From akimototso@gt.chugai-pharm.co.jp Wed Feb 18 03:12:39 1998 Received: from ns.chugai-pharm.co.jp for akimototso@gt.chugai-pharm.co.jp by www.ccl.net (8.8.3/950822.1) id DAA07164; Wed, 18 Feb 1998 03:08:25 -0500 (EST) Received: by ns.chugai-pharm.co.jp; (5.65v3.2/1.3/10May95) id AA11475; Wed, 18 Feb 1998 17:10:57 +0900 Received: from unix0216.gt.chugai-pharm.co.jp by toyow019.chugai-pharm.co.jp (5.65v4.0/1.1.8.2/24Jun96-0306PM) id AA32540; Wed, 18 Feb 1998 17:13:45 +0900 Received: from mac1030.gt.chugai-pharm.co.jp by gtsrv03.gt.chugai-pharm.co.jp; (5.65v3.2/1.1.8.2/21Jun96-0309PM) id AA31472; Wed, 18 Feb 1998 17:13:50 +0900 Message-Id: <9802180813.AA31472@gtsrv03.gt.chugai-pharm.co.jp> Date: Thu, 19 Feb 1998 17:30:50 +0900 To: chemistry@www.ccl.net From: akimototso@gt.chugai-pharm.co.jp (Toshio Akimoto) X-Sender: akimototso@gtsrv03.gt.chugai-pharm.co.jp Subject: correlation evaluation of vectors Mime-Version: 1.0 Content-Type: text/plain; charset=iso-2022-jp X-Mailer: Eudora-J(1.3.8.5-J13) >Date: Thu, 19 Feb 1998 17:28:33 +0900 >To:chemistry@www.ccl.net >From:akimototso@gt.chugai-pharm.co.jp (Toshio Akimoto) >Subject:correlation evaluation of vectors > >Dear People >I'd like to know the evaluation of the correlation of 2 vectors groups.The >summation of inner-products of 2 direction cosine is expected too week. Thank >you. >Name : Toshio Akimoto >E-mail Adress: akimototso@gtsrv03.gt.chugai-pharm.co.jp > From bruno@antas.agraria.uniss.it Wed Feb 18 04:12:40 1998 Received: from cinymp.cineca.it for bruno@antas.agraria.uniss.it by www.ccl.net (8.8.3/950822.1) id EAA07343; Wed, 18 Feb 1998 04:08:51 -0500 (EST) Received: from antas.agraria.uniss.it by cinymp.cineca.it (5.61/UNICOS-PP) id AA93175; Wed, 18 Feb 98 10:08:20 +0100 Date: Wed, 18 Feb 1998 10:05:22 +0100 (NFT) From: "Dr. Bruno Manunza" To: Fenglou Mao Cc: "CHEMISTRY@www.ccl.net" Subject: Re: CCL:Add Water to Proteins In-Reply-To: Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII On Wed, 18 Feb 1998, Fenglou Mao wrote: > Hi, cclers, > Will anyone introduce any programs or papers about adding water > to proteins? > Thanks! > > Sincerely Yours, > > FengLou Mao > ******************************* Dear FengLou, there is a program to do this: it's Solvate. You'll find a link to its home page on the software links page of our web site http://antas.agraria.uniss.it Hope it helps Regards Bruno Dr Bruno Manunza DISAABA (Dept. of Agricultural Environm. Sci) University of Sassari V.le Italia 39 07100 Sassari, ITALY phone: 39 79 229215 fax: 39 79 229276 e-mail: bruno@antas.agraria.uniss.it e-mail: bruno@tharros.dipchim.uniss.it e-mail: gx6bot81@cray.cineca.it web: http://antas.agraria.uniss.it From duca@tigger.cc.uic.edu Wed Feb 18 10:12:46 1998 Received: from tigger.cc.uic.edu for duca@tigger.cc.uic.edu by www.ccl.net (8.8.3/950822.1) id JAA08847; Wed, 18 Feb 1998 09:38:04 -0500 (EST) Received: from tigger.cc.uic.edu (SLIP4B-01.DIALIN.UIC.EDU [128.248.10.149]) by tigger.cc.uic.edu (8.8.5/8.8.5) with ESMTP id IAA252274 for ; Wed, 18 Feb 1998 08:37:27 -0600 Message-ID: <34EAF20B.9E75EC80@tigger.cc.uic.edu> Date: Wed, 18 Feb 1998 08:36:59 -0600 From: Jose Santiago Duca Organization: Laboratory of Molecular Modeling and Design - College of Pharmacy - University of Illinois at Chicago X-Mailer: Mozilla 4.03 [en] (Win95; I) MIME-Version: 1.0 To: CCL Subject: Calcium parameters Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear CCLers; I would like to know where to find good MMFF parameters for