From hebant@ext.jussieu.fr Thu Sep 26 03:57:55 1996 Received: from shiva.jussieu.fr for hebant@ext.jussieu.fr by www.ccl.net (8.7.5/950822.1) id DAA04679; Thu, 26 Sep 1996 03:45:47 -0400 (EDT) Received: from idf.ext.jussieu.fr (idf.ext.jussieu.fr [134.157.81.129]) by shiva.jussieu.fr (8.7.6/jtpda-5.2) with ESMTP id JAA14322 ; Thu, 26 Sep 1996 09:45:41 +0200 (METDST) Received: from [134.157.11.16] by idf.ext.jussieu.fr (8.6.10/jtpda-4.0) with SMTP; Thu, 26 Sep 1996 09:45:39 +0200 Date: Thu, 26 Sep 1996 09:45:39 +0200 X-Sender: hebant@idf.ext.jussieu.fr Message-Id: Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" To: smb@smb.chem.niu.edu (Steven Bachrach) From: hebant@ext.jussieu.fr (Pascal HEBANT) Subject: 3-ECCC Proceedings Cc: chemistry@www.ccl.net, admin@hackberry.chem.niu.edu, smb@smb.chem.niu.edu Dear Sir, Can you tell me where the proceeding of the 3-ECC Conference will be published. Regards ***************************************************************************** Pascal HEBANT Laboratoire d'Electrochimie et de Chimie Analytique Ecole Nationale Superieure de Chimie de Paris 11 rue Pierre et Marie Curie 75005 Paris FRANCE tel: 33 (1) 44 27 66 94 fax: 33 (1) 44 27 67 50 http://alcyone.enscp.jussieu.fr/Pages/LECA/Electrochimie.html http://alcyone.enscp.jussieu.fr/Pages/LECA/GP/Pascal.html ***************************************************************************** From qibvigap@lg.ehu.es Thu Sep 26 07:57:56 1996 Received: from lgsx01.lg.ehu.es for qibvigap@lg.ehu.es by www.ccl.net (8.7.5/950822.1) id HAA05566; Thu, 26 Sep 1996 07:26:42 -0400 (EDT) Received: from lgdx02.lg.ehu.es by lgsx01.lg.ehu.es (4.1/4.7 ) id AA15579; Thu, 26 Sep 96 13:25:23 +0100 Received: by lgdx02.lg.ehu.es (5.65/4.7) id AA29723; Thu, 26 Sep 1996 13:33:25 +0100 Date: Thu, 26 Sep 1996 13:33:25 +0100 (WET DST) From: Pablo Vitoria Garcia X-Sender: qibvigap@lgdx02 To: ccl Subject: Summary of answers Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII From qibvigap@lg.ehu.esWed Sep 25 19:57:20 1996 Date: Wed, 25 Sep 1996 19:56:35 +0100 (WET DST) From: Pablo Vitoria Garcia To: "Angelica G. Zacarias" Subject: Re: your mail Dear Netters, Here is a summary of the answers to my question about problems with SCF convergence in G94. Thanks a lot to everyone who answered. My question was: >> Could anybody tell me what the marked (>>>>) messages mean (I understand >> the English :-))when they appear in the .out file of a Gaussian job? >> >> 96 alpha electrons 96 beta electrons >> nuclear repulsion energy 2467.2165270904 Hartrees. >> One-electron integrals computed using PRISM. >> The smallest eigenvalue of the overlap matrix is 1.527D-01 >> Projected Huckel Guess. >> Requested convergence on RMS density matrix=1.00D-08 within 64 cycles. >> Requested convergence on MAX density matrix=1.00D-06. >> Integral accuracy reduced to 1.0D-05 until final iterations. >> >>>> Problem detected with inexpensive integrals. >> >>>> Switching to full accuracy and repeating last cycle. ----------------------------------------------------------------------- Date: Tue, 24 Sep 1996 13:17:07 -0400 From: David Heisterberg During the initial stages of direct scf integrals are calculated with pretty loose tolerances and cutoffs to speed things up. However, this can lead to problems sometimes. Gaussian detects this and tightens up the integral evaluation if necessary. Did the job eventually converge? Dave Heisterberg ----------------------------------------------------------------------- Date: Tue, 24 Sep 1996 13:21:26 -0400 (EDT) From: carlos@UDel.Edu Hola, El mensaje que tienes se refiere a un calculo directo, por defecto el Gaussian en un calculo de este tipo reduce la precision de calculo la integrales bielectronicas que incluye en el proceso scf, hasta que se alcanza una convergencia en la funcion de onda determinada a partir de entonces cambia a precision normal En tu calculo el programa no alcanza la convergencia con el primer criterio (en el capitulo 4 del manual dice que el primer paso se termina despues de 21 iteraciones se alcanze o no la convergencia) y cambia al criterio estricto. Puede que aun asi se alcanze la convergencia en el SCF pero bastantes veces da problemas. Como primera opcion, si la funcion de onda no converge es usar SCF=NoVarAcc con lo que se realiza todo el calculo con alta precision desde el principio. Espero que te sirva de ayuda. Carlos Manuel Estevez Valcarcel ----------------------------------------------------------------------- Date: Tue, 24 Sep 1996 19:36:37 +0200 (METDST) From: Steen Hammerum Nothing to worry about. The program just tells you that the cheap way of doing it didn't work, and that it is therefore switching to the more accurate (but more time-consuming) method. Happens often. Steen ----------------------------------------------------------------------- Date: Tue, 24 Sep 1996 15:04:39 -0400 (EDT) From: Carlos Manuel Estevez Valcarcel Hola de nuevo: Es normal que tarde bastante, por el trozo de salida de tu primer mensaje supongo que tienes algun metal de transicion en la molecula (el programa hace una densidad de prueba (guess en ingles, nunca se como traducirlo) con un Huckel en vez de con un INDO que es lo normal para molecular organicas. Ten paciencia yo te recomendaria que en tu entrada pusies #p en vez de #n con lo uqe te sale mucha mas informacion, en particular