From chemistry-request@server.ccl.net Wed Jan 17 02:22:19 2001 Received: from pollux.chem.umn.edu (pollux.chem.umn.edu [128.101.156.56]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f0H7MJd02821 for ; Wed, 17 Jan 2001 02:22:19 -0500 Received: (from cramer@localhost) by pollux.chem.umn.edu (8.9.3/8.9.3) id BAA22758; Wed, 17 Jan 2001 01:19:44 -0600 (CST) From: Christopher Cramer Message-Id: <200101170719.BAA22758@pollux.chem.umn.edu> Subject: Re: CCL:Solvent in G98W To: quanph@hcmuns.edu.vn (Phung Quan) Date: Wed, 17 Jan 2001 01:19:44 -0600 (CST) Cc: truhlar@chem.umn.edu (Don Truhlar), chemistry@ccl.net In-Reply-To: <002201c07fc5$1923df00$41041dac@chem.hcmuns.edu.vn> from "Phung Quan" at Jan 16, 2001 09:03:27 PM X-Mailer: ELM [version 2.5 PL2] MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dr. Quan, AMSOL will do this for you at semiempirical levels, GAMESOL at ab initio levels. Both are distributed by us after signing a license agreement (GAMESOL is a plug-in to GAMESS, which must be obtained from Mark Gordon's group at Iowa State, and both are free). For more information see the MC^2 software page linked at comp.chem.umn.edu Chris Cramer Phung Quan > > Dear CCLers, > We are using G98W. > We'd like to calculate free energy (delta G) of an organic compound in > many kinds of solvents. However we could only do this in some solvents > which are available in Gaussian 98. In case we want to operate in other > solvent such as cyclopentanon, what should we do? > We really need your help! > Best regards > -- Below are our temporary addresses during our sabbatical year in Barcelona (July 23, 2000 - August 1, 2001). Chris at Univ. of Barcelona Cramer Family in Barcelona --------------------------- -------------------------- c/o Professor Javier Luque Via Augusta 228 4/3 Fac. Farmacia, Dept. Fis. Quim. 08021 Barcelona Universitat de Barcelona SPAIN Joan XXIII, s/n Phone: (34) 93 209 4776 08028 Barcelona SPAIN Phone (my mobile): (34) 62 043 1176 Permanent data: Christopher J. Cramer University of Minnesota Department of Chemistry 207 Pleasant St. SE Minneapolis, MN 55455-0431 -------------------------- Phone: (612) 624-0859 || FAX: (612) 626-2006 cramer@pollux.chem.umn.edu http://pollux.chem.umn.edu/~cramer From chemistry-request@server.ccl.net Wed Jan 17 05:43:23 2001 Received: from lancelot.imb-jena.de (lancelot.imb-jena.de [192.124.248.76]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f0HAhMd03257 for ; Wed, 17 Jan 2001 05:43:23 -0500 Received: (from pineda@localhost) by lancelot.imb-jena.de (SGI-8.9.3/8.8.8) id LAA05375 for chemistry@ccl.net; Wed, 17 Jan 2001 11:43:23 +0100 (CET) From: pineda@imb-jena.de (Felipe Pineda) Message-Id: <10101171143.ZM5363@lancelot.imb-jena.de> Date: Wed, 17 Jan 2001 11:43:23 +0000 X-Mailer: Z-Mail (3.2.3 08feb96 MediaMail) To: chemistry@ccl.net Subject: Cluster analysis Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Dear CCL'ers! i would be very grateful for any pointer to a software tool (utility in commercial or academic s/w, standalone tool) which is able to perform such an analysis on a set of conformers typically sampled by some FF MD protocol (e.g.,simmulated annealing) and to build families of conformations displaying similarity to each other with respect to an user defined structural feature (backbone conformation, for example) to a given extent (some rmsd threshold) specified by the user. i used some years ago an insightII macro called family.bcl written by Don Mackay, 1991, which do this with the help of an external program called also family: # The external program "family" is a "C" program and is available from # Don Mackay # Biosym Technologies, Inc. # 10065 Barnes Canyon Rd. # San Diego CA 92121 but in the meantime there are maybe new, more efficient tools out there. many thanks in advance for any tip and best regards felipe -- ********************************************************************** * Felipe Pineda,PhD * * Institut fuer Molekulare Biotechnologie * * AG Theoretische Biophysik * * Beutenbergstrasse 11, Jena Vox: +49-3641-65-6491 * * Postfach 100 813, D-07708 Jena, Germany Fax: -6495 * * web: www.imb-jena.de/~pineda * *"In the world predominates the suffering and prevails the injustice"* * G. Garcia Marquez, colombian writer, Lit. Nobel Prize laureat * ********************************************************************** ********************************************************************** * DISCLAIMER: Unless indicated otherwise, everything in this note is * * my personal opinion, not an official statement of my employer * ********************************************************************** From chemistry-request@server.ccl.net Wed Jan 17 03:07:57 2001 Received: from post.tau.ac.il (post.tau.ac.il [132.66.16.11]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f0H87ud02916 for ; Wed, 17 Jan 2001 03:07:56 -0500 Received: from post.tau.ac.il (pico.tau.ac.il [132.66.145.20]) by post.tau.ac.il (8.9.3/8.9.3) with ESMTP id KAA00696 for ; Wed, 17 Jan 2001 10:07:56 +0200 (IST) Sender: silviu@post.tau.ac.il Message-ID: <3A6552DC.72588369@post.tau.ac.il> Date: Wed, 17 Jan 2001 08:07:56 +0000 From: Zilberman Silviu Organization: TAU To: ccl Subject: rasmol movies Hi everyone, I'm trying to use Rasmol to read coordinate files in xyz format. These files contains several fraims and I would like to be able either to display it as a movie or to be able just to look at each frame. I know it can be done with other softwares (e.g. gOpenMol) but is there a way to do it with Rasmol scripts? I did not find clear answers in their home page. Thanks, Silviu. -- %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% Zilberman Silviu School of Chemistry, Tel Aviv University Ramat Aviv, Tel-Aviv, Israel 61391 Phones 972-3-6407634 972-3-6409293 (fax 1) 972-3-6423765 (fax 2) mailto:silviu@post.tau.ac.il Home Page: http://femto.tau.ac.il/~silviu %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% From chemistry-request@server.ccl.net Wed Jan 17 08:57:59 2001 Received: from rzumail2.unizh.ch (rzumail2.unizh.ch [130.60.128.10]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f0HDvwd04523 for ; Wed, 17 Jan 2001 08:57:58 -0500 Received: from toukie.zzmk.unizh.ch (zzmkfw.unizh.ch [130.60.67.4]) by rzumail2.unizh.ch (8.9.3/8.9.3/08) with ESMTP id OAA11417; Wed, 17 Jan 2001 14:57:57 +0100 (MET) Message-Id: <4.3.2.7.0.20010117150519.00aa33c0@ziaix-imap.unizh.ch> X-Sender: toukie@ziaix-imap.unizh.ch (Unverified) X-Mailer: QUALCOMM Windows Eudora Version 4.3.2 Date: Wed, 17 Jan 2001 15:06:50 +0100 To: chemistry@server.ccl.net From: "Hr. Dr. S. Shapiro" Subject: ? re partial atomic charge units Cc: toukie@zui.unizh.ch Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii"; format=flowed Dear Colleagues; What are the dimensional units for Mulliken partial atomic charges calculated using MOPAC? Thanks in advance to all responders, S. Shapiro toukie@zui.unizh.ch From chemistry-request@server.ccl.net Wed Jan 17 10:40:11 2001 Received: from schrodinger.com (root@thermidore.schrodinger.com [192.156.98.99]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f0HFeAd04940 for ; Wed, 17 Jan 2001 10:40:11 -0500 Received: from tandoori.schrodinger.com (root@tandoori.schrodinger.com [216.216.237.99]) by schrodinger.com (8.8.5/8.8.5) with ESMTP id HAA19295 for ; Wed, 17 Jan 2001 07:40:10 -0800 Received: from sally.schrodinger.com (shenkin@sally.schrodinger.com [216.216.237.92]) by tandoori.schrodinger.com (8.8.5/8.8.5) with ESMTP id KAA28355 for ; Wed, 17 Jan 2001 10:40:04 -0500 Received: from localhost (shenkin@localhost) by sally.schrodinger.com (8.8.8/8.8.5) with ESMTP id KAA28660 for ; Wed, 17 Jan 2001 10:41:05 -0500 X-Authentication-Warning: