From chemistry-request@ccl.net Thu Oct 21 17:46:41 2004 Received: from hotmail.com (bay10-f49.bay10.hotmail.com [64.4.37.49]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i9LMkeqN009211 for ; Thu, 21 Oct 2004 17:46:40 -0500 Received: from mail pickup service by hotmail.com with Microsoft SMTPSVC; Thu, 21 Oct 2004 15:57:57 -0700 Received: from 199.106.16.3 by by10fd.bay10.hotmail.msn.com with HTTP; Thu, 21 Oct 2004 22:57:57 GMT X-Originating-IP: [199.106.16.3] X-Originating-Email: [tomc1234.-at-.hotmail.com] X-Sender: tomc1234.-at-.hotmail.com From: "Tom Cao" To: chemistry.-at-.ccl.net Subject: Choice of Force field and charge Date: Thu, 21 Oct 2004 15:57:57 -0700 Mime-Version: 1.0 Content-Type: text/plain; format=flowed Message-ID: X-OriginalArrivalTime: 21 Oct 2004 22:57:57.0937 (UTC) FILETIME=[68488210:01C4B7C1] X-Spam-Status: No, hits=1.5 required=7.5 tests=FROM_ENDS_IN_NUMS autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Dear All, I have another question about the choice of force field or charge for the study systems. I found there are multiple choice of force fields when I want to make some calculations, could you please tell me some general rule, which force field is better for which system? (for example, marcomolecules, small molecules ...). What's about the choice of charges for different systems? Thanks a lot for your help Sincerely Tom _________________________________________________________________ Get ready for school! Find articles, homework help and more in the Back to School Guide! http://special.msn.com/network/04backtoschool.armx From chemistry-request@ccl.net Thu Oct 21 16:36:08 2004 Received: from smtp2.Stanford.EDU (smtp2.Stanford.EDU [171.67.16.125]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i9LLa7e6004778 for ; Thu, 21 Oct 2004 16:36:07 -0500 Received: from alphahelix (alphahelix.Stanford.EDU [171.64.126.26]) by smtp2.Stanford.EDU (8.12.11/8.12.11) with ESMTP id i9LLmLS2004666; Thu, 21 Oct 2004 14:48:22 -0700 Reply-To: From: "Joseph Han" To: "'Daniel Svozil'" , Subject: RE: How do you organize your *.pdf files? Date: Thu, 21 Oct 2004 14:48:19 -0700 Message-ID: <00fc01c4b7b7$af655b50$1a7e40ab@alphahelix> MIME-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: 7bit X-Priority: 3 (Normal) X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook, Build 10.0.6626 X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2800.1409 In-Reply-To: <33166.62.24.92.191.1098380003.squirrel~at~marge.uochb.cas.cz> Importance: Normal X-Spam-Status: No, hits=2.5 required=7.5 tests=FORGED_YAHOO_RCVD, FROM_ENDS_IN_NUMS autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net I'm sure that many researchers have similar dilemmas. Here's my solution. I use JabRef. It's a free java based reference organizer. (http://jabref.sourceforge.net) I find it to be comparable to Endnote for organizing references; however, if you are using MS Word to create articles, then the citation creation in Endnote is better. Just the opposite is true if you are using LaTex. Within the database, one can place links to a web address and/or a pdf document. However, it still doesn't solve the problem of how to get the reference information without manual entry. For that, I just have to be diligent when using a citation search engine. For example, when I find a reference of interest on SciSearch or Web of Science, I export the reference. I can then import this reference into