Calcium(+2). I need to run some simulations using the CO2(-2)Ca(+2) moiety. Thanks in advance, Jose S. Duca From boufer@cennas.nhmfl.gov Wed Feb 18 10:37:41 1998 Received: from cennas.nhmfl.gov for boufer@cennas.nhmfl.gov by www.ccl.net (8.8.3/950822.1) id JAA08967; Wed, 18 Feb 1998 09:55:47 -0500 (EST) Received: from localhost (boufer@localhost) by cennas.nhmfl.gov (8.8.5/8.8.5) with SMTP id JAA07694 for ; Wed, 18 Feb 1998 09:55:48 -0500 (EST) Date: Wed, 18 Feb 1998 09:55:48 -0500 (EST) From: Ahmed Bouferguene X-Sender: boufer@cennas To: chemistry@www.ccl.net Subject: Scattering code. Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi all, Is there anybody who know where I can get a code that can be used to modelize electron/molecule scattering at low energy impact ? thanks. -- Ahmed Bouferguene ----------------------------------------------------------------------- Ce n'est pas par ce que les choses sont difficiles que nous n'osons pas les faire. C'est parce que nous n'osons pas les faire qu'elles sont difficiles. From jhjensen@blue.weeg.uiowa.edu Wed Feb 18 11:12:44 1998 Received: from ns-mx.uiowa.edu for jhjensen@blue.weeg.uiowa.edu by www.ccl.net (8.8.3/950822.1) id KAA09223; Wed, 18 Feb 1998 10:40:08 -0500 (EST) Received: from [128.255.138.237] (his.chem.uiowa.edu [128.255.138.237]) by ns-mx.uiowa.edu (8.8.8/8.8.5) with ESMTP id JAA53310 for ; Wed, 18 Feb 1998 09:39:58 -0600 Message-Id: Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Wed, 18 Feb 1998 09:40:52 -0500 To: chemistry@www.ccl.net From: "Jan H. Jensen" Subject: DQS Hello, I would appreciate hearing from anyone who has experience with the DQS program from Florida State. Specifically I am trying to port DQS-2.1 to a linux machine and I am running into some trouble with reserved tcp ports. I have written the people at Florida State already but have not heard from them. If anyone has succeeded with such a port and would like to help I can supply further details. Best regards, Jan Jensen =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=- Jan H. Jensen Assistant Professor Department of Chemistry jan-jensen@uiowa.edu University of Iowa Phone:(319) 335-1108 Iowa City, IA 52242 FAX: (319) 335-1270 http://www.uiowa.edu/~chemdept/faculty/jensen/ =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=- From bo@argo.urv.es Wed Feb 18 12:12:50 1998 Received: from argo.urv.es for bo@argo.urv.es by www.ccl.net (8.8.3/950822.1) id LAA09596; Wed, 18 Feb 1998 11:25:33 -0500 (EST) Received: (from bo@localhost) by argo.urv.es (950413.SGI.8.6.12/950213.SGI.AUTOCF) id RAA00090 for chemistry@www.ccl.net; Wed, 18 Feb 1998 17:17:05 +0100 From: bo@argo.urv.es (Carles Bo) Message-Id: <199802181617.RAA00090@argo.urv.es> Subject: IR frequencies & Intensities To: chemistry@www.ccl.net Date: Wed, 18 Feb 1998 17:17:05 +0100 (MET) X-Mailer: ELM [version 2.4 PL24 ME5a] MIME-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Dear CCLers: Does anybody has at hand references on calculated IR intensities by ab initio/DFT methods compared to experimental ones ? We are interested in systems containg transition metals and carbonyls, but any information will be appreciated. Regards, Carles ________________________________________________________________ Carles Bo Dept. de Quimica Fisica i Inorganica Universitat Rovira i Virgili Voice (34) (77) 55 95 69 Pl. Imperial Tarraco, 1 FAX (34) (77) 55 95 63 43005 - Tarragona SPAIN http://www.quimica.urv.es/~w3qfi http://www.quimica.urv.es/cgi-bin/card?bo+qfi ________________________________________________________________ From eloranta@endor.chem.jyu.fi Wed Feb 18 13:12:44 1998 Received: from endor.chem.jyu.fi for eloranta@endor.chem.jyu.fi by www.ccl.net (8.8.3/950822.1) id MAA09907; Wed, 18 Feb 1998 12:15:46 -0500 (EST) Received: (from eloranta@localhost) by endor.chem.jyu.fi (8.8.5/8.8.5) id TAA27262 for CHEMISTRY@www.ccl.net; Wed, 18 Feb 1998 19:20:09 +0200 From: Jussi Eloranta Message-Id: <199802181720.TAA27262@endor.chem.jyu.fi> Subject: GAMSS UK To: CHEMISTRY@www.ccl.net Date: Wed, 18 Feb 1998 19:20:09 +0200 (EET) Content-Type: text Dear Netters, Does anyone know who to contact for information on GAMESS UK program? (WWW pointers, E-mail or anything) Best regards, Jussi Eloranta Dept. of Chemistry University of Jyvaskyla Finland From rvenable@deimos.cber.nih.gov Wed Feb 18 15:12:46 1998 Received: from deimos.cber.nih.gov for rvenable@deimos.cber.nih.gov by www.ccl.net (8.8.3/950822.1) id PAA10805; Wed, 18 Feb 1998 15:08:53 -0500 (EST) Received: from localhost by deimos.cber.nih.gov with SMTP (1.37.109.14/16.2) id AA173642450; Wed, 18 Feb 1998 15:07:30 -0500 Date: Wed, 18 Feb 1998 15:07:30 -0500 (EST) From: Rick Venable To: Laurence Lavelle Cc: chemistry@www.ccl.net Subject: Re: CCL:Switching functions and double cutoffs In-Reply-To: <3.0.32.19980217174344.00a62a60@mbi.ucla.edu> Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII On Tue, 17 Feb 1998, Laurence Lavelle wrote: >The same cannot be said for the infamous spherical bag of waters; a simulation >of that system represents a solute in an isolated droplet of a vacuum aerosol, >and not a protein in solution. The pressure is not exactly determined, and >there are electrostatic artefacts induced by the dielectric boundary >(water/vacuum); charges behave as if there were an image of the charge on the >the vacuum side of the boundary. While I don't have the page number, I've >been told the reference for the "image charge" phenomenon is a paper by >Onsager in Vol. 1, No. 1 of either J. Chem. Phys. or J. Phys. Chem.; I haven't found that one either, but here's the one on reaction fields: Electric Moments of Molecules in Liquids, L. Onsager, JACS 58:1486-93 (1936) -- Rick Venable =====\ |=| "Eschew Obfuscation" FDA/CBER Biophysics Lab |____/ |=| Bethesda, MD U.S.A. | \ / |=| ( Not an official statement or rvenable@deimos.cber.nih.gov | \ / |=| position of the FDA; for that, http://nmr1.cber.nih.gov/ \/ |=| see http://www.fda.gov ) http://www.erols.com/rvenable From daizadeh@kappa.ucdavis.edu Wed Feb 18 18:12:45 1998 Received: from kappa.ucdavis.edu for daizadeh@kappa.ucdavis.edu by www.ccl.net (8.8.3/950822.1) id RAA11486; Wed, 18 Feb 1998 17:13:40 -0500 (EST) Received: (from daizadeh@localhost) by kappa.ucdavis.edu (950413.SGI.8.6.12/950213.SGI.AUTOCF) id OAA23042 for CHEMISTRY@www.ccl.net; Wed, 18 Feb 1998 14:18:49 -0800 From: "Iraj Daizadeh" Message-Id: <9802181418.ZM23040@kappa.ucdavis.edu> Date: Wed, 18 Feb 1998 14:18:49 -0800 X-Mailer: Z-Mail (3.2.3 08feb96 MediaMail) To: CHEMISTRY@www.ccl.net Subject: G94 output -> MATlab/Mathematica Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Hello. A Collegue (sp) of mine is searching for a script that converts standard G94 output into Matlab/mathematica input. Any information on this matter would be appreciated. Thanks in advance. Iraj. -- Iraj Daizadeh Department of Chemistry University of California One Shields Ave. Davis, CA 95616-5295 Phone: 530.754.8695 Fax: 530.752.8995 email: daizadeh@kappa.ucdavis.edu