From owner-chemistry@ccl.net Tue Mar 26 03:18:48 1996 Received: from bedrock.ccl.net for owner-chemistry@ccl.net by www.ccl.net (8.7.1/950822.1) id CAA10937; Tue, 26 Mar 1996 02:49:51 -0500 (EST) Received: from goliat.ugr.es for aentrena@goliat.ugr.es by bedrock.ccl.net (8.7.1/950822.1) id CAA20276; Tue, 26 Mar 1996 02:49:45 -0500 (EST) Received: from quimfarm2 (quimfarm2.ugr.es [150.214.65.52]) by goliat.ugr.es (8.6.10/8.6.12) with SMTP id IAA03694 for ; Tue, 26 Mar 1996 08:51:06 GMT Date: Tue, 26 Mar 1996 08:51:06 GMT Message-Id: <199603260851.IAA03694@goliat.ugr.es> X-Sender: aentrena@goliat.ugr.es Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" To: chemistry@ccl.net From: aentrena@goliat.ugr.es (Antonio Entrena Guadix ) Subject: Phase angle X-Mailer: Hello to all: I am loocking for a program to calculate the phase angle in a five- six or seven-membered rings. As a input data I would like to use the MM3 output coordinates. Please, e-mail directly and I will send the summary to the net. Thanks in advance A. Entrena From chmjdr@nus.sg Tue Mar 26 03:41:53 1996 Received: from sable.nus.sg for chmjdr@nus.sg by www.ccl.net (8.7.1/950822.1) id CAA10882; Tue, 26 Mar 1996 02:30:28 -0500 (EST) Received: from leonis.nus.sg (leonis.nus.sg [137.132.1.18]) by sable.nus.sg (8.6.10/8.6.9) with ESMTP id PAA27646 for ; Tue, 26 Mar 1996 15:30:05 +0800 Received: from [137.132.36.67] ([137.132.36.67]) by leonis.nus.sg (8.6.10/8.6.9/CNS-3.5) with SMTP id PAA05714 for ; Tue, 26 Mar 1996 15:29:59 +0800 X-Sender: chmjdr@leonis.nus.sg Message-Id: Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Tue, 26 Mar 1996 15:33:35 +0800 To: chemistry@www.ccl.net From: chmjdr@leonis.nus.sg (Ranford J D) Subject: SQUAD and PSEQUAD programs Dear all, We are trying to locate a program which will determine binding and stability constants (metal and proton) for a series of ligands with transition metal complexes. Because of the poor aqueous solubility of our system we must work at low concentrations with ca. 25 % DMSO which requires us to use electronic spectra to determine the constants. Does anyone know of a sit which contains freeware versions of the programs SQUAD or PSEQUAD (or equivalent) for Mac or PC? Any help would be much appreciated. John ********************************* John Ranford Department of Chemistry National University of Singapore Kent Ridge Crescent Singapore 119260 FAX 7791691 E-mail chmjdr@nus.sg ********************************* From rander@mesaani.uku.fi Tue Mar 26 03:54:37 1996 Received: from mesaani.uku.fi for rander@mesaani.uku.fi by www.ccl.net (8.7.1/950822.1) id CAA10923; Tue, 26 Mar 1996 02:46:33 -0500 (EST) Received: by mesaani.uku.fi (AIX 3.2/UCB 5.64/4.03) id AA16099; Tue, 26 Mar 1996 09:49:22 +0200 Date: Tue, 26 Mar 1996 09:49:21 +0200 (WET) From: Reimo Rander To: chemistry@www.ccl.net Subject: CCL: Could you help me(Cd parameters)? Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear CCL-ers! I am working with metallothioneins. In my case I have only Cd metals. Now, could anybody tell me how can I get the parameters for Cd and how to explane to CHARMm (I'm working with Quanta and CHARMm) that I got Cd-s in my protein and that they are bonded to Cys S groups? Thanks in advance Reimo Rander ============================================================================ Reimo Rander student of BIOCHEMISTRY, 3rd grade, University of Tartu, ESTONIA Office: Room 127, Inst of Molecular and Cell Biology, Dpment of Biochemistry Vanemuise 46 EE2400 Tartu Estonia Phone: (372) 7430-235 Fax: (372) 7430-235 Email: reimo@mega.chem.ut.ee ============================================================================ From