From chemistry-request@server.ccl.net Fri Apr 14 04:27:12 2000 Received: from iris.sipp.ac.cn ([202.127.25.14]) by server.ccl.net (8.8.7/8.8.7) with SMTP id EAA26695 for ; Fri, 14 Apr 2000 04:25:21 -0400 Received: from iris.sipp.ac.cn (202.127.25.133) by iris.sipp.ac.cn (EMWAC SMTPRS 0.81) with SMTP id ; Fri, 14 Apr 2000 16:27:59 +0800 Sender: user@ccl.net Message-ID: <38F6C7B5.1B4B00B4@iris.sipp.ac.cn> Date: Fri, 14 Apr 2000 16:24:37 +0900 From: Mao Xiang Organization: iris.sipp.ac.cn X-Mailer: Mozilla 4.51C-SGI [en] (X11; I; IRIX 6.3 IP32) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net Subject: problem in promd of gromos96 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hello, everyone: Does anyone have the experience that what I should do when I met the following informations in gromos96,when I run promd? ------------------------------------------------- NONBML: WARNING, NOT ALL EXCLUDED NEIGHBOUR WERE SCANNED IN THE PAIR-LIST NONBML: WARNING, NOT ALL THIRD NEIGHBOUR WERE SCANNED IN THE PAIR-LIST ------------------------------------------------ Thanks a lot. regards, mao ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | Mao Xiang | | Lab of Molecular Regulation for Microbial Secondary Metabolism | | Shanghai institute of Plant Physiology, Academia Sinica | | 300 Fenglin Road, Shanghai, China, 200032 | | Tel: +86-21-64042090-4791 | | Fax: +86-21-64042385 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ From chemistry-request@server.ccl.net Fri Apr 14 04:28:29 2000 Received: from sg2.csrsrc.mi.cnr.it (sg2.csrsrc.mi.cnr.it [155.253.3.253]) by server.ccl.net (8.8.7/8.8.7) with SMTP id EAA26707 for ; Fri, 14 Apr 2000 04:28:22 -0400 Received: from csrsrc.mi.cnr.it by sg2.csrsrc.mi.cnr.it via ESMTP (940816.SGI.8.6.9/940406.SGI.AUTO) for id HAA13283; Fri, 14 Apr 2000 07:36:20 -0700 Sender: alex@csrsrc.mi.cnr.it Message-ID: <38F6D8A3.CE2B77B7@csrsrc.mi.cnr.it> Date: Fri, 14 Apr 2000 10:36:52 +0200 From: Alessandro Pandini X-Mailer: Mozilla 4.03 [en] (X11; I; AIX 4.1) MIME-Version: 1.0 To: chemistry@ccl.net Subject: CCL: Protonated Side-chains Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear all, I have a protein obtained by homology modelling. I'd like to properly protonate the sidechain of the active site. I have some good ideas, but I'm looking for guidelines. Does anyone know a good review about? Is there anyone around who has already dealt with this problem? Thanks Alex From chemistry-request@server.ccl.net Fri Apr 14 05:21:42 2000 Received: from smtprelay.ruc.dk (smtprelay.ruc.dk [130.225.220.22]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id FAA27114 for ; Fri, 14 Apr 2000 05:21:41 -0400 Received: from virgil.ruc.dk (virgil.ruc.dk [130.225.220.110]) by smtprelay.ruc.dk (8.9.3/8.9.3) with ESMTP id LAA10645; Fri, 14 Apr 2000 11:17:35 +0200 (MET DST) Received: from VIRGIL/SpoolDir by virgil.ruc.dk (Mercury 1.44); 14 Apr 00 11:28:11 +0100 Received: from SpoolDir by VIRGIL (Mercury 1.44); 14 Apr 00 11:28:06 +0100 From: "Jens Spanget-Larsen" Organization: Roskilde Universitetscenter To: Jochen Kuepper , Brian Space , chemistry@ccl.net Date: Fri, 14 Apr 2000 11:27:41 +0100 Subject: Re: CCL:Reduced Mass Priority: normal X-mailer: Pegasus Mail for Windows (v2.23) Message-ID: <151073384C@virgil.ruc.dk> Jochen Kuepper : > Jens Spanget-Larsen gave a nice reply to a question: > > > In Gaussian output how is the reduced mass defined? > > Well, I put it into LaTeX - do whatever you want with the > document. Probably it can be put somewhere on the CCL webpages ? Dear Jochen, thank you for