JabRef. Joseph > -----Original Message----- > From: Computational Chemistry List > [mailto:chemistry-request~at~ccl.net] On Behalf Of Daniel Svozil > Sent: Thursday, October 21, 2004 10:33 AM > To: chemistry~at~ccl.net > Subject: CCL:How do you organize your *.pdf files? > > > Hi all, > > though my posting is not only computational chemistry > related, I think the > discussion may be of general interest. > > I would like to know, if there is any free linux solution > that would help > in organizing pdf files with the articles downloaded from the > web. I was > looking for some application/script, but I didn't find anything. > > My question is, if it is possible to build a database (e.g. > BibTeX) of pdf > files (articles) that would include information such as title, author, > journal, abstract etc. + path to the pdf file taken automatically from > *.pdf. It seems to me, that thi is may be even not possible, > as pdf format > is not a markup language (as XML) and is not suitable to such a task. > Maybe the best way would be to convert pdf to text (pdftotext > in Linux), > and than to parse the text file for the information. But such a script > would be very complicated, as format of text data differs journal from > journal, and many possibilities would have to be taken into account. > > I found one free application that makes life with my pdf mess > much easier, > it is called Quaneko (http://quaneko.sourceforge.net/), and it is > available both for Linux and Windows. What Quaneko does it > takes pdf by > pdf, converts them to text files, and than indexes those, so one can > easily query information using keywords and logical expressions. The > possibility to view a text preview or full pdf by acroread is also > avilable. Quaneko proved to be very useful and I rely on it > quite heavy. > > And what is the way you organize your pdf articles in computer? > > Thanks in advance > Dan > > P.S.; Please, post your responses to the list, so the whole > community > can benefit from them. > > > -- > Daniel Svozil, PhD > Institute of Organic Chemistry and Biochemistry > and Center for Complex Molecular Systems and Biomolecules > http://www.molecular.cz/ > Czech Republic > > phone: +420-220 410 312 > > > -= This is automatically added to each message by the mailing > script =- > To send e-mail to subscribers of CCL put the string CCL: on > your Subject: line > and send your message to: CHEMISTRY~at~ccl.net > > Send your subscription/unsubscription requests to: > CHEMISTRY-REQUEST~at~ccl.net > HOME Page: http://www.ccl.net | Jobs Page: http://www.ccl.net/jobs > > If your mail is bouncing from CCL.NET domain send it to the > maintainer: > Jan Labanowski, jlabanow~at~nd.edu (read about it on CCL Home Page) > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ > -+-+-+-+-+ > > > > > From chemistry-request@ccl.net Fri Oct 22 10:01:39 2004 Received: from supertimor.sciences.univ-nantes.fr (supertimor.sciences.univ-nantes.fr [193.52.109.8]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i9MF1bM3031132 for ; Fri, 22 Oct 2004 10:01:38 -0500 Received: from localhost (supertimor [127.0.0.1]) by supertimor.sciences.univ-nantes.fr (Postfix) with ESMTP id 27DD25F858; Fri, 22 Oct 2004 17:09:24 +0200 (CEST) Received: from supertimor.sciences.univ-nantes.fr ([127.0.0.1]) by localhost (supertimor [127.0.0.1]) (amavisd-new, port 10024) with ESMTP id 09137-07; Fri, 22 Oct 2004 17:09:23 +0200 (CEST) Received: from [193.52.103.102] (quantum.chimie.sciences.univ-nantes.fr [193.52.103.102]) by supertimor.sciences.univ-nantes.fr (Postfix) with ESMTP id 857605F855; Fri, 22 Oct 2004 17:09:23 +0200 (CEST) Message-ID: <41792425.3080002{at}univ-nantes.fr> Date: Fri, 22 Oct 2004 17:15:49 +0200 From: Bertrand Illien Reply-To: Bertrand.Illien{at}univ-nantes.fr User-Agent: Mozilla Thunderbird 0.7.3 (Windows/20040803) X-Accept-Language: fr, en MIME-Version: 1.0 To: CHEMISTRY{at}ccl.net Subject: summary :g03c 64bits vs 32 bits for opteron/athlon 64 Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 8bit X-Virus-Scanned: by amavisd-new at sciences.univ-nantes.fr X-Spam-Status: No, hits=2.5 required=7.5 tests=NO_RDNS2,SMILEY autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net FIRST MESSAGE >> >> we would like to buy a new computer for use with G03/linux. >> have you got few benchs time results of g03revC. test files ( >> test397 is fine) >> with 1/ g03 64bits compiled for opteron (or/and athlon 64) >> 2/ g03 32 bits (compiled for pentium 4) on the same opteron >> (or/and athlon 64) >> > >> does the 64bits compilation vs 32 bits improve performances ? >> >> does the new intel xeon with EM 64 perform better than P4 (1MB in >> L2) with G03 32 bits program ? >> thanks for your help. >> sincerely yours >> >> Bertrand > SUMMARY timing for test397.com : 2Ghz AMD64 (3200+, L2:1MB, socket 754) running Fedora Core 2 . Codes compiled using portland 5.1 <> - 32 bits: 10678.677u - 64 bits: 10459.699u <> Negligibly faster in 64 bits, but with advantage of large scratch files (>16 Gb) and more than 2Gb memory handling for large jobs. END SUMMARY We also take an interest in test397 timings for others CPU : opteron 248 or 250 xeon 3.0 Or 3.2GHz (FSB 533, L2=512KB, L3=1MB) Thanks in advance Bertrand ______________________________________________________________________ Bertrand ILLIEN Laboratoire de Spectrochimie et Modilisation EA 1149 - FR CNRS 2465 Faculti des Sciences et Techniques 2, rue de la Houssinihre BP 92208 44322 Nantes Cedex 3 FRANCE Tel :(+33)(0)2 51 12 55 65 - Fax : 55 67 http://www.sciences.univ-nantes.fr/spectro From chemistry-request@ccl.net Fri Oct 22 07:23:51 2004 Received: from web53910.mail.yahoo.com (web53910.mail.yahoo.com [206.190.36.220]) by server.ccl.net (8.12.8/8.12.8) with SMTP id i9MCNo3p020918 for ; Fri, 22 Oct 2004 07:23:50 -0500 Message-ID: <20041022123609.73506.qmail{at}web53910.mail.yahoo.com> Received: from [129.128.136.71] by web53910.mail.yahoo.com via HTTP; Fri, 22 Oct 2004 08:36:09 EDT Date: Fri, 22 Oct 2004 08:36:09 -0400 (EDT) From: "A. Boufarik" Subject: Background Charge To: "Comp. Chem. List" MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="0-96128173-1098448569=:72721" X-Spam-Status: No, hits=2.8 required=7.5 tests=FROM_ENDS_IN_NUMS,HTML_20_30, HTML_MESSAGE,MK_BAD_HTML_04 autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net --0-96128173-1098448569=:72721 Content-Type: text/plain; charset=us-ascii Hi all, I understand when charge is used, the charge is specified as a multiple of the electron charge (atomic units). However, if I wanted to set a proton at say 0.0 0.0 3(atomic unit) charge, should I say: 0.0 0.0 3.0 1.0 or 0.0 0.0 -1.0 I am just confused as regarrd the sign. Cheers Boufarik --------------------------------- Post your free ad now! Yahoo! Canada Personals --0-96128173-1098448569=:72721 Content-Type: text/html; charset=us-ascii
Hi all,
 