sally.schrodinger.com: shenkin owned process doing -bs Date: Wed, 17 Jan 2001 10:41:05 -0500 (EST) From: Peter Shenkin To: CHEMISTRY@ccl.net Subject: Re: CCL:Cluster analysis In-Reply-To: <10101171143.ZM5363@lancelot.imb-jena.de> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi, MacroModel, from Schrodinger, Inc., includes XCluster, which is described in J. Comp. Chem., v15, #8, 899-916 (1994). See www.schrodinger.com for some more details (including the manual). -P. On Wed, 17 Jan 2001, Felipe Pineda wrote: > Dear CCL'ers! > > i would be very grateful for any pointer to a software tool (utility in > commercial or academic s/w, standalone tool) which is able to perform such an > analysis on a set of conformers typically sampled by some FF MD protocol > (e.g.,simmulated annealing) and to build families of conformations displaying > similarity to each other with respect to an user defined structural feature > (backbone conformation, for example) to a given extent (some rmsd threshold) > specified by the user. i used some years ago an insightII macro called > family.bcl written by Don Mackay, 1991, which do this with the help of an > external program called also family: > > # The external program "family" is a "C" program and is available from > # Don Mackay > # Biosym Technologies, Inc. > # 10065 Barnes Canyon Rd. > # San Diego CA 92121 > > but in the meantime there are maybe new, more efficient tools out there. > > many thanks in advance for any tip and best regards > > felipe > > -- > ********************************************************************** > * Felipe Pineda,PhD * > * Institut fuer Molekulare Biotechnologie * > * AG Theoretische Biophysik * > * Beutenbergstrasse 11, Jena Vox: +49-3641-65-6491 * > * Postfach 100 813, D-07708 Jena, Germany Fax: -6495 * > * web: www.imb-jena.de/~pineda * > *"In the world predominates the suffering and prevails the injustice"* > * G. Garcia Marquez, colombian writer, Lit. Nobel Prize laureat * > ********************************************************************** > ********************************************************************** > * DISCLAIMER: Unless indicated otherwise, everything in this note is * > * my personal opinion, not an official statement of my employer * > ********************************************************************** > > -= 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 Wed Jan 17 13:01:37 2001 Received: from apex.ibpc.fr (apex.ibpc.fr [193.49.234.1]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f0HI1Yd05182 for ; Wed, 17 Jan 2001 13:01:35 -0500 Received: from pinson.galaxy.ibpc.fr (pinson.galaxy.ibpc.fr [193.49.27.21]) by apex.ibpc.fr (8.9.3/jtpda-5.3.3) with ESMTP id SAA02720 for ; Wed, 17 Jan 2001 18:59:32 +0100 (MET) Date: Wed, 17 Jan 2001 18:59:32 +0100 (CET) From: Peter Varnai X-Sender: varnai@pinson.galaxy.ibpc.fr To: CHEMISTRY@ccl.net Subject: octahedral box in AMBER/CHARMM Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear CCLers, I would like to hear about experiences with simulations in a truncated octahedral box using PME versus cubic box in AMBER 6 and/or CHARMM 27. Thank you for your help. Peter Varnai From chemistry-request@server.ccl.net Wed Jan 17 10:58:52 2001 Received: from hotmail.com (f94.law7.hotmail.com [216.33.237.94]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f0HFwqd05000 for ; Wed, 17 Jan 2001 10:58:52 -0500 Received: from mail pickup service by hotmail.com with Microsoft SMTPSVC; Wed, 17 Jan 2001 07:58:07 -0800 Received: from 130.91.65.29 by lw7fd.law7.hotmail.msn.com with HTTP; Wed, 17 Jan 2001 15:58:07 GMT X-Originating-IP: [130.91.65.29] From: "JAYASRI DASSARMA" To: chemistry@ccl.net Subject: Format conversion Date: Wed, 17 Jan 2001 10:58:07 -0500 Mime-Version: 1.0 Content-Type: text/plain; format=flowed Message-ID: X-OriginalArrivalTime: 17 Jan 2001 