your effort. I attach a Word97 version. Yours, Jens >--< =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= JENS SPANGET-LARSEN Phone: +45 4674 2000 (RUC) Department of Chemistry +45 4674 2710 (direct) Roskilde University (RUC) Fax: +45 4674 3011 P.O.Box 260 E-Mail: JSL@virgil.ruc.dk DK-4000 Roskilde, Denmark http://www.rub.ruc.dk/dis/chem/psos/ =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= From chemistry-request@server.ccl.net Fri Apr 14 05:21:56 2000 Received: from smtprelay.ruc.dk (smtprelay.ruc.dk [130.225.220.22]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id FAA27123 for ; Fri, 14 Apr 2000 05:21:55 -0400 Received: from virgil.ruc.dk (virgil.ruc.dk [130.225.220.110]) by smtprelay.ruc.dk (8.9.3/8.9.3) with ESMTP id LAA10648; Fri, 14 Apr 2000 11:17:35 +0200 (MET DST) Received: from VIRGIL/SpoolDir by virgil.ruc.dk (Mercury 1.44); 14 Apr 00 11:28:12 +0100 Received: from SpoolDir by VIRGIL (Mercury 1.44); 14 Apr 00 11:28:06 +0100 From: "Jens Spanget-Larsen" Organization: Roskilde Universitetscenter To: Jochen Kuepper , Brian Space , chemistry@ccl.net Date: Fri, 14 Apr 2000 11:27:40 +0100 X-pmuue: redmass.doc X-finfo: DOS,"redmass.doc",,,,Binary Subject: Re: CCL:Reduced Mass Priority: normal X-mailer: Pegasus Mail for Windows (v2.23) Message-ID: <15107334A9@virgil.ruc.dk> * This message contains the file 'redmass.doc', which has been * uuencoded. If you are using Pegasus Mail, then you can use * the browser's eXtract function to lift the original contents * out to a file, otherwise you will have to extract the message * and uudecode it manually. begin 660 redmass.doc MT,\1X*&Q&N$`````````````````````/@`#`/[_"0`&```````````````! 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M````$@`*\`@````!!`````X``%,`"_`>````OP$``!``RP$`````_P$```@` M!`,)````/P,!``$````1\`0````!````,0<``/__%````!,`2@!E`&X`0`@`',`80!V`&4`(`!O`&8`(`!2 M`&4`9`!-`&$` M`$,`.@!<`%<`20!.`$0`3P!7`%,`7`!$`&4`0!M`&(`;P!L````,R:0`0```@L&!`("`@("!`,````` M```````````````!`````````$$`<@!I`&$`;````#\UD`$```('`PD"`@4" M!`0#`````````````````````0````````!#`&\`=0!R`&D`90!R`"``3@!E M`'<````B``0`,0B(&```T`(``&@!``````MM1(8+;42&!VU$A@(```````D! M``#K!0```0`#````!``#$`P```````````````$``0````$`````````(0,` M```````````````````````````````````````````````````````````` M```````````````````````````````````````````````````````````` M```````````````````````````````````````````````````````````` M```````````````````````````````````````````````````````````` M```````````````````````````````````````````````````````````` M```````````````````````````````````````````````````````````` M```````````````````````````````````````````````````````````` MI0;`![0`M`"``!(P```0`!D`9````!D```!$!P`````````````````````` M```````````````````````````````````````````````````````````` M``````(``````/__$@``````(`!$`#H`7`!-`%,`3P!F`&8`:0!C`&4`7`!4 M`&4`;0!P`&P`80!T`&4` Received: by studs3.sci.kun.nl via egonw@localhost id LAA11984 (8.8.8/3.1); Fri, 14 Apr 2000 11:57:58 +0200 (MET DST) Date: Fri, 14 Apr 2000 11:57:58 +0200 (MET DST) Message-Id: <200004140957.LAA11984@studs3.sci.kun.nl> To: CHEMISTRY@ccl.net, chatt@tniri.go.jp Subject: re: New Journal > Because it is a free online journal, papers published in IJMS will > receive very high publicity. Authors who have published in MDPI's other > journals (e.g., MOLECULES at http://www.mdpi.org/molecules/) have informed us that they > receive many more reprint requests than for other papers. Don't take this question to be negative... I like MOLECULES very much, and think it is an important step towards the new economy.... You