I understand when charge is used, the charge is specified as a multiple of the electron charge (atomic units). However, if I wanted to set a proton at say 0.0 0.0 3(atomic unit) charge, should I say:
 
0.0 0.0 3.0 1.0 or 0.0 0.0 -1.0
 
I am just confused as regarrd the sign.
 
Cheers
 
Boufarik


Post your free ad now! Yahoo! Canada Personals
--0-96128173-1098448569=:72721-- From chemistry-request@ccl.net Fri Oct 22 02:42:17 2004 Received: from av3-2-sn1.fre.skanova.net (av3-2-sn1.fre.skanova.net [81.228.11.110]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i9M7gF3p004600 for ; Fri, 22 Oct 2004 02:42:16 -0500 Received: by av3-2-sn1.fre.skanova.net (Postfix, from userid 502) id 7600737E44; Fri, 22 Oct 2004 09:54:33 +0200 (CEST) Received: from smtp3-2-sn1.fre.skanova.net (smtp3-2-sn1.fre.skanova.net [81.228.11.164]) by av3-2-sn1.fre.skanova.net (Postfix) with ESMTP id 6224E37F14 for ; Fri, 22 Oct 2004 09:54:33 +0200 (CEST) Received: from htu.se (h232n2fls33o1006.telia.com [217.209.70.232]) by smtp3-2-sn1.fre.skanova.net (Postfix) with ESMTP id 4D5CF37E5B for ; Fri, 22 Oct 2004 09:54:28 +0200 (CEST) Message-ID: <4178BCB4.3060901:at:htu.se> Date: Fri, 22 Oct 2004 09:54:28 +0200 From: Steven Kirk User-Agent: Mozilla/5.0 (X11; U; Linux i686; en-US; rv:1.5) Gecko/20031115 Thunderbird/0.3 X-Accept-Language: en-us, en MIME-Version: 1.0 To: CHEMISTRY:at:ccl.net Subject: How do you organize your PDF files Content-Type: text/plain; charset=us-ascii; format=flowed Content-Transfer-Encoding: 7bit X-Spam-Status: No, hits=2.6 required=7.5 tests=RCVD_IN_DYNABLOCK, RCVD_IN_SORBS autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Some more tools: Docco - http://tockit.sourceforge.net/docco/ This is written in Java, andindexes Word, Excel, OpenOffice and a few other formats as well as PDF. It is based on the Lucene toolkit http://jakarta.apache.org/lucene/docs/index.html There is also a .NET port of Lucene http://openlucene.net/ and the developing Beagle package http://www.gnome.org/projects/beagle/ Regards, Steve Kirk From chemistry-request@ccl.net Fri Oct 22 05:20:24 2004 Received: from sainfoin.extra.cea.fr (sainfoin.extra.cea.fr [132.166.172.103]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i9MAKN3p013976 for ; Fri, 22 Oct 2004 05:20:23 -0500 Received: from araneus.saclay.cea.fr (araneus.saclay.cea.fr [132.166.192.110]) by sainfoin.extra.cea.fr (8.12.10/8.12.10/CEAnet-Internet.4.0) with ESMTP id i9MAWiFI015848 for ; Fri, 22 Oct 2004 12:32:44 +0200 (MEST) Received: from nenuphar.saclay.cea.fr (unverified) by araneus.saclay.cea.fr (Content Technologies SMTPRS 4.3.14) with ESMTP id ; Fri, 22 Oct 2004 12:32:41 +0200 Received: from llb.saclay.cea.fr (llb.saclay.cea.fr [132.166.17.100]) by nenuphar.saclay.cea.fr (8.12.10/8.12.10/CEAnet-internes.4.0) with ESMTP id i9MAWhGV011774; Fri, 22 Oct 2004 12:32:43 +0200 (MEST) Received: from [132.166.18.220] (llb1220.saclay.cea.fr [132.166.18.220]) by llb.saclay.cea.fr (8.12.10/jtpda-5.3.2) with ESMTP id i9MAWZ7L013314 ; Fri, 22 Oct 2004 12:32:40 +0200 (MEST) In-Reply-To: <4178205A.6070300:at:ucla.edu> References: <33166.62.24.92.191.1098380003.squirrel:at:marge.uochb.cas.cz> <4178205A.6070300:at:ucla.edu> Mime-Version: 1.0 (Apple Message framework v619) Content-Type: text/plain; charset=ISO-8859-1; format=flowed Message-Id: Cc: CCL computational chemistry list (E-mail) From: hinsen:at:llb.saclay.cea.fr Subject: Re: CCL:How do you organize your *.pdf files? Date: Fri, 22 Oct 2004 12:33:45 +0200 To: Douglas Sievers X-Mailer: Apple Mail (2.619) X-Spam-Status: No, hits=1.0 required=7.5 tests=NO_REAL_NAME autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id i9MAKO3p013981 On Oct 21, 2004, at 22:47, Douglas Sievers wrote: > Supposedly, you can do a "reverse DOI lookup" to obtain the metadata, > which is in XML format, and that could be used to create a local > database. Unfortunately, the only Are you sure such a system exists? DOIs resolve to URLs (they can be considered "permanent URLs") and can thus point to lots of different information. A system that recognizes DOIs that point to publications and can then return a standardized bibliographical reference is not trivial to create. -- --------------------------------------------------------------------- Konrad Hinsen Laboratoire Lion Brillouin, CEA Saclay, 91191 Gif-sur-Yvette Cedex, France Tel.: +33-1 69 08 79 25 Fax: +33-1 69 08 82 61 E-Mail: hinsen:at:llb.saclay.cea.fr --------------------------------------------------------------------- From chemistry-request@ccl.net Fri Oct 22 01:56:43 2004 Received: from mallaury.noc.nerim.net (smtp-105-friday.noc.nerim.net [62.4.17.105]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i9M6uR3p002240 for ; Fri, 22 Oct 2004 01:56:37 -0500 Received: from greenpharma02 (greenpharma.net1.nerim.net [62.212.109.242]) by mallaury.noc.nerim.net (Postfix) with SMTP id A2C0762E3B; Fri, 22 Oct 2004 09:08:35 +0200 (CEST) Message-ID: <002b01c4b806$fdfd5890$0201a8c0@greenpharma02> Reply-To: "Quoc-Tuan Do" From: "Quoc-Tuan Do" To: "Daniel Svozil" Cc: References: Subject: Re: CCL:How do you organize your *.pdf files? Date: Fri, 22 Oct 2004 09:16:03 +0200 Organization: GreenPharma 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 6.00.2800.1106 X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2800.1106 X-Spam-Status: No, hits=0.0 required=7.5 tests=none autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Dear Daniel, Though this software is for Windows only, it is free and very handy: PaperWorks is by Tom Hall and can be downloaded here: http://www.mbio.ncsu.edu/BioEdit/library/library.html It can manage pdf files, abstracts from medline etc... Hope this is helpful. Best regards, Quoc-Tuan ============================================ Quoc-Tuan DO GreenPharma S.A. 3, Allie du Titane 45100 Orlians FRANCE Til : +33.2.38.25.99.80 Fax : +33.2.38.25.99.65 mail: quoctuan.do[at]greenpharma.com web : http://www.greenpharma.com ----- Original Message ----- From: "Jeff Nauss" To: "Daniel Svozil" Cc: ; "Computational Chemistry List" Sent: Thursday, October 21, 2004 10:09 PM Subject: CCL:How do you organize your *.pdf files? > "Computational Chemistry List" wrote on > 10/21/2004 10:33:23 AM: > > > And what is the way you organize your pdf articles in computer? > > For almost 15 years now, I have used a reference manager program. The > program indexes each document by a reference number and has associated > with it information such as author, title, keywords, etc. I then file > each document by the index number, whether hard copy or electronic PDF. In > the reference manager, I can search by keyword, abstract, author, date, > and so forth. I get the index number and find the document in my file. > > I first used Papyrus which was cheap, easy to use, and pretty good. But > it was not maintained well enough with updates to be useful with later > versions of MS Word. I switched to EndNote a few years ago and have been > quite happy with it. > > With EndNote I can download PubMed entries directly into the database. You > can also download information from quite a few other databases as well. > > I suppose you could do something similar with a LINUX based database > manager if not a reference manager program. > > Jeff > -- > Jeffrey L. Nauss, Ph.D. > Lead Training Scientist > > Accelrys > 9685 Scranton Road > San Diego, CA 92121-1761 > > Phone: 858-799-5555 > Fax: 858-799-5100 > E-mail: jnauss[at]accelrys.com > http://www.accelrys.com/training > > > > > -= This is automatically added to each message by the mailing script =- > To send e-mail to subscribers of CCL put the string CCL: on your Subject: line > and send your message to: CHEMISTRY[at]ccl.net > > Send your subscription/unsubscription requests to: CHEMISTRY-REQUEST[at]ccl.net > HOME Page: http://www.ccl.net | Jobs Page: http://www.ccl.net/jobs > > If your mail is bouncing from CCL.NET domain send it to the maintainer: > Jan Labanowski, jlabanow[at]nd.edu (read about it on CCL Home Page) > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ > > > > > From chemistry-request@ccl.net Fri Oct 22 10:07:03 2004 Return-Path: Message-ID: <784B3A3328E3754DB82027F6BA16467F1F8080!at!atd-ntd.atd.acs.org> From: William Shepherd To: chemistry!at!ccl.net Subject: Journal of Chemical Theory and Computation on the Web Date: Fri, 22 Oct 2004 09:19:39 -0400 Dear CCL subscribers and ACS Computers in Chemistry Division Members The Journal of Chemical Theory and Computation is now available online as Articles ASAP at http://pubs.acs.org/JCTC . In addition, you can register now to receive your personal print copy of the January 2005 inaugural issue at http://pubs.acs.org/promo/jctcsample/ . The Journal of Chemical Theory and Computation (JCTC) publishes papers reporting new theories, methodology and/or important applications in quantum