15:58:07.0968 (UTC) FILETIME=[48B98600:01C0809E] Hello, Can anyone suggest any free software which can convert an image in Postscript format to JPG format in Windows or Unix. Thanks a lot. Sarma. _________________________________________________________________ Get your FREE download of MSN Explorer at http://explorer.msn.com From chemistry-request@server.ccl.net Wed Jan 17 14:16:38 2001 Received: from cqf.co.cu (cqf.co.cu [63.170.172.34]) by server.ccl.net (8.11.0/8.11.0) with SMTP id f0HJGVd05310 for ; Wed, 17 Jan 2001 14:16:33 -0500 Received: (qmail 837 invoked from network); 17 Jan 2001 17:46:48 -0000 Received: from unknown (HELO pdc.cqf.co.cu) (10.1.10.2) by 10.1.10.1 with SMTP; 17 Jan 2001 17:46:48 -0000 Received: from padrongj (MOD-1 [10.1.10.26]) by pdc.cqf.co.cu with SMTP (Microsoft Exchange Internet Mail Service Version 5.5.1960.3) id DA2LBW8T; Wed, 17 Jan 2001 11:55:19 -0500 Message-ID: <00ea01c080ad$e1e73f20$1a0a010a@padrongj> From: "Juan Alexander Padron Garcia" To: "Daniel Severance" , "CCL (E-mail)" Cc: "Daniel Severance" Subject: RE: CCL:Viewing multiple structure files Date: Wed, 17 Jan 2001 11:49:24 -0600 MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 4.72.3110.5 X-MimeOLE: Produced By Microsoft MimeOLE V4.72.3110.3 Greatings Daniel: I dont know if this program is may be too powerfull for your needs, but Deep View (spdbviewer) can do that and much more, is fast, free and relatively small. It includes a lot of others options, but I am sure that you might use it for what you want. Seek him in www.expasy.ch . Hope this help Juan Alexander Padron Garcia Molecular Modeling Laboratories Pharmaceutical Chemistry Center La Habana, Cuba >Greetings CClers, > I've generated a set of conformations of a molecule and want to send it >to some chemists at a remote site. >Is there a simple application (Windows NT) for simply scrolling through the >set of conformations one at >a time (visually, with 3D rotation ability) so they can see the results? It >needs to do nothing else, although it >might be nice to be able to dump out the current conformation into a new >file, it wouldn't be required. > Is there anything available to do this (either academic or commercial is >fine)? > Thanks! > Dan > From chemistry-request@server.ccl.net Wed Jan 17 17:19:23 2001 Received: from email.nist.gov (email.nist.gov [129.6.2.7]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f0HMJNd05865 for ; Wed, 17 Jan 2001 17:19:23 -0500 Received: from bratsche.nist.gov (bratsche.nist.gov [129.6.194.154]) by email.nist.gov (8.9.3/8.9.3) with ESMTP id RAA21861 for ; Wed, 17 Jan 2001 17:19:24 -0500 (EST) Message-Id: <5.0.0.25.2.20010117163650.00a946b0@mailserver3.nist.gov> X-Sender: irikura@mailserver3.nist.gov X-Mailer: QUALCOMM Windows Eudora Version 5.0 Date: Wed, 17 Jan 2001 16:40:43 -0500 To: chemistry@ccl.net From: Karl Irikura Subject: G98W from the command line? Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii"; format=flowed How can I run Gaussian98 for Windows from a DOS command line? I have a script that invokes G98 repeatedly. It's fine under UNIX, but I would like to do it under Windows also. Do I have to invoke individual links explicitly? Thanks for any help! Karl ---------------------------------------------- Dr. Karl K. Irikura National Institute of Standards and Technology 100 Bureau Drive, Stop 8380 Gaithersburg, MD 20899-8380 voice: 301-975-2510 fax: 301-869-4020 e-mail: karl.irikura@nist.gov http://www.nist.gov/compchem/ ---------------------------------------------- From chemistry-request@server.ccl.net Wed Jan 17 16:22:26 2001 Received: from mr2.wpafb.af.mil (mr2o.wpafb.af.mil [129.48.104.214]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f0HLMQd05785 for ; Wed, 17 Jan 2001 16:22:26 -0500 Received: from ml-firewall.ml.wpafb.af.mil (ml-firewall.ml.wpafb.af.mil [134.131.90.33]) by