mention "receive very high publicity", but how high is that? Do you have numbers on average amount of readers per articles per month for example? And how does that compare to other (paper) journals? Just wondering... Egon Willighagen From chemistry-request@server.ccl.net Fri Apr 14 04:16:14 2000 Received: from yogi.pc1.uni-duesseldorf.de (yogi.pc1.uni-duesseldorf.de [134.99.152.44]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id EAA26663 for ; Fri, 14 Apr 2000 04:16:13 -0400 Received: (from jochen@localhost) by yogi.pc1.uni-duesseldorf.de (8.9.3/8.9.3) id KAA10229; Fri, 14 Apr 2000 10:16:09 +0200 MIME-Version: 1.0 Content-Type: multipart/mixed; boundary="jVOBVk3WYM" Content-Transfer-Encoding: 7bit Message-ID: <14582.54217.108808.196894@yogi.pc1.uni-duesseldorf.de> Date: Fri, 14 Apr 2000 10:16:09 +0200 (CEST) From: Jochen Kuepper To: Jens Spanget-Larsen Cc: Brian Space , chemistry@ccl.net Subject: CCL:Reduced Mass In-Reply-To: <2A1037412@virgil.ruc.dk> References: <2A1037412@virgil.ruc.dk> X-Mailer: VM 6.72 under 21.1 (patch 9) "Canyonlands" XEmacs Lucid --jVOBVk3WYM Content-Type: text/plain; charset=iso-8859-1 Content-Description: message body text Content-Transfer-Encoding: quoted-printable Jens Spanget-Larsen gave a nice reply to a question: > > In Gaussian output how is the reduced mass defined? Well, I put it into LaTeX - do whatever you want with the document. Probably it can be put somewhere on the CCL webpages ? Jochen --=20 Heinrich-Heine-Universit=E4t Institut f=FCr Physikalische Chemie I Jochen K=FCpper Universit=E4tsstr. 1, Geb. 26.43 Raum 02.29 40225 D=FCsseldorf, Germany phone ++49-211-8113681, fax ++49-211-8115195 http://www.Jochen-Kuepper.de --jVOBVk3WYM Content-Type: text/plain; charset=iso-8859-1 Content-Disposition: attachment; filename="GaussianOutput.tex" Content-Transfer-Encoding: quoted-printable \documentclass[12pt,a4paper]{article} \usepackage{amsfonts} \usepackage[intlimits]{amsmath} \usepackage{amssymb} \usepackage{ccfonts} \usepackage[T1]{fontenc} \usepackage[vmargin=3D20mm,hmargin=3D25mm]{geometry} \usepackage[latin1]{inputenc} \usepackage{units} % Dirac Notation, Kommutator, ... \newcommand{\ket}[1] {\vert #1 \rangle} % | psi > \newcommand{\bra}[1] {\langle #1 \vert} % < psi | \newcommand{\braket}[2] {\langle #1 \mid #2 \rangle} % < psi | psi= > \newcommand{\braopket}[3] {\left< #1 \left| #2 \right| #3 \right>} %= < psi | op | psi > \newcommand{\commutate}[2] {\left[ #1 , #2 \right]} % [ A, B ] \begin{document} \title{Understanding Gaussian Output} \author{Jochen K=FCpper} \date{\today} \maketitle \section{Reduced masses in Gaussian output} \hspace*{10mm} \begin{minipage}[l]{100mm} \begin{verbatim} From: Jens Spanget-Larsen Subject: CCL:Reduced Mass Date: Thu, 13 Apr 2000 17:01:54 +0100 \end{verbatim} \end{minipage} \\[2mm] \noindent Let the r'th normal mode vector of unit length be given as \begin{align} Q_r & =3D \sum_i c_{ir} q_i \\ q_i & =3D \sqrt{m_i} x_i \end{align} where the sum is over the 3N mass-weighted atomic displacement coordinates $q$. $m$ are the corresponding atomic masses in \unit{amu}, and $x$ the cartesian displacement coordinates (in \AA{}ngstrom). The "reduced mass" $M$ in \unit{amu} may then be obtained as \begin{equation} M_r =3D \sum_i \frac{m_i}{c_{ir}^2} \end{equation} The "normal coordinates" printed by Gaussian apparently correspond to cartesian vectors (in \AA{}ngstrom) normalized to unit length; in order to obtain the proper length of this vector, the printed coefficients d must be multiplied by the inverse square root of the reduced mass: \begin{equation} d_{ir} =3D \frac{1}{\sqrt{M_r}} d_{ir}^{\text{printed}} \end{equation} The proper cartesian displacement vector is then obtained as \begin{equation} X_r =3D \sum_i d_{ir} x_i \end{equation} The coefficients $c$ and $d$ are related by \begin{equation} d_{ir} =3D c_{ir} \frac{1}{\sqrt{m_i}} \end{equation} and we have the following relation \begin{equation} \left| X_r \right| =3D \left| Q_r \right| \frac{1}{\sqrt{M_r}} \end{equation} The inverse square root of the reduced mass is simply the length of the cartesian displacement vector $X$ for unit displacement along norma= l mode $Q$. \end{document} --jVOBVk3WYM-- From chemistry-request@server.ccl.net Fri Apr 14 09:34:12 2000 Received: from atc.atccu.chula.ac.th (un@atc.atccu.chula.ac.th [192.207.64.1]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id JAA29425 for ; Fri, 14 Apr 2000 09:34:09 -0400 Received: from localhost (un@localhost) by atc.atccu.chula.ac.th (8.9.1/8.9.1) with ESMTP id UAA07141 for ; Fri, 14 Apr 2000 20:47:15 +0700 Date: Fri, 14 Apr 2000 20:47:15 +0700 (ICT) From: chinapong kritayakornupong To: chemistry@ccl.net Subject: van der walls radius Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear all, What's program that can calculate van der walls radius of functional groups such as CH3, i-Pr, t-Bu group? How can I find van der walls radius of functional from expermental data? Sincerely Your, Chinapong %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% %% Chinapong Kritayakornupong %% %% M.Sc. student %% %% Department of Chemistry %% %% Faculty of Science %% %% Chulalongkorn University %% %% Thailand 10330 %% %% Office Room (66)(2)2185221-2 %% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% From chemistry-request@server.ccl.net Fri Apr 14 12:36:21 2000 Received: from eeyore.cc.uic.edu (eeyore.cc.uic.edu [128.248.171.51]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id MAA30572 for ; Fri, 14 Apr 2000 12:36:21 -0400 Received: from [131.193.195.200] (4146ses.chem.uic.edu [131.193.195.200]) by eeyore.cc.uic.edu (8.9.3/8.9.3) with ESMTP id LAA01034 for ; Fri, 14 Apr 2000 11:33:09 -0500 (CDT) Mime-Version: 1.0 X-Sender: cai@mailserv.uic.edu Message-Id: Date: Fri, 14 Apr 2000 11:30:31 -0500 To: chemistry@ccl.net From: Lisheng Cai Subject: presentation of structures in chemical journals Content-Type: text/plain; charset="us-ascii" ; format="flowed" Dear Sir/Madam: I am trying to present a lot of structures from quantum mechanics calculations in chemical journals. The structures should be represented by open circles connected by hollow tubes, with atomic symbol within the circle. Selected bond lengths and angles could be added in those diagrams. I believe that this is the most economic way to present a lot of information in a limited space. A lot of papers published in the literature related calculations have these. I can not find a program to do so. For example, cerius2, insightII, and chemdraw, and the like do not present such structures. Ideally, I need a program which can also import either Cartesian coordinates or internal coordinates. Sincerely Lisheng Cai email: cai@uic.edu From chemistry-request@server.ccl.net Fri Apr 14 13:57:03 2000 Received: from wodc7-1.relay.mail.uu.net (wodc7-1.relay.mail.uu.net [199.171.54.114]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id NAA31131 for ; Fri, 14 Apr 2000 13:57:02 -0400 Received: from wodc7-1.uucp-gw.mail.uu.net by wodc7mr0.ffx.ops.us.uu.net with ESMTP (peer crosschecked as: wodc7-1.uucp-gw.mail.uu.net [199.171.54.178]) id QQikxj19278 for ; Fri, 14 Apr 2000 17:56:47 