unipune.ernet.in!gadre@iucaa.ernet.in Tue Mar 26 05:18:48 1996 Received: from sangam.ncst.ernet.in for unipune.ernet.in!gadre@iucaa.ernet.in by www.ccl.net (8.7.1/950822.1) id FAA12769; Tue, 26 Mar 1996 05:07:18 -0500 (EST) Received: from iucaa.UUCP (uucp@localhost) by sangam.ncst.ernet.in (8.6.12/8.6.6) with UUCP id PAA01774 for CHEMISTRY@www.ccl.net; Tue, 26 Mar 1996 15:39:47 +0530 Received: from unipune.ernet.in by iucaa (4.1/SMI-4.1) id AA13298; Tue, 26 Mar 96 15:30:46+050 Received: by unipune.ernet.in (5.0/SMI-SVR4.1.0) id AA27465; Tue, 26 Mar 1996 15:18:10 +0500 Date: Tue, 26 Mar 1996 15:18:10 +0500 From: gadre@unipune.ernet.in (Faculty) Message-Id: <9603262018.AA27465@unipune.ernet.in> To: CHEMISTRY@www.ccl.net Subject: Professor Kuczkowski Cc: gadre@unipune.ernet.in Dear Sirs : I'll appreciate receiving e-mail address of Professor Robert L. Kuczkowski, Department of Chemistry, Michigan University. Thanks a lot! .............................................Professor Shridhar R. Gadre gadre@parcom.ernet.in March 25, 1996. gadre@unipune.ernet.in From patrick@hartree2.rug.ac.be Tue Mar 26 10:18:50 1996 Received: from mserv.rug.ac.be for patrick@hartree2.rug.ac.be by www.ccl.net (8.7.1/950822.1) id JAA16932; Tue, 26 Mar 1996 09:44:02 -0500 (EST) Received: from allserv.rug.ac.be by mserv.rug.ac.be with SMTP id AA00615 (5.67b/IDA-1.5 for ); Tue, 26 Mar 1996 15:43:53 +0100 Received: from hartree2.rug.ac.be by allserv.rug.ac.be (5.x/SMI-SVR4) id AA27401; Tue, 26 Mar 1996 15:43:51 +0100 Received: by hartree2.rug.ac.be (AIX 4.1/UCB 5.64/4.03) id AA10264; Tue, 26 Mar 1996 15:43:33 +0100 Date: Tue, 26 Mar 1996 15:43:33 +0100 (NFT) From: Patrick Bultinck To: CCL Subject: Dipole moment origin and electrostatics Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear, I have a simple general question, which is troubling me. In an article by a well-known author several complexes are compared, and a Kitaura-Morokuma decomposition analysis carried out. From this analysis we see that the electrostatic interaction is the most important. Okay so far, but the author then calculates the dipole moment to explain this, and he calculates the dipole moment. This is important since the M-O distance is smaller than M-N, while for the N case the electrostatic interaction is stronger. He finds that the dipole moment for NH3 is closer to M than in case of H2O which should then explain a) the bond lengths and b) the stronger electrostatic interaction, and this despite mu (H2O) > mu (NH3). (Z*mu)/r^2 you know. All this explains everything very good, but... I have a problem with this. All of the ion-ligand interaction is moved into the ion-dipole interaction, what about the rest of the multipoles ? This is especially interesting since when repeating some calculations by him, I found that he simply put the origin of the dipole in the center of mass. I would think that if you want to reduce the ion-ligand interaction to an ion-dipole model, you should choose your origin such that most of the higher order poles are minimal, so that you make the smallest mistake. If you do not do so, it would seems to me that one could think of some ligand, which has a smaller interaction energy, but still has it's dipole closer to the ion because you chose things so that the center of mass was closer to the ion (say, throw a CH3 instead of H in it)... If you want to compare some electrostatic interactions between different ligands with the same ion, and you want to make use of ion-dipole interactions to explain your observations, then how should you take the ORIGIN of the dipole vector ? Simply taking it in the center of mass seems like 'forget about the electrons, just have