sobre los ciclos SCF, puedes ver como va la conergencia y si vale la pena esperar, tambien puedes tratar varios algoritmos de convergencia como VShift (que separa artificialmente el HOMO del LUMO una cantidad determinada y es conveniente en los metales de transicion donde estos orbitales suelen estar muy proximos (esto no tiene ningun efecto sobre los orbitales finales es solo para el principio de las iteraciones) tambien puedes usar quadratic Convergence (qc) que suele converger mejor pero que tarda mucho mas. Bueno nada mas, que los duendes de los ciclos SCF no se porten muy mal Carlos ----------------------------------------------------------------------- From choic@gusun.georgetown.edu Thu Sep 26 10:57:58 1996 Received: from gusun.acc.georgetown.edu for choic@gusun.georgetown.edu by www.ccl.net (8.7.5/950822.1) id KAA06420; Thu, 26 Sep 1996 10:21:52 -0400 (EDT) Received: from localhost by gusun.acc.georgetown.edu (SMI-8.6/SMI-SVR4) id KAA09773; Thu, 26 Sep 1996 10:16:43 -0400 Date: Thu, 26 Sep 1996 10:16:43 -0400 (EDT) From: Cheol Choi X-Sender: choic@gusun To: chemistry@www.ccl.net Subject: Summary of X Server for Quanta and Cerius2 Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Here is a summary of the answers I have received to my query about the X Server software for Quanta and Cerius2 program. Thanks to everyone who responded. My original query was : > Dear CCLers, > We are using the Quanta and Cerius2 programs with the SGI workstations. > Since there are a lot of users, we are considering having X Servers > (usually PC based computer with Windows or Mac) with X terminal > emulator. > But we couldn't find any X terminal emulator which is capable of DGL. > Please, let us know a proper X terminal emulator if there is any > especially for Quanta and Cerius2. > This is a summary of the answers. From soperpd@nylon.es.dupont.com Wed Sep 18 15:30:12 1996 Return-Path: Received: from gatekeeper.es.dupont.com by gusun.acc.georgetown.edu (SMI-8.6/SMI-SVR4) id PAA07096; Wed, 18 Sep 1996 15:30:11 -0400 Received: by gatekeeper.es.dupont.com; id PAA16144; Wed, 18 Sep 1996 15:35:12 -0400 Received: by esds01.es.dupont.com; id AA25785; Wed, 18 Sep 96 15:35:10 -0400 Received: by nylon.es.dupont.com (940816.SGI.8.6.9/920502.SGI) id PAA00392; Wed, 18 Sep 1996 15:35:21 -0400 Date: Wed, 18 Sep 1996 15:35:21 -0400 Message-Id: <199609181935.PAA00392@nylon.es.dupont.com> From: Paul Soper To: choic@gusun.acc.georgetown.edu Subject: Re: CCL:X Server for Quanta and Cerius2 ? Content-Length: 665 Status: RO X-Status: A Cheolho, Any X-Windows terminal emulator should work with Cerius2. The "Cerius2 Installation and Administration Guide" lists a number of them on pp 31-32. I have personally run it from a Windows 3.1 PC using Hummingbird's Exceed 4. Good luck, Paul Soper ----------------------------------------------------------------- Paul Soper All the usual disclaimers apply DuPont Central Research soperpd@esvax.dnet.dupont.com P.O. Box 80328 Tel (302)-695-1757 Wilmington, DE 19880-0328 FAX (302)-695-2112 ----------------------------------------------------------------- From Gary_Lickfield@quickmail.clemson.edu Wed Sep 18 17:58:22 1996 Return-Path: Received: from CLEMSON.EDU by gusun.acc.georgetown.edu (SMI-8.6/SMI-SVR4) id RAA03640; Wed, 18 Sep 1996 17:58:21 -0400 Received: from quickmail.clemson.edu (quickmail.clemson.edu [130.127.8.57]) by CLEMSON.EDU (8.7.5/8.7.3) with SMTP id SAA16126 for ; Wed, 18 Sep 1996 18:03:20 -0400 (EDT) Message-ID: Date: 18 Sep 1996 18:08:56 -0500 From: "Gary Lickfield" Subject: Re: CCL-X Server for Quanta To: "Cheol Choi" X-Mailer: Mail*Link SMTP-QM 3.0.2 Content-Length: 2453 Status: RO X-Status: A Reply to: RE>CCL:X Server for Quanta and Cerius2 ? Cheol Choi, I also use Cerius2, and I have been using MacX 1.2 on my power mac. This has worked ok with Cerius2 version 1.6. However, I am currently having a problem with the new version - Cerius2 2.0. Good Luck, Gary Lickfield (LGARY@CLEMSON.EDU) ------------------ RFC822 Header Follows ------------------ Received: by quickmail.clemson.edu with SMTP;18 Sep 1996 14:59:44 -0500 Received: from www.ccl.net (www.ccl.net [128.146.36.5]) by CLEMSON.EDU (8.7.5/8.7.3) with ESMTP id OAA29176; Wed, 18 Sep 1996 14:56:00 -0400 (EDT) Received: for chemistry-request@www.ccl.net by www.ccl.net (8.7.5/950822.1) id OAA22789; Wed, 18 Sep 1996 14:23:37 -0400 (EDT) Received: from gusun.acc.georgetown.edu for choic@gusun.georgetown.edu by www.ccl.net (8.7.5/950822.1) id NAA22647; Wed, 18 Sep 1996 13:42:54 -0400 (EDT) Received: from localhost by gusun.acc.georgetown.edu (SMI-8.6/SMI-SVR4) id NAA17533; Wed, 18 Sep 1996 13:37:51 -0400 Date: Wed, 18 Sep 1996 13:37:50 -0400 (EDT) From: Cheol Choi X-Sender: choic@gusun To: chemistry@www.ccl.net Subject: CCL:X Server for Quanta and Cerius2 ? Message-ID: Sender: Computational Chemistry List Errors-To: ccl@www.ccl.net Precedence: bulk From M.Biggs@surrey.ac.uk Thu Sep 19 03:49:40 1996 Return-Path: Received: from mailc.surrey.ac.uk by gusun.acc.georgetown.edu (SMI-8.6/SMI-SVR4) id DAA16087; Thu, 19 Sep 1996 03:49:39 -0400 Message-Id: <199609190749.DAA16087@gusun.acc.georgetown.edu> Received: from surrey.ac.uk by mailc.surrey.ac.uk id <08184-0@mailc.surrey.ac.uk>; Thu, 19 Sep 1996 08:54:41 +0100 Subject: Re: CCL:X Server for Quanta and Cerius2 ? To: choic@gusun.georgetown.edu (Cheol