GMT Received: from wodc7uc0.ffx.ops.us.uu.net by wodc7ug0.ffx.ops.us.uu.net with SMTP (peer crosschecked as: wodc7-2.uucp.uu.net [199.171.54.180]) id QQikxj14656 for ; Fri, 14 Apr 2000 17:56:47 GMT Received: from m10.UUCP by wodc7uc0.ffx.ops.us.uu.net with UUCP/RMAIL ; Fri, 14 Apr 2000 17:56:47 +0000 Received: from gershwin by m10.gaussian.com; Fri, 14 Apr 2000 13:25:16 -0400 Received: (from ochtersk@localhost) by gershwin (980427.SGI.8.8.8/980728.SGI.AUTOCF) id NAA25347 for CHEMISTRY@ccl.net; Fri, 14 Apr 2000 13:24:21 -0400 (EDT) Date: Fri, 14 Apr 2000 13:24:20 -0400 From: Joseph Ochterski To: CHEMISTRY@ccl.net Subject: Re: CCL:Reduced Mass Message-ID: <20000414132420.F127134@gershwin> Reply-To: gaussian.com!ochtersk@gaussian.com References: <38F4BDCB.F8B8CD0D@space1.chemistry.duq.edu> Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii X-Mailer: Mutt 0.95.4i In-Reply-To: <38F4BDCB.F8B8CD0D@space1.chemistry.duq.edu>; from Brian Space on Wed, Apr 12, 2000 at 02:17:47PM -0400 On Wed, Apr 12, at 02:17:47PM -0400, Brian Space wrote: > > In Gaussian output how is the reduced mass defined? I have written a white paper on this subject, which explains in detail both how and why the reduced mass is calculated this way. It also has other useful information closely related to this subject, like what to do when the low frequency modes for translation and rotation are too large. It is available on the Gaussian, Inc. web site: http://www.gaussian.com/vib.htm -- Joseph Ochterski, Ph.D Senior Customer Service Scientist help@gaussian.com From chemistry-request@server.ccl.net Fri Apr 14 17:50:13 2000 Received: from ccl.net (atlantis.ccl.net [192.148.249.4]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id RAA32179 for ; Fri, 14 Apr 2000 17:50:13 -0400 Received: from mail.jakinternet.co.uk (qmailr@[212.41.41.61]) by ccl.net (8.9.3/8.9.3/OSC 2.0) with SMTP id RAA10527 for ; Fri, 14 Apr 2000 17:50:09 -0400 (EDT) Received: (qmail 25406 invoked from network); 14 Apr 2000 21:58:59 -0000 Received: from unknown (HELO smtp.jakinternet.co.uk) (root@212.41.41.7) by smtp.jakinternet.co.uk with SMTP; 14 Apr 2000 21:58:59 -0000 Received: from l7p8h3 ([195.217.160.22]) by smtp.jakinternet.co.uk ; Fri, 14 Apr 2000 16:13:02 -0000 From: "W a t e r B o a r d . C o m" To: Date: Fri, 14 Apr 2000 16:02:53 +0000 Subject: W a t e r B o a r d . C o m Reply-To: info@waterboard.com Organization: WaterBoard.com MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Priority: 3 Message-ID: <95572518201@smtp.jakinternet.co.uk> Interested in the Water Industry ? http://www.waterboard.com/ The Search Engine for the Water Industry! Thank You From chemistry-request@server.ccl.net Fri Apr 14 17:50:29 2000 Received: from mail.jakinternet.co.uk (qmailr@[212.41.41.61]) by server.ccl.net (8.8.7/8.8.7) with SMTP id RAA32193 for ; Fri, 14 Apr 2000 17:50:28 -0400 Received: (qmail 25725 invoked from network); 14 Apr 2000 21:59:52 -0000 Received: from unknown (HELO smtp.jakinternet.co.uk) (root@212.41.41.7) by smtp.jakinternet.co.uk with SMTP; 14 Apr 2000 21:59:52 -0000 Received: from l7p8h3 ([195.217.160.22]) by smtp.jakinternet.co.uk ; Fri, 14 Apr 2000 16:13:18 -0000 From: "W a t e r B o a r d . C o m" To: Date: Fri, 14 Apr 2000 16:03:09 +0000 Subject: W a t e r B o a r d . C o m Reply-To: info@waterboard.com Organization: WaterBoard.com MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Priority: 3 Message-ID: <95572519801@smtp.jakinternet.co.uk> Interested in the Water Industry ? http://www.waterboard.com/ The Search Engine for the Water Industry! Thank You