a look at nuclei'. Is the fact that things are so well explained by the center-of-mass-origin coincidence, or am I missing the point (which is probably true). Thanks, Patrick Bultinck Quantum chemistry University of Ghent Belgium From risser@boisdarc.etsu.edu Tue Mar 26 14:19:10 1996 Received: from boisdarc.etsu.edu for risser@boisdarc.etsu.edu by www.ccl.net (8.7.1/950822.1) id NAA21182; Tue, 26 Mar 1996 13:45:01 -0500 (EST) Received: by boisdarc.etsu.edu (AIX 4.1/UCB 5.64/4.03) id AA42196; Tue, 26 Mar 1996 12:42:47 -0600 Date: Tue, 26 Mar 1996 12:42:47 -0600 (CST) From: Steven M Risser To: chemistry@www.ccl.net Subject: Dipole moment origin and electrostatics Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Patrick Bultinck recently asked about the choice of the origin for the dipole moment. The choice of origin will not matter if the net charge on the system is zero. The dipole moment of a neutral system is independent of the origin. The higher order terms, however, will depend on the choice of the origin. ______________________________________________________________________________ Dr. Steven M. Risser Department of Physics East Texas State University Commerce, TX 75429 USA EML : risser@boisdarc.etsu.edu ______________________________________________________________________________ From ross@cgl.ucsf.EDU Tue Mar 26 14:40:34 1996 Received: from socrates.ucsf.EDU for ross@cgl.ucsf.EDU by www.ccl.net (8.7.1/950822.1) id OAA21342; Tue, 26 Mar 1996 14:08:21 -0500 (EST) From: Received: (from ross@localhost) by socrates.ucsf.EDU (8.7.3/GSC4.25) id LAA23202 for chemistry@www.ccl.net; Tue, 26 Mar 1996 11:08:14 -0800 (PST) Date: Tue, 26 Mar 1996 11:08:14 -0800 (PST) Message-Id: <199603261908.LAA23202@socrates.ucsf.EDU> To: chemistry@www.ccl.net Subject: mass-weighted RMS I am interested in people's opinions on use of RMS comparisons of different conformations of the same molecule. To my mind, the mass-weighted approach is more appropriate than the unweighted, geometric approach. I.e. mass-weighted: RMS = sqrt( (d1^2 * mass1 + d2^2 * mass2 + d3^2 * mass3 ...) / total_mass) as opposed to geometric: RMS = sqrt(d1^2 + d2^2 + d3^2 ...) where 'd1' is the distance between the positions of atom 1 in 2 conformers. The rationale for 'preferring' heavier atoms is that they are less mobile (it takes more energy to get them moving at a given velocity) and therefore more indicative of structure. Is there any situation where mass-weighting would not be desirable? This issue arose when someone compared the results of my trajectory analysis program, Carnal (part of AMBER), with RMS measurements obtained using another program package, which does not do mass weighting. Bill Ross From lawson@argus.cem.msu.edu Tue Mar 26 15:18:53 1996 Received: from argus.cem.msu.edu for lawson@argus.cem.msu.edu by www.ccl.net (8.7.1/950822.1) id PAA22090; Tue, 26 Mar 1996 15:07:33 -0500 (EST) From: Received: from bohr.cem.msu.edu by argus.cem.msu.edu via ESMTP (950215.SGI.8.6.10/940406.SGI) for id PAA09588; Tue, 26 Mar 1996 15:07:28 -0500 Received: by bohr.cem.msu.edu (940816.SGI.8.6.9/) for chemistry@www.ccl.net id PAA26772; Tue, 26 Mar 1996 15:07:29 -0500 Date: Tue, 26 Mar 1996 15:07:29 -0500 Message-Id: <199603262007.PAA26772@bohr.cem.msu.edu> To: chemistry@www.ccl.net Subject: moment >The choice of origin will not matter if the net charge on the system is >zero. The dipole moment of a neutral system is independent of the >origin. The higher order terms, however, will depend on the choice of >the origin. Unless the molecule has no dipole. Then the quadrupole moment will be independent of the origin, for only the first nonvanishing multipole is independent