From akimototso@gt.chugai-pharm.co.jp Wed Feb 18 18:20:05 1998 Received: from ns.chugai-pharm.co.jp for akimototso@gt.chugai-pharm.co.jp by www.ccl.net (8.8.3/950822.1) id SAA11646; Wed, 18 Feb 1998 18:04:57 -0500 (EST) Received: by ns.chugai-pharm.co.jp; (5.65v3.2/1.3/10May95) id AA12590; Thu, 19 Feb 1998 08:07:23 +0900 Received: from unix0216.gt.chugai-pharm.co.jp by toyow019.chugai-pharm.co.jp (5.65v4.0/1.1.8.2/24Jun96-0306PM) id AA04743; Thu, 19 Feb 1998 08:10:12 +0900 Received: from mac1030.gt.chugai-pharm.co.jp by gtsrv03.gt.chugai-pharm.co.jp; (5.65v3.2/1.1.8.2/21Jun96-0309PM) id AA02543; Thu, 19 Feb 1998 08:10:17 +0900 Message-Id: <9802182310.AA02543@gtsrv03.gt.chugai-pharm.co.jp> Date: Fri, 20 Feb 1998 08:27:19 +0900 To: chemistry@www.ccl.net From: akimototso@gt.chugai-pharm.co.jp (Toshio Akimoto) X-Sender: akimototso@gtsrv03.gt.chugai-pharm.co.jp Subject: Evaluation of cross crrelation of 2 sets of vectors Cc: youkla@inpharmatics.com Mime-Version: 1.0 Content-Type: text/plain; charset=iso-2022-jp X-Mailer: Eudora-J(1.3.8.5-J13) Dear People I'd like to know the mathematical method to evaluate the similarity of 2 sets of vetors. To caluculate the superposition of 2 sets of vectors is very exact, but it takes time to try calculate 100000 times(because I have to change the position and orientation on the molecular surface). But only calulate summation of inner-product is perhaps too weak fuction . I am working for a pharmaceutical company and we don't have enough math books. I'd appreciate your help. Name: Toshio Akimoto E-Mail Adress: akimototso@gtsrv03.gt.chugai-pharm.co.jp From tvd@msi.com Wed Feb 18 19:12:45 1998 Received: from bioc1.msi.com for tvd@msi.com by www.ccl.net (8.8.3/950822.1) id SAA11991; Wed, 18 Feb 1998 18:50:51 -0500 (EST) Received: by bioc1.msi.com (931110.SGI/930416.SGI) for CHEMISTRY@www.ccl.net id AA16146; Wed, 18 Feb 98 14:56:22 -0800 Received: from biff.msi.com(146.202.0.225) by bioc1.msi.com via smap (V2.0) id xma016138; Wed, 18 Feb 98 14:56:07 -0800 Received: from win95-pc.msi.com by biff.biosym.com (4.1/SMI-4.1) id AA02831; Wed, 18 Feb 98 14:54:36 PST Message-Id: <3.0.32.19980218145737.00a600fc@146.202.0.225> X-Sender: tvd@146.202.0.225 X-Mailer: Windows Eudora Pro Version 3.0 (32) Date: Wed, 18 Feb 1998 14:57:38 +0000 To: CHEMISTRY@www.ccl.net From: Ton van Daelen Subject: Cerius2 SDK workshops, West coast US Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Dear all - MSI is organizing two 2-day workshops on the Cerius2 software developer's kit on the US West coast. This is a course for current and future customers and it is very practically oriented. Experience tells us that by the end of the second day, most trainees will have completed a basic user interface to a stand alone program or made significant progress with a new modeling application. See the URL's below for details. A European workshop is tentatively planned for April/May in Cambridge, England. Let me know if you would be interested in that one. Regards - Ton March 10-11, 1998: Santa Clara http://www.msi.com/info/training/training_sdk_sc.html March 12-13, 1998: San Diego http://www.msi.com/info/training/training_sdk_sd.html Ton van Daelen, Ph.D. Product Manager Software Developer's Kit __o E: tvd@msi.com _`\<,_ Molecular Simulations, Inc P: -1-619-546-5329 (*)/ (*) 9685 Scranton Road F: -1-619-458-0136 /\/\/\/\/\/\ San Diego, CA 92121 W: http://www.msi.com Check out What's New in SDK on the SDK web pages at http://www.msi.com/support/sdk/