mr2.wpafb.af.mil (8.11.0/8.11.0) with SMTP id f0HLMSf07918 for ; Wed, 17 Jan 2001 16:22:28 -0500 (EST) Received: by ml-firewall.ml.wpafb.af.mil; id QAA08145; Wed, 17 Jan 2001 16:22:28 -0500 Received: from unknown(134.131.35.6) by ml-firewall.ml.wpafb.af.mil via smap (V5.5) id xma008068; Wed, 17 Jan 01 16:22:02 -0500 Received: from Picard.ml.wpafb.af.mil (picard.ml.wpafb.af.mil [134.131.35.26]) by nsrhost.ml.wpafb.af.mil (8.8.6 (PHNE_14041)/8.8.6) with ESMTP id QAA09492 for ; Wed, 17 Jan 2001 16:22:01 -0500 (EST) Received: (from duanx@localhost) by Picard.ml.wpafb.af.mil id QAA25799; Wed, 17 Jan 2001 16:21:49 -0500 (EST) Date: Wed, 17 Jan 2001 16:21:46 -0500 (EST) From: "Xianofeng . Duan MLBP CON" To: chemistry@ccl.net Subject: HELP:Compiling GAMESS with PGI compiler Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi, CCLers! I compiled GAMESS with pgf77 and pgfcc on our linux cluster (RH 6.2, Pentium II/III). The compiling was going all right and the executable ran without any errors. However the problem was with the examples. I tested exam01, exam02 and exam03, for all of them I got much lower SCF energies. For instance, in exam02 the final energy is supposed to be -37.2810867258, but I got -37.343158728.(Even for initial energy, it's about 0.06 a.u. lower). The settings I used are: comp: pgf77 -c -tp p6 -fast $MODULE.f lked: LDR='pgf77' LIBRARIES='libpgfnrtl.a' BLAS='blas.o' VECTOR=' ' QUICHE='zunix.o' Could someone tell me how to fix the problem? Thanks! **************************************** Xiaofeng Duan, Ph.D. AFRL/MLBP, Bldg. 654 2941 P St. Ste. 1 Wright-Patterson AFB, OH 45433 (937)255-9164 duanx@Picard.ml.wpafb.af.mil **************************************** From chemistry-request@server.ccl.net Wed Jan 17 21:18:03 2001 Received: from yakko.cimav.edu.mx (IDENT:root@[207.248.161.2]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f0I2I0d06407 for ; Wed, 17 Jan 2001 21:18:01 -0500 Received: from glossman ([207.248.161.69]) by yakko.cimav.edu.mx (8.11.0/8.11.0) with SMTP id f0I2IHE30221 for ; Wed, 17 Jan 2001 19:18:17 -0700 Message-ID: <002a01c080fd$42ea33a0$45a1f8cf@cimav.edu.mx> From: "Dr. Daniel Glossman" To: "Computational Chemistry List" Subject: ONIOM hyperpolarizabilities Date: Wed, 17 Jan 2001 19:17:59 -0800 MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 8bit X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 5.50.4522.1200 Disposition-Notification-To: "Dr. Daniel Glossman" X-MimeOLE: Produced By Microsoft MimeOLE V5.50.4522.1200 Dear netters: I am trying to calculate hyperpolarizabilities of organic molecules and I have the following question: Is it possible to calculate hyperpolarizabilities withing Gaussian98 using ONIOM and DFT? To put it on another way: I know that in order to compute the hyperpolarizabilities in Gaussian 98, using DFT it is necessary to resort to the keyword Polar=EnOnly, performing a numerical differentiation. This works by calculating the energy with different applied fields and it´s done automatically. But what happen if one uses ONIOM? Is it possible to use Polar=EnOnly together with ONIOM and DFT? I have tried it myself and found that the calculations goes into an endless loop, increasing the field in only one direction (x) with the default step and never finishing. What am I doing wrong? Thanks in advance for your help. Dr. Daniel Glossman Mitnik ************************************************************************** Dr. Daniel Glossman Mitnik Centro de Investigacion en Materiales Avanzados (CIMAV) LAQUICOM - Laboratorio de Química Computacional Miguel de Cervantes 120 Complejo Industrial Chihuahua Chihuahua, Chih. 31109 Mexico Phone: (52) 14 391151 FAX: (52) 14 391112 E-mail: glossman@mail.cimav.edu.mx glossman@hotmail.com dglossman@yahoo.com **************************************************************************