of the choice of origin. Dan Lawson lawson@argus.cem.msu.edu Michigan State University From hinsenk@ERE.UMontreal.CA Tue Mar 26 15:37:21 1996 Received: from harfang.CC.UMontreal.CA for hinsenk@ERE.UMontreal.CA by www.ccl.net (8.7.1/950822.1) id PAA22082; Tue, 26 Mar 1996 15:04:56 -0500 (EST) Received: from eole.ERE.UMontreal.CA (eole.ERE.UMontreal.CA [132.204.10.20]) by harfang.CC.UMontreal.CA with ESMTP id PAA29195 (8.6.11/IDA-1.6); Tue, 26 Mar 1996 15:03:33 -0500 Received: from cyclone.ERE.UMontreal.CA by eole.ERE.UMontreal.CA (951211.SGI.8.6.12.PATCH1042/5.17) id PAA19809; Tue, 26 Mar 1996 15:03:32 -0500 Received: by cyclone.ERE.UMontreal.CA (951211.SGI.8.6.12.PATCH1042/5.17) id OAA06565; Tue, 26 Mar 1996 14:59:09 -0500 Date: Tue, 26 Mar 1996 14:59:09 -0500 Message-Id: <199603261959.OAA06565@cyclone.ERE.UMontreal.CA> To: risser@boisdarc.etsu.edu CC: chemistry@www.ccl.net In-reply-to: (message from Steven M Risser on Tue, 26 Mar 1996 12:42:47 -0600 (CST)) Subject: Re: CCL:Dipole moment origin and electrostatics From: hinsenk@ERE.UMontreal.CA (Konrad HINSEN) > Patrick Bultinck recently asked about the choice of the origin for the > dipole moment. > > The choice of origin will not matter if the net charge on the system is > zero. The dipole moment of a neutral system is independent of the > origin. The higher order terms, however, will depend on the choice of > the origin. More generally, the lowest non-vanishing multipole moment is independent of the choice of the origin. But if I have understood the original question correctly, this is not the point. The question was about the choice of an origin for a multipole expansion, not about the origin dependence of one group of its coefficients. When you use multipole expansions, you choose an origin, calculate multipole moments up to a certain order for this origin, and calculate energies, forces, or whatever using a set of point multipoles located at this origin. And even if the multipole moments for two origins happen to be the same, the potential of the point multipoles can be quite different. As an example, take a multipole expansion for a set of two opposite charges up to the dipole. The dipole moment will be the same for each origin, even for an origin 10 meters away from the charges, but the potential of a point dipole with this moment will nevertheless depend very much on this. It will represent the potential of the original charges best if the origin is right between the two charges. The reason is that for this position the combined potential of the neglected higher-order multipoles is smallest. ------------------------------------------------------------------------------- Konrad Hinsen | E-Mail: hinsenk@ere.umontreal.ca Departement de chimie | Tel.: +1-514-343-6111 ext. 3953 Universite de Montreal | Fax: +1-514-343-7586 C.P. 6128, succ. Centre-Ville | Deutsch/Esperanto/English/Nederlands/ Montreal (QC) H3C 3J7 | Francais (phase experimentale) ------------------------------------------------------------------------------- From ng570@andechs.pnl.gov Tue Mar 26 16:18:56 1996 Received: from andechs.pnl.gov for ng570@andechs.pnl.gov by www.ccl.net (8.7.1/950822.1) id PAA22687; Tue, 26 Mar 1996 15:50:42 -0500 (EST) Received: by andechs.pnl.gov (AIX 3.2/UCB 5.64/4.03) id AA14783; Tue, 26 Mar 1996 12:51:20 -0800 From: ng570@andechs.pnl.gov (Kirk Peterson) Message-Id: <9603262051.AA14783@andechs.pnl.gov> Subject: CCL:Dipole moment origin and electrostatics To: chemistry@www.ccl.net (Computational Chemistry List) Date: Tue, 26 Mar 1996 12:51:18 -0800 (PST) X-Mailer: ELM [version 2.4 PL23] Content-Type: text Just to note, when the net charge on the system IS nonzero, the