From chemistry-request@server.ccl.net Tue Jul 2 15:12:43 2002 Received: from net.bluemoon.net (root@[63.237.147.10]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g62JChx07559 for ; Tue, 2 Jul 2002 15:12:43 -0400 Received: from localhost (fantom@localhost) by net.bluemