future of Pharmacophore Research
27. Future Directions in Pharmacophore Discovery J.H.VanDrie

---
Osman F. Güner, Ph.D.
Director,  Lead Identification & Optimization
Molecular Simulations Inc.   (858) 799-5341
osman@msi.com        http://www.msi.com --=====================_8604898==_.ALT-- From chemistry-request@server.ccl.net Mon Mar 13 11:38:18 2000 Received: from coyote.iupui.edu (coyote.iupui.edu [134.68.220.82]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id LAA14350 for ; Mon, 13 Mar 2000 11:38:17 -0500 Received: from macgw.chem.iupui.edu (macgw.chem.iupui.edu [134.68.137.71]) by coyote.iupui.edu (8.9.3/8.9.3/1.2IUPUIPO) with SMTP id LAA30153; Mon, 13 Mar 2000 11:36:12 -0500 (EST) Message-ID: Date: 13 Mar 2000 11:47:50 -0500 From: "Boyd" Subject: re: Pd parameters To: "Bonnet, Pascal" , "OSC CCL" X-Mailer: Mail*Link SMTP for Quarterdeck Mail; Version 4.1.0 Hi Pascal, You can find references for molecular mechanics parameters for Pd in Ken Lipkowitz's appendix to Vol. 14 of Reviews in Computational Chemistry. Thanks, Don Donald B. Boyd, Ph.D. Editor, Reviews in Computational Chemistry http://chem.iupui.edu/rcc/rcc.html Editor, Journal of Molecular Graphics and Modelling (publication of the ACS COMP division and MGMS) http://chem.iupui.edu/~boyd/jmgm.html Department of Chemistry Indiana University-Purdue University at Indianapolis 402 North Blackford Street Indianapolis, Indiana 46202-3274, U.S.A. Telephone 317-274-6891, FAX 317-274-4701 E-mail boyd@chem.iupui.edu From chemistry-request@server.ccl.net Mon Mar 13 14:19:31 2000 Received: from ns.mnc.md (root@ns.mnc.md [212.0.192.2]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id OAA15461 for ; Mon, 13 Mar 2000 14:19:29 -0500 Received: from 212.0.193.178 ([212.0.193.178]) by ns.mnc.md (8.8.7/8.8.7) with ESMTP id VAA32127 for ; Mon, 13 Mar 2000 21:19:12 +0200 Date: Mon, 13 Mar 2000 21:05:08 +0200 From: Mike Peleah X-Mailer: The Bat! (v1.41) Reply-To: Mike Peleah X-Priority: 3 (Normal) Message-ID: <3878.000313@mnc.md> To: chemistry@ccl.net Subject: =?koi8-r?B?T3NjaWxsYXRvciBTdHJlbmd0aCB2cyBllTEwXi00?= Mime-Version: 1.0 Content-Type: text/plain; charset=koi8-r Content-Transfer-Encoding: 8bit +======================---------------- --- -- - - - - . | Dear chemistry, : . I calculate electronic spectrum and obtain results in such form (I use INDO/1s implemetation in ArgusLab 1.0): -----------------[ cut ]---------------------------------------------- 4 ( 1)->( 4) Energy 26939.9 State Dipole 1.6582 Oscillator Strength length 0.0074 -----------------[ cut ]---------------------------------------------- I would like to know if I could compare this Oscillator Strength results with experimental epsilon x 10^-4 intensity value. Thanks. Best regards, Mike mailto:mike@mnc.md . : | . - - - - -- --- ----------------======================+ From chemistry-request@server.ccl.net Mon Mar 13 17:27:24 2000 Received: from mercury.chem.csiro.au (mercury.chem.CSIRO.AU [138.194.50.8]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id RAA16254 for ; Mon, 13 Mar 2000 17:27:20 -0500 Received: from [138.194.53.105] (mac-53105.chem.CSIRO.AU [138.194.53.105]) by mercury.chem.csiro.au (8.9.3/8.9.3) with ESMTP id JAA00903 for ; Tue, 14 Mar 2000 09:27:10 +1100 (EST) X-Sender: bae008@mail.chem.csiro.au Message-Id: Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Tue, 14 Mar 2000 09:27:05 +1100 To: chemistry@ccl.net From: Jonathan Baell Subject: MMF94s and dielectric Dear All Does anyone one have any references on the use of MMF94 ( with modified amide parameters for static minimizations, a la MMF94s as implemented in sybyl 6.5) for minimization of a crystal structure of a small molecule such as, for example, a substituted benzanilide? This is especially in regard to choice of dielectric function (e.g. distance-dependent with base diel. of 4?) to best approximate the solid-state electrostatic environment. Our interest is in seeing how different or similar the minimized xtl structure is to the xtl structure itself (and checking out of course that it's not stuck in a theoretical local minimum). jonathan baell