conventional choice of the origin for the dipole moment is the center of mass. Cheers, Kirk Peterson ------- Kirk A. Peterson Assistant Professor Department of Chemistry / Email: ng570@andechs.pnl.gov Washington State University / Office: (509) 375-6350, (509) 372-7282 and / Fax: (509) 375-6631 Theory, Modeling, and Simulation Environmental Molecular Sciences Laboratory Pacific Northwest National Laboratory, K1-83 Richland, WA 99352 > > Patrick Bultinck recently asked about the choice of the origin for the > dipole moment. > > The choice of origin will not matter if the net charge on the system is > zero. The dipole moment of a neutral system is independent of the > origin. The higher order terms, however, will depend on the choice of > the origin. > > ______________________________________________________________________________ > Dr. Steven M. Risser > Department of Physics > East Texas State University > Commerce, TX 75429 USA > EML : risser@boisdarc.etsu.edu > ______________________________________________________________________________ > > From owner-chemistry@ccl.net Tue Mar 26 19:18:55 1996 Received: from bedrock.ccl.net for owner-chemistry@ccl.net by www.ccl.net (8.7.1/950822.1) id TAA24328; Tue, 26 Mar 1996 19:00:03 -0500 (EST) Received: from trex.centroin.com.br for Carlos.Andre@bbs.centroin.com.br by bedrock.ccl.net (8.7.1/950822.1) id SAA06338; Tue, 26 Mar 1996 18:59:54 -0500 (EST) Received: from bbs.UUCP (bbs@localhost) by trex.centroin.com.br (8.6.12/8.6.12) with UUCP id VAA22509 for chemistry@ccl.net; Tue, 26 Mar 1996 21:03:35 -0300 Received: by bbs.centroin.com.br (CentroIn Internet Gateway v0.33) id 23QL011700082368 Tue Mar 26, 1996 21:00:13 -0300 From: Carlos.Andre@bbs.centroin.com.br (Carlos Andre) Message-Id: <199603262100.23QL011700082368@bbs.centroin.com.br> Date: Tue Mar 26, 1996 20:14:08 -0300 To: chemistry@ccl.net Subject: chemistry-request@ccl.net Organization: CentroIn BBS, +55-21-205-0281, Rio de Janeiro, Brazil Alo All!!!! Sou estudante de Engenharia Quimica pela UFRJ e gostaria de participar de conversas sobre a area. Como e que eu faco? Grato, Carlos. OBS: o meu e-mail segue a msg. carlos.andre@bbs.centroin.com.br ___ * UniQWK #2461* "Gosto de viver pobre... porem com muito dinheiro" Pablo Picasso From amasunov@shiva.Hunter.CUNY.EDU Tue Mar 26 20:19:19 1996 Received: from hcrelay.hunter.cuny.edu for amasunov@shiva.Hunter.CUNY.EDU by www.ccl.net (8.7.1/950822.1) id TAA24521; Tue, 26 Mar 1996 19:40:38 -0500 (EST) Received: from shiva.hunter.cuny.edu (amasunov@shiva.hunter.cuny.edu [146.95.128.96]) by hcrelay.hunter.cuny.edu (8.6.12/george0995) with SMTP id TAA11696; Tue, 26 Mar 1996 19:39:57 -0500 Date: Tue, 26 Mar 1996 19:41:46 -0500 (EST) From: Artem Masunov To: Computational Chemistry List cc: Artem Masunov , Patrick Bultinck Subject: RE: Dipole moment origin and electrostatic Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Patrick Bultinck wrote: >All of the ion-ligand interaction is moved into the ion-dipole >interaction, what about the rest of the multipoles ? This is especially >interesting since when repeating some calculations by him, I found that >he simply put the origin of the dipole in the center of mass. I would >think that if you want to reduce the ion-ligand interaction to an >ion-dipole model, you should choose your origin such that most of the >higher order poles are minimal, so that you make the smallest mistake. Nothing surprising. Why bother choosing origin if center of mass gives you the value good enough? Most of the electrostatic calculations are driven by wishful thinking. That is why Kitaura-Morokuma decomposition analysis is so popular: it almost always