Choi) Date: Thu, 19 Sep 1996 08:54:40 +0100 (BST) In-Reply-To: from "Cheol Choi" at Sep 18, 96 01:37:50 pm X-Mailer: ELM [version 2.4 PL25] MIME-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit From: Dr Mark J Biggs Sender: M.Biggs@surrey.ac.uk Content-Length: 1122 Status: RO X-Status: Try Vista eXceed (I am not sure how you would get it). It is not public domain but I don't think it is too expensive. Regards Mark From pakman@donald.hanhyo.co.kr Wed Sep 18 20:56:39 1996 Return-Path: Received: from donald.hanhyo.co.kr by gusun.acc.georgetown.edu (SMI-8.6/SMI-SVR4) id UAA02599; Wed, 18 Sep 1996 20:56:21 -0400 Received: by donald.hanhyo.co.kr (940816.SGI.8.6.9/930416.SGI) id JAA03280; Thu, 19 Sep 1996 09:53:45 +0900 From: "Sang Soo Pak" Message-Id: <9609190953.ZM3278@donald.hanhyo.co.kr> Date: Thu, 19 Sep 1996 09:53:44 +0000 In-Reply-To: Cheol Choi "CCL:X Server for Quanta and Cerius2 ?" (Sep 18, 1:37pm) References: X-Mailer: Z-Mail (3.2.0 26oct94 MediaMail) To: Cheol Choi Subject: Re: CCL:X Server for Quanta and Cerius2 ? Cc: sspak@donald.hanhyo.co.kr Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Length: 2081 Status: RO X-Status: Dear Mr. Choi, You can use any X-terminal for Cerius2. Cerius2 will run in X-window mode automatically. However, for Quanta, it's best to buy an SGI indy and use it as an terminal. If you can get your MSI representative to give you a floating license, then with you newly aquired indy, you can run Quanta on your machine with the existing license of Quanta. Hope the above help. By the way, I sell Quanta and C2 in Korea. Sincerely, Sang -- Sang Soo Pak (!! we moved again !!) Molecular Design Laboratory Hanhyo Institute of Technology Hanhyo Institute of Technology Kukje Center Building, 27th Floor San 6, Daeya-Dong, Shihung-Shi, 191 Hankang-Ro 2 Ka, Yongsan-Ku Kyungki-Do, 429-010, Korea Seoul, 140-702, Korea Tel: +82-32-691-2955 Tel: +82-2-791-1704 Fax: +82-32-692-0415 Fax: +82-2-791-1705 e-mail: sspak@donald.hanhyo.co.kr Web: http://www.hanhyo.co.kr From support@msi.com Thu Sep 19 15:38:14 1996 Return-Path: Received: from bioc1.msi.com by gusun.acc.georgetown.edu (SMI-8.6/SMI-SVR4) id PAA09178; Thu, 19 Sep 1996 15:38:13 -0400 Received: from iris76.biosym.com by bioc1.msi.com (5.64/0.0) id AA05461; Thu, 19 Sep 96 12:43:10 -0700 Received: by iris76.msi.com (950413.SGI.8.6.12/930416.SGI) for choic@gusun.georgetown.edu id MAA07240; Thu, 19 Sep 1996 12:43:09 -0700 Message-Id: <199609191943.MAA07240@iris76.msi.com> From: Response Center Date: Thu, 19 Sep 1996 12:43:09 -0700 Reply-To: Response Center Organization: Molecular Simulations Inc. Phone: (619) 546-5509 To: choic@gusun.acc.georgetown.edu Subject: X Server for QUANTA and Cerius2 Content-Length: 1274 Status: RO X-Status: Dear Dr. Choi, I don't know of anything which supports DGL other than another SGI workstation. However: Cerius2 can be run in X11 mode to display on X-terminals even if they do not support DGL; you should try to arrange a trial of the X-terminal software before purchasing any since not all software completely supports the X11 protocol. QUANTA will not run on a remote display even if it is DGL-capable. The program will run extremely slowly and some portions do not work. MSI does not support remote display capabilities for QUANTA on any platform. Regards, Bob Funchess -- You can get the latest patches for Insight II 95.0 from our website http://www.msi.com/support/life/insight/ North America: Europe: Scientific Support Scientific Support Molecular Simulations Molecular Simulations 9685 Scranton Road 240/250 The Quorum, Barnwell Road San Diego, CA 92121-3752 Cambridge, CB5 8RE, England +1 (619) 546-5509 +44 1223 413 304 >>>>> Please use the addresses given below for electronic mail <<<<< E-Mail (Europe) support@msicam.co.uk E-Mail (North America) support@msi.com From amanda@msi.com Wed Sep 25 10:07:58 1996 Return-Path: Received: from bioc1.msi.com by gusun.acc.georgetown.edu (SMI-8.6/SMI-SVR4) id KAA11485; Wed, 25 Sep 1996 10:07:57 -0400 Received: from biff.msi.com by bioc1.msi.com (5.64/0.0) id AA16747; Wed, 25 Sep 96 07:13:03 -0700 Received: from DialupEudora (iris21) by biff.biosym.com (4.1/SMI-4.1) id AA13520; Wed, 25 Sep 96 07:12:57 PDT Date: Wed, 25 Sep 96 07:12:55 PDT X-Sender: aporzio@146.202.0.225 Message-Id: Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" To: Cheol Choi From: amanda@msi.com (Amanda Porzio) Subject: Re: SGI emulator ? Content-Length: 1729 Status: RO X-Status: Dear Cheolho Choi, Thanks for your message. My e-mail has been down for the last 3 weeks so I apologize for the delay in responding. Cerius2 does support X-terminal emulation but Quanta unfortunately does not. We do not have any plans to make Quanta accesssible at this point as evenetually Quanta's functionality will be incorporated in a new architecture similar to C2 that will support x-term communication. A solution could be visit our home page and download a free copy of our WebLab Viewer. This Viewer is free and allows you to import Quanta's files into the program for viewing only. The other option is to switch from Quanta to Insight and purchase the module called AXXESS that allows a user to drive Insight from an x-terminal. Thanks, Amanda From choic@gusun.georgetown.edu Thu Sep 26 12:57:58 1996 Received: from gusun.acc.georgetown.edu for choic@gusun.georgetown.edu by