chemistry, molecular dynamics, and statistical mechanics. Topics in this bi-monthly journal include: - advances in ab initio quantum mechanics - density functional theory - molecular design - properties of new materials - surface science - Monte Carlo simulations - solvation models - QM/MM calculations - biomolecular structure prediction - molecular dynamics in the broadest sense including gas-phase dynamics, ab initio dynamics, biomolecular dynamics, and protein folding Offering the ACS Paragon System for online manuscript submission, JCTC allows you to access a personalized Web page tailored to your preferences, submit manuscripts in environments customized for the journal and the community it serves, quickly learn the status of your manuscript, and submit files in a wide range of supported formats. Complete a brief, one-time registration at http://paragon.acs.org . The JCTC also offers two free options for e-mail notification of new articles published on the Web. With ASAP Alerts, you can receive daily or weekly e-mail messages alerting you as soon as individual articles are released on the Web. With Table of Contents Alerts, you receive e-mail alerts of the table of contents of complete issues on the day they are posted on the Web. Go to http://pubs.acs.org/journals/asap to sign up. Register for your personal print issue today at http://pubs.acs.org/promo/jctcsample/ , and go to the journal homepage at http://pubs.acs.org/JCTC to access Articles ASAPSM. From chemistry-request@ccl.net Fri Oct 22 10:58:43 2004 Received: from web20226.mail.yahoo.com (web20226.mail.yahoo.com [216.136.227.3]) by server.ccl.net (8.12.8/8.12.8) with SMTP id i9MFwgM3003822 for ; Fri, 22 Oct 2004 10:58:42 -0500 Message-ID: <20041022161058.11446.qmail{at}web20226.mail.yahoo.com> Received: from [193.205.5.2] by web20226.mail.yahoo.com via HTTP; Fri, 22 Oct 2004 18:10:58 CEST Date: Fri, 22 Oct 2004 18:10:58 +0200 (CEST) From: PB Coto Subject: CCL: Neutral arginine parameters for amber To: CHEMISTRY{at}ccl.net MIME-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit X-Spam-Status: No, hits=1.5 required=7.5 tests=FROM_ENDS_IN_NUMS autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Dear All, Could anyone please send me a reference where I can find amber parameters for neutral arginine? Thanks in advance Pedro. ______________________________________________ Renovamos el Correo Yahoo!: !100 MB GRATIS! Nuevos servicios, mas seguridad http://correo.yahoo.es From chemistry-request@ccl.net Fri Oct 22 14:37:23 2004 Received: from web53906.mail.yahoo.com (web53906.mail.yahoo.com [206.190.36.216]) by server.ccl.net (8.12.8/8.12.8) with SMTP id i9MJbMM3015901 for ; Fri, 22 Oct 2004 14:37:22 -0500 Message-ID: <20041022194939.42199.qmail|at|web53906.mail.yahoo.com> Received: from [129.128.136.71] by web53906.mail.yahoo.com via HTTP; Fri, 22 Oct 2004 15:49:39 EDT Date: Fri, 22 Oct 2004 15:49:39 -0400 (EDT) From: "A. Boufarik" Subject: Gaussian : Charge and potential energy matrix To: "Comp. Chem. List" MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="0-915337882-1098474579=:40499" X-Spam-Status: No, hits=1.8 required=7.5 tests=FROM_ENDS_IN_NUMS,HTML_MESSAGE, MK_BAD_HTML_04 autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net --0-915337882-1098474579=:40499 Content-Type: text/plain; charset=us-ascii Hi all, I am trying to understand how the charge keyword works in particular the meaning of Potential Energy Matrix tha G03 outputs when IOp(3/33=1) is requested. It does not seem to correspond to < X_i | 1 / |r - x| | X_j >. In fact, if this were the case then using a positive and negative charge should produce the same matrix (within a sign). Any comment as for the meaning of Potential Energy Matrix ? Cheers Boufarik --------------------------------- Post your free ad now! Yahoo! Canada Personals --0-915337882-1098474579=:40499 Content-Type: text/html; charset=us-ascii
Hi all,
 
I am trying to understand how the charge keyword works in particular the meaning of Potential Energy Matrix tha G03 outputs when IOp(3/33=1) is requested.
 
It does not seem to correspond to < X_i  | 1 / |r - x| | X_j >. In fact, if this were the case then using a positive and negative charge should produce the same matrix (within a sign).
 
Any comment as for the meaning of Potential Energy Matrix ?
 
Cheers
 
Boufarik


Post your free ad now! Yahoo! Canada Personals
--0-915337882-1098474579=:40499--