points to electrostatic. When it tells you H3B-NH3 complex is strong electrostatic in nature (it does indeed), do you believe that too? Did you try NBO analysis (it usually points to charge transpher) or geminal analysis (which stresses polarization)? Any multipole decomposition is giong to add even more confusion. What I would do is numerical integration of the charge density to get rid of all this multipolar approximations. It even takes less effort to do this. In Gaussian94 you just use GRID to represent electron density as the set of point charges and then CHARGE to calculate interaction of these charges with anything else. Artem > __ _________ > / \ / _ _ \ Artem Masunov - amasunov@shiva.hunter.cuny.edu > / \\ \\ \\ \ Chemistry Department, Hunter College > / /\ \\ \\ \\ \ City University of New York > / ____ \\ \\ \\ \ 695 Park Avenue, New York, NY 10021 > /__/\__/\__\\__\\__\\__\ Tel: (212) 725-0317, Fax: (212) 772-5332 > \__\/ \/__//__//__//__/ > I know you believe you understand what you think I said, but I am not sure > you realize that what you heard is not what I meant. (Gaussian92) From owner-chemistry@ccl.net Tue Mar 26 23:18:57 1996 Received: from bedrock.ccl.net for owner-chemistry@ccl.net by www.ccl.net (8.7.1/950822.1) id WAA26978; Tue, 26 Mar 1996 22:45:53 -0500 (EST) Received: from ce.ifisicam.unam.mx.ifisicam.unam.mx for ramon@ce.ifisicam.unam.mx by bedrock.ccl.net (8.7.1/950822.1) id WAA08660; Tue, 26 Mar 1996 22:45:52 -0500 (EST) Message-Id: <199603270345.WAA08660@bedrock.ccl.net> Received: by ce.ifisicam.unam.mx (1.38.193.3/16.2) id AA11475; Tue, 26 Mar 96 21:43:08 -0600 From: Ramon Garduno Subject: Q:How to install from a CDROM? To: chemistry@ccl.net (POST MSG's) Date: Tue, 26 Mar 96 21:43:08 CST Mailer: Elm [revision: 70.85] Dear fellow netters: May be this is not an appropiate place to put this question, but I figured that many of you might have faced the same problem I am facing now. So, I it won't hurt if I try to find the answer here (Jan,... please stop me if I am wrong ). I want to install a comercial software (BIOSYM) in my SGI INDY, but I do not have a CDROM attached to it. Since we also have a SGI POWER CHALLENGE with an internal CDROM unit, I figured that it could be a piece of cake to mount the later on my INDY using the feature "NFS Mount Manager" in order to install the software in this way. So I did, but I did not get the results I wanted. HELP !!!! This is what I did chronologically: 1) Added line /CDROM in the file /etc/exports on the POWER CHALLENGE. 2) Opened the feature NFS Mount Manager on INDY. 3) Chose host:/CDROM to be mounted on /CDROM (on INDY). 4) Introduced cdrom with software on hosts (POWER CHALLENGE). 5) With instruction "df" I can see that host:/CDROM is mounted. chicoce:/CDROM nfs 3265974 2544695 721279 78% /CDROM 6) Now I change directory to /CDROM (INDY) and list what is on it. 7) Wow!, the directory /CDROM is empty. 8) Scratch my head and wonder, Could CCL help me?. Here is the catch 22. POWER CHALLENGE has IRIX 6.1, INDY has IRIX 5.2. Could this be part of the problem? Any hints to solve my problem will be appreciated. PLEASE RESPOND DIRECTLY TO ME, IN ORDER TO SAVE BANDWIDTH !! Cheers, Ramon -- ____________________________________________________________________________ Dr. Ramon Garduno-Juarez Research Professor in Biophysics INSTITUTO DE FISICA | EMAIL: ramon@ce.ifisicam.unam.mx UNIVERSIDAD NAL. AUTONOMA DE MEXICO | rgard@redvax1.dgsca.unam.mx Laboratorio de Cuernavaca | VOICE: (73)175388 Apdo. Postal 48-3 | (73)111611 62251 Cuernavaca, Morelos | FAX: (73)111603 MEXICO | (73)173077 ___________________________________ EOF _____________________________________