www.ccl.net (8.7.5/950822.1) id MAA07406; Thu, 26 Sep 1996 12:23:06 -0400 (EDT) Received: from localhost by gusun.acc.georgetown.edu (SMI-8.6/SMI-SVR4) id MAA29275; Thu, 26 Sep 1996 12:17:52 -0400 Date: Thu, 26 Sep 1996 12:17:51 -0400 (EDT) From: Cheol Choi X-Sender: choic@gusun To: chemistry@www.ccl.net Subject: Summary of X Server for Quanta and Cerius2 (2) (Sorry) Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Sorry. I think I made a mistake in sending a summary. This is a summary of the answers. Thanks, Cheol Ho Choi Dep. of Chem. Georgetown Univ. ----------------------------------------------------------------- Any X-Windows terminal emulator should work with Cerius2. The "Cerius2 Installation and Administration Guide" lists a number of them on pp 31-32. I have personally run it from a Windows 3.1 PC using Hummingbird's Exceed 4. Good luck, Paul Soper ----------------------------------------------------------------- Paul Soper All the usual disclaimers apply DuPont Central Research soperpd@esvax.dnet.dupont.com P.O. Box 80328 Tel (302)-695-1757 Wilmington, DE 19880-0328 FAX (302)-695-2112 ----------------------------------------------------------------- Reply to: RE>CCL:X Server for Quanta and Cerius2 ? Cheol Choi, I also use Cerius2, and I have been using MacX 1.2 on my power mac. This has worked ok with Cerius2 version 1.6. However, I am currently having a problem with the new version - Cerius2 2.0. Good Luck, Gary Lickfield (LGARY@CLEMSON.EDU) Try Vista eXceed (I am not sure how you would get it). It is not public domain but I don't think it is too expensive. Regards Mark Dear Mr. Choi, You can use any X-terminal for Cerius2. Cerius2 will run in X-window mode automatically. However, for Quanta, it's best to buy an SGI indy and use it as an terminal. If you can get your MSI representative to give you a floating license, then with you newly aquired indy, you can run Quanta on your machine with the existing license of Quanta. Hope the above help. By the way, I sell Quanta and C2 in Korea. Sincerely, Sang -- Sang Soo Pak (!! we moved again !!) Molecular Design Laboratory Hanhyo Institute of Technology Hanhyo Institute of Technology Kukje Center Building, 27th Floor San 6, Daeya-Dong, Shihung-Shi, 191 Hankang-Ro 2 Ka, Yongsan-Ku Kyungki-Do, 429-010, Korea Seoul, 140-702, Korea Tel: +82-32-691-2955 Tel: +82-2-791-1704 Fax: +82-32-692-0415 Fax: +82-2-791-1705 e-mail: sspak@donald.hanhyo.co.kr Web: http://www.hanhyo.co.kr Dear Dr. Choi, I don't know of anything which supports DGL other than another SGI workstation. However: Cerius2 can be run in X11 mode to display on X-terminals even if they do not support DGL; you should try to arrange a trial of the X-terminal software before purchasing any since not all software completely supports the X11 protocol. QUANTA will not run on a remote display even if it is DGL-capable. The program will run extremely slowly and some portions do not work. MSI does not support remote display capabilities for QUANTA on any platform. Regards, Bob Funchess -- You can get the latest patches for Insight II 95.0 from our website http://www.msi.com/support/life/insight/ North America: Europe: Scientific Support Scientific Support Molecular Simulations Molecular Simulations 9685 Scranton Road 240/250 The Quorum, Barnwell Road San Diego, CA 92121-3752 Cambridge, CB5 8RE, England +1 (619) 546-5509 +44 1223 413 304 >>>>> Please use the addresses given below for electronic mail <<<<< E-Mail (Europe) support@msicam.co.uk E-Mail (North America) support@msi.com Dear Cheolho Choi, Thanks for your message. My e-mail has been down for the last 3 weeks so I apologize for the delay in responding. Cerius2 does support X-terminal emulation but Quanta unfortunately does not. We do not have any plans to make Quanta accesssible at this point as evenetually Quanta's functionality will be incorporated in a new architecture similar to C2 that will support x-term communication. A solution could be visit our home page and download a free copy of our WebLab Viewer. This Viewer is free and allows you to import Quanta's files into the program for viewing only. The other option is to switch from Quanta to Insight and purchase the module called AXXESS that allows a user to drive Insight from an x-terminal. Thanks, Amanda From zfeng@mdh.bim.anl.gov Thu Sep 26 13:13:54 1996 Received: from mdh.bim.anl.gov for zfeng@mdh.bim.anl.gov by www.ccl.net (8.7.5/950822.1) id MAA07457; Thu, 26 Sep 1996 12:33:49 -0400 (EDT) Received: from pyp.bim.anl.gov (pyp.bim.anl.gov [146.139.36.45]) by mdh.bim.anl.gov (8.6.11/8.6.11) with ESMTP id QAA24801 for ; Thu, 26 Sep 1996 16:33:50 GMT Received: (zfeng@localhost) by pyp.bim.anl.gov (8.6.11/8.6.11) id QAA01358 for CHEMISTRY@www.ccl.net; Thu, 26 Sep 1996 16:33:49 GMT From: "Zhou Feng" Message-Id: <9609261133.ZM1356@pyp.bim.anl.gov> Date: Thu, 26 Sep 1996 11:33:48 -0500 X-Mailer: Z-Mail (3.2.2 10apr95 MediaMail) To: CHEMISTRY@www.ccl.net Subject: summary: implicit solvation programs Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Dear ccl: I posted a message inquiring programs which can do implicit solvent model while performing energy minimization & molecular dynamics. Here is a summary of the responses I have got. Thanks to all who replied! On Sep 23, 11:32am, Zhou Feng wrote: > Subject: CCL:(no subject) > Hi: > > I am looking for a reasonably accurate implicit solvation energy program which > can do some simple energy minimization or low temperature MD to predict the > energies of a biomoleular system, there are moderate conformational changes > which has to be predicted along with the energies. IS there anyone who can give > me some suggestions? We have CHARMM & Delphi, but we need to do some dynamics > with the implicit solvent model. MacroModel/BatchMin has GB/SA solvation, which will probably do what you need. See the URL below for info. on cost and availability, and also for literature references to GB/SA. -P. -- ****** ********** In Memoriam, Bill Monroe, 1911 - 1996 ****************** * 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.cc.columbia.edu/cu/chemistry/mmod/mmod.html From: "Robert Fraczkiewicz" Message-Id: <9609231336.ZM10061@pauli.utmb.edu> Date: Mon, 23 Sep 1996 13:36:11 -0500 In-Reply-To: Zhou Feng "CCL:(no subject)" (Sep 23, 11:32am) References: <199609231632.QAA00698@pyp.bim.anl.gov> X-Mailer: Z-Mail (3.2.3 08feb96 MediaMail) To: Zhou Feng , chemistry@www.ccl.net Subject: Re: CCL:(no subject) Cc: werner@nmr.utmb.edu Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Status: RO On Sep 23, 11:32am, Zhou Feng wrote: > Subject: CCL:(no subject) > Hi: > > I am looking for a reasonably accurate implicit solvation energy program which > can do some simple energy minimization or low temperature MD to predict the > energies of a biomoleular system, there are moderate conformational changes > which has to be predicted along with the energies. IS there anyone who can give > me some suggestions? We have CHARMM & Delphi, but we need to do some dynamics > with the implicit solvent model. > > Feng Zhou > Argonne National Lab. An excellent program FANTOM written by Werner Braun and co-workers can do that. Please, refer to the following web page for information: http://www.hbcg.utmb.edu/faculty/braun/fm_home.html FANTOM is free of charge for academic users. Regards, Robert Fraczkiewicz, University of Texas Medical Branch From: zauhar@elara.tripos.com ************************************************************************* Received: (from news@localhost) by gatekeeper.tripos.com (8.6.12/8.6.12) id NAA05017 for <@gatekeeper.tripos.com:zfeng@mdh.bim.anl.gov>; Mon, 23 Sep 1996 13:59:56 -0500 Received: from elara.tripos.com(192.160.145.60) by gatekeeper.tripos.com via smap (V1.3) id sma005013; Mon Sep 23 13:59:49 1996 Received: from xhost2 by elara via ESMTP (951211.SGI.8.6.12.PATCH1042/951211.SGI.AUTO) for id NAA16615; Mon, 23 Sep 1996 13:34:30 -0500 Received: by xhost2 (951211.SGI.8.6.12.PATCH1042) id NAA22093; Mon, 23 Sep 1996 13:34:29 -0500 Date: Mon, 23 Sep 1996 13:34:29 -0500 Message-Id: <199609231834.NAA22093@xhost2> To: Zhou Feng Subject: Solvent model in mole. mech. Status: RO Dear Feng, The Incorporation of Hydration Forces Determined by Continuum Electrostatics into Molecular Mechanics Simulations, R.J. Zauhar, J. Comp. Chem., 12, 575-83 (1991). I do not yet have this working with my new code, but it is not difficult to make the modifications. Let me know if you are interested in this. Best regards, Randy All opinions expressed here are mine, not my employer's ///////////////////////////////////////////////////////////////////////// \\ Randy J. Zauhar, PhD | E-mail: zauhar@tripos.com // \\ Tripos, Inc. | : zauhar@inlink.com // \\ 1699 S. Hanley Rd., Suite 303 | Phone: (314) 647-1099 Ext. 3382 // \\ St. Louis, MO 63144 | // ///////////////////////////////////////////////////////////////////////// ** ** ** "If you have conceptions of things that you can have no conception ** ** of, then the conception and the thing appear to co-incide." ** ** --- C.G. Jung ** >From rino@ibc.wustl.edu Mon Sep 23 14:01:27 1996 Received: from mdh.bim.anl.gov by enzyme.bim.anl.gov (AIX 3.2/UCB 5.64/4.03) id AA13494; Mon, 23 Sep 1996 14:01:26 -0500 Received: from wugate.wustl.edu (wugate.wustl.edu [128.252.120.1]) by mdh.bim.anl.gov Received: from mdh.bim.anl.gov by enzyme.bim.anl.gov (AIX 3.2/UCB 5.64/4.03) id AA13494; Mon, 23 Sep 1996 14:01:26 -0500 Received: from wugate.wustl.edu (wugate.wustl.edu [128.252.120.1]) by mdh.bim.anl.gov (8.6.11/8.6.11) with ESMTP id TAA19168 for ; Mon, 23 Sep 1996 1 9:00:21 GMT Received: from ibc.wustl.edu (ibc.wustl.edu [128.252.122.174]) by wugate.wustl.edu (8. 7.5/8.7.3) with SMTP id OAA17628 for ; Mon, 23 Sep 1996 14:01:0 3 -0500 Received: by ibc.wustl.edu (SMI-8.6/SMI-SVR4) id OAA13447; Mon, 23 Sep 1996 14:00:55 -0500 Date: Mon, 23 Sep 1996 14:00:55 -0500 (CDT) From: Rino Ragno To: Zhou Feng Subject: Re: CCL:(no subject) In-Reply-To: <199609231632.QAA00698@pyp.bim.anl.gov> Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Status: RO On Mon, 23 Sep 1996, Zhou Feng wrote: > Hi: > > I am looking for a reasonably accurate implicit solvation energy program which > can do some simple energy minimization or low temperature MD to predict the > energies of a biomoleular system, there are moderate conformational changes > which has to be predicted along with the energies. IS there anyone who can give > me some suggestions? We have CHARMM & Delphi, but we need to do some dynamics > with the implicit solvent model. > > > > Feng Zhou > Argonne National Lab. > > Hi, Have a look to the TINKER program which is free: http://dasher.wustl.edu/tinker/ It has a GB/SA module! Rino ++---------------------------------------------------------------------------++ ++---------------------------------------------------------------------------++ || || || Dr. Rino Ragno E-mail: rino@wucmd.wustl.edu || || Institute for Biomedical Computing or: rino@ibc.wustl.edu || || Center for Molecular Design Phone : 314-362-2273 || || Box 8036, Washington University FAX : 314-362-0234 || || 700 South Euclid Avenue || || St. Louis, Missouri 63110 || || U. S. A. || || || ++---------------------------------------------------------------------------++ ++---------------------------------------------------------------------------++ From: Craig Burkhart Organization: Goodyear Research X-Mailer: Mozilla 2.0S (X11; I; IRIX 6.2 IP22) Mime-Version: 1.0 To: Zhou Feng Subject: Re: CCL:(no subject) References: <199609231632.QAA00698@pyp.bim.anl.gov> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit > > I am looking for a reasonably accurate implicit solvation energy program which > can do some simple energy minimization or low temperature MD to predict the > energies of a biomoleular system, there are moderate conformational changes > which has to be predicted along with the energies. IS there anyone who can give > me some suggestions? We have CHARMM & Delphi, but we need to do some dynamics > with the implicit solvent model. > Try contacting Clark Still's group at Columbia. Macromodel may do what you need... -- ---------------------------------------------------------------------------- ** GO TRIBE! GO TRIBE! GO TRIBE! GO TRIBE! GO TRIBE! GO TRIBE! GO TRIBE! *** ----------------------------------+----------------------------------------- Papernet: Craig W. Burkhart |** 1996 AL CENTRAL DIVISION CHAMPIONS ** Goodyear Research |*Record: 95-60* MLB RANK: 1* Last Nite: 142 Goodyear Blvd. |Indians beat the Royals 6-5...McDowell,P. Akron, OH 44305 |Tribe trailing 5-3 in bottom of 7th, Mouthnet: 330.796.3163 |scores 3 as Royals blow it with 2 E's. Faxnet: .3304 |Seitzer (3-4) .390 in 18 gms; Jack gets W Internet: cburkhart@goodyear.com |(13-9), Mesa 1-2-3 in 9th for 36th save. ----------------------------------+----------------------------------------- WAHOO! WAHOO! WAHOO! WAHOO! WAHOO! WAHOO! WAHOO! WAHOO! WAHOO! WAHOO! WAHOO! ---------------------------------------------------------------------------- From: JOE KLIMKOWSKI Subject: Implicit Solvation To: zfeng@mdh.bim.anl.gov Cc: KLIMKOWSKI V JOE Message-Id: <5916511124091996/A45986/MCVAX4/11A9C2F20E00*@MHS> Autoforwarded: false Mime-Version: 1.0 Content-Type: TEXT/PLAIN; CHARSET=US-ASCII Content-Transfer-Encoding: 7BIT Importance: normal Priority: normal Sensitivity: Company-Confidential Ua-Content-Id: 11A9C2F20E00 X400-Mts-Identifier: [;5916511124091996/A45986/MCVAX4] Hop-Count: 2 Status: RO Feng, I saw you message on the Computational chemistry BB. Since you have CHARMM you should consider the ASP (atomic solvation parameter) method of Wesson and Eisenberg. It is implemented in both the academic and MSI versions of CHARMM. Unfortunatly the documentation for it is almost nonexistent. A grep in the /quanta/data/doc subdirectory will confirm it's existance, but not much else. Another good package you might want to consider is Jay Ponder's TINKER. It includes Still's GB/SA method. Possibly some others. Best Regards, V. Joe Klimkowski Eli Lilly and Company From: Thomas Simonson Message-Id: <9609250824.AA05887@schlitz.u-strasbg.fr> To: zfeng@mdh.bim.anl.gov Subject: Re: CCL:(no subject) Status: RO Dear Feng, Xplor has a simple and fast excluded volume implicit solvent model, although this may not yet be in the official version. But there's just a small piece of code to add, which you can probably obtain from Axel Brunger. The original reference for this model is Colonna & Sander, 1990, Biophys.J. 57:1103, and Chris Sander has published more recent papers using it. It's similar to an accessible surface area, but faster. Tom Simonson Regards,From: A J Turner To: Zhou Feng Subject: Re: CCL:(no subject) In-Reply-To: <199609231632.QAA00698@pyp.bim.anl.gov> Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Status: RO Hi! Have you check out the new polarisable boundary terms in mff in CHARMM 24? Cheers Alex ------------------------------------------------------------------- |Alexander J Turner |A.J.Turner@bath.ac.uk | |Post Graduate |http://www.bath.ac.uk/~chpajt/home.html| |School of Chemistry |+144 1225 8262826 ext 5137 | |University of Bath | | |Bath, Avon, U.K. |Field: QM/MM modeling | ------------------------------------------ From: "Ernest Chamot" Subject: Re: CCL:(no subject) To: "Zhou Feng" X-Mailer: VersaTerm Link v1.1.6 Status: RO Hi Feng, > I am looking for a reasonably accurate implicit solvation energy program which >can do some simple energy minimization or low temperature MD to predict the >energies of a biomoleular system, there are moderate conformational changes >which has to be predicted along with the energies. There are a couple very effective implicit solvation models that I know of and can recommend, but they are both implemented for semiempirical QM methods, rather than molecular mechanics. COSMO by Klamt in MOPAC and SM2 (or SM5 now?) by Cramer and Truhlar in Amsol have picked up some pretty subtle geometric effects that are completely missed by simpler SCRF models (which assume only a spherical cavity.) Is your system small enough to model semiempirically? EC --- Chamot Laboratories, Inc. 530 E. Hillside Rd. Naperville, Illinois 60540 Phone/Fax: (630) 637-1559 echamot@xnet.com http://www.xnet.com/~chamotlb ------------------------- From owner-chemistry@ccl.net Thu Sep 26 14:58:09 1996 Received: from bedrock.ccl.net for owner-chemistry@ccl.net by www.ccl.net (8.7.5/950822.1) id OAA08410; Thu, 26 Sep 1996 14:55:14 -0400 (EDT) Received: from Arizona.EDU for momot@iris5.chem.Arizona.EDU by bedrock.ccl.net (8.7.6/950822.1) id OAA29664; Thu, 26 Sep 1996 14:55:12 -0400 (EDT) Received: from iris5.chem.Arizona.EDU by Arizona.EDU (PMDF V5.0-5 #2381) id <01I9XMHZHUDC94E6VX@Arizona.EDU> for CHEMISTRY@ccl.net; Thu, 26 Sep 1996 11:55:07 -0700 (MST) Received: by iris5.chem.Arizona.EDU (920330.SGI/911001.SGI) for @maggie.telcom.Arizona.EDU:CHEMISTRY@ccl.net id AA04781; Thu, 26 Sep 1996 12:14:37 -0700 Date: Thu, 26 Sep 1996 12:14:36 +42000 From: Konstantin Momot Subject: Spartan questions summary To: Computational Chemistry List Message-id: MIME-version: 1.0 Content-type: TEXT/PLAIN; charset=US-ASCII Content-transfer-encoding: 7BIT Hello everybody, yesterday I posted 2 questions about Spartan. A large number of people responded; my thanks to all of them. The original questions and summary of replies follow. Cheers -- Konstantin Momot momot@iris5.chem.arizona.edu http://aruba.ccit.arizona.edu/~momot/research.html ========================================================================== 1) "How to start a Spartan job from a non-graphical terminal ?" The proper command is spartan -x jobname & One needs not worry about the Spartan path or env. variables. Do not use sp_abinitio etc.; spartan will take care of that. jobname should be a directory containinng files _spartan, input, and propin. They can be created from either interactive version by setting up (but not submitting) a job, or by a text editor if you know the proper format. In an unlikely case when you start interactive Spartan by a command other than spartan, you probably need to use that command instead: interactive-spartan-alias -x jobname & ====================================================================== 2) "Why PURED keyword did not work on Fe atom with 3-21G ?" As I was told, the keyword was intended to work on diffuse functions of main group elements, but not on d-elements. This does not apply to STO-3G, where PURED will work with d-elements. ============================================================================ From zfeng@enzyme.bim.anl.gov Thu Sep 26 16:58:00 1996 Received: from enzyme.bim.anl.gov for zfeng@enzyme.bim.anl.gov by www.ccl.net (8.7.5/950822.1) id QAA09092; Thu, 26 Sep 1996 16:22:58 -0400 (EDT) Received: by enzyme.bim.anl.gov (AIX 3.2/UCB 5.64/4.03) id AA18879; Thu, 26 Sep 1996 15:24:07 -0500 Date: Thu, 26 Sep 1996 15:24:07 -0500 From: zfeng@enzyme.bim.anl.gov (Zhou Feng) Message-Id: <9609262024.AA18879@enzyme.bim.anl.gov> To: CHEMISTRY@www.ccl.net, zfeng@mdh.bim.anl.gov Subject: Re: CCL:M:summary: implicit solvation programs Dear Ernest: Thanks very mych for your message. We are currently looking for mostly MM programs, eben though an AMSOL calculation might be possible (~200 atoms, possible?) for our system. Feng Zhou From korkin@qtp.ufl.edu Thu Sep 26 17:09:10 1996 Received: from qtp.ufl.edu for korkin@qtp.ufl.edu by www.ccl.net (8.7.5/950822.1) id QAA09049; Thu, 26 Sep 1996 16:13:11 -0400 (EDT) Received: from white7.qtp.ufl.edu by qtp.ufl.edu (SMI-8.6/SMI-SVR4) id QAA13102; Thu, 26 Sep 1996 16:13:09 -0400 From: "Anatoli Korkin" Received: by white7.qtp.ufl.edu (SMI-8.6/4.11) id PAA18066; Thu, 26 Sep 1996 15:12:55 -0500 Date: Thu, 26 Sep 1996 15:12:55 -0500 Message-Id: <199609262012.PAA18066@white7.qtp.ufl.edu> Subject: IR data bases on internet and in books To: chemistry@www.ccl.net Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Content-MD5: 4jEMEeCh0CdvjLA/mCxHWQ== Dear colleagues, I am sorry, if I repeat someone's recent question. Can you advise the IR data bases on internet or good data collections in easy available books? I am particularly interested in small organic and inorganic molecules. Normally, I find them via citations in theoretical papers in QCLDB, but it does not work all the time. Thanks, Anatoli Korkin From owner-chemistry@ccl.net Thu Sep 26 17:12:03 1996 Received: from bedrock.ccl.net for owner-chemistry@ccl.net by www.ccl.net (8.7.5/950822.1) id QAA09045; Thu, 26 Sep 1996 16:13:09 -0400 (EDT) Received: from copland.udel.edu for sbennett@wotan.duch.udel.edu by bedrock.ccl.net (8.7.6/950822.1) id QAA04848; Thu, 26 Sep 1996 16:13:03 -0400 (EDT) Received: from wotan.duch.udel.edu (wotan.duch.udel.edu [128.175.54.25]) by copland.udel.edu (8.7.6/8.7.3) with SMTP id QAA02598 for <@brahms.udel.edu:chemistry@ccl.net>; Thu, 26 Sep 1996 16:13:03 -0400 (EDT) Received: by wotan.duch.udel.edu (940816.SGI.8.6.9/930416.SGI) id PAA10600; Thu, 26 Sep 1996 15:46:33 -0400 Date: Thu, 26 Sep 1996 15:46:33 -0400 (EDT) From: Steve Bennett To: CCL Users Subject: Polarizability summary Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII In response to my recent post on determining polarizabilities, I'll summarize with the following. Thanks to all the respondents. The GAMESS program can calculate static linear polarizabilities and hyperpolarizabilities with the runtype=FFIELD, or you can use runtype=TDHF to get either static or time-dependent polarizabilities and hyperpolarizabilities. Or, when doing an analytic hessian calculation, set POLAR=.TRUE. in the $CPHF group and you will get the static linear polarizabilities. All these methods are available at the ab initio Hartree-Fock level, and I believe that FFIELD is also available with the semiempirical methods (AM1, PM3, MNDO). GAMESS can be obtained free of charge (including source code) from Mike Schmidt: mike@si.fi.ameslab.gov Hope this helps. Paul Dr Paul N. Day Commercial: (513) 255-6671, Ext 3106-- Visiting Scientist FAX: (513) 255-1128 Laser Hardened Materials Branch WL/MLPJ E-Mail: daypaul@biotech.ml.wpafb.af.mil Wright-Patterson AFB, OH 45433 (134.131.35.30) ----- See Miller (JACS *112*, 8533 (1990)) for such a method. We've implemented this in our ChemPlus QSAR Properties module, using additional parameters from Bondi (_J. Phys. Chem._ *68*, 441 (1964)) and Shannon and Prewitt (_Acta Cryst._ *B25*, 925 (1969)) to handle at least some organometallics. For example, I optimized ferrocene with ZINDO/1 in HyperChem and calculated its polarizability with ChemPlus as 14.50 A^3. Joel Polowin, Ph.D. Manager, Scientific Support Email to: polowin@hyper.com Hypercube Inc, 419 Phillip St, Waterloo, Ont, Canada N2L 3X2 (519)725-4040 Info requests to: info@hyper.com Support questions to: support@hyper.com http://www.hyper.com/ ---- It sounds like you may be looking for a fast, approximate method. If, however, you are willing to include ab initio approaches, the commercial program PS-GVB put out by Schrodinger Inc. (http://www.psgvb.com) will compute linear and first nonlinear polarizabilities at the HF level very quickly. Not quickly compared to evaluating an empirical analytical function but quickly in comparison to the same level of theory found in other commercial codes. The program in general has been fine-tuned to handle the complications which arise from transition metal calculations as well (like in the initial guess of the wavefunction and range of effective core potentials available). You can also hand-pick a series of uniform zero-frequency fields to apply to the molecule of interest to do calculations of higher order polarizabilities via a finite field procedure. Dr. Bryan Marten-- Ciba Pharmaceuticals martebr2@ussu.ciba.com ------ For ab-initio HONDO, by Michel Dupuis, IBM, Kingston is best. Also try Gaussian or GAMESS. Semi-empirical try ZINDo, Mike Zerner, Quantum Theory Project, Univ. of Florida. I am separately sending you my CNDO-EB-CHF + data and output. Good luck, John Dr. John Waite, e-mail: chem8@york.ac.uk or The National Hellenic Research Foundation, rosen@cyclades.nrcps.ariadne-t.gr Organic and Pharaceutical Institute, phone: ++30-1-7238958 (direct) Vas. Konstantinou 48, phone: ++30-1-7247913(secrtry. Mary) Athens 116-35, fax: ++30-1-7247913 Greece or NCRS "Democritos", phone: ++30-1-6513112-5 X219 c/o Dr. G.Kordas, e-mail john@john.nrcps.ariadne-t.gr Material Science Institute, Aghia Paraskevi, Attikis, Athens 153-10, Greece ------ DGauss is a commericial density functional program that can compute static optical polarizabilities. It is a part of the UniChem molecular modeling package that is offered by the Oxford Molecular Group. It will be able to predict polarizabilities for organometallics as well as organics, and, since it computes these using analytic 2nd derivatives, it will compute them relatively efficiently. If you'd interested, I can send additional information regarding UniChem & DGauss. Regards, Mark Mark S. Stave, Ph.D. Computational Scientist e-mail: mstave@oxmol.com Oxford Molecular Group, Inc. office: (612) 894-2510 ----- Gaussian 94 can compute polarizabilities and hyperpolarizabilities at HF, DFT and traditional correlation levels. For the HF and DFT methods these are analytic, for MP2 and beyond they are a mixture of analytic and numerical. Douglas J. Fox Director of Technical Support help@gaussian.com From fgonzale@lauca.usach.cl Thu Sep 26 18:57:59 1996 Received: from ralun.usach.cl for fgonzale@lauca.usach.cl by www.ccl.net (8.7.5/950822.1) id SAA09877; Thu, 26 Sep 1996 18:50:43 -0400 (EDT) Received: from lauca.usach.cl (lauca.usach.cl [158.170.64.28]) by ralun.usach.cl (8.6.11/8.6.9) with ESMTP id SAA05205 for ; Thu, 26 Sep 1996 18:54:32 -0500 Received: (from fgonzale@localhost) by lauca.usach.cl (8.6.12/8.6.12) id SAA29073; Thu, 26 Sep 1996 18:56:08 -0400 From: Fdo Danilo Gonzalez Nilo Message-Id: <199609262256.SAA29073@lauca.usach.cl> Subject: Formation Constant for metal ions Complexation To: chemistry@www.ccl.net Date: Thu, 26 Sep 96 18:56:08 AST Cc: fgonzale@lauca.usach.cl Dear Friends: We are looking for any way of Calculating "Formation Constant for Complexes" between Organic Macrocycles and Metal ions using Molecular Dynamics and Quantum Mechanics. Please send me any kind of information about these problems. How can I get those Formation Constants???. I will summarize all the answers. Thanks a LOT!!! Fernando Danilo Gonzalez N. Universidad de Santiago de Chile Facultad de Quimica y Biologia Casilla 40, Correo 33, Santiago, Chile fono: 681 2575 E-mail : fgonzale@lauca.usach.cl fax : (562) 681 2108 danilo@quantum.usach.cl URL : http://quantum.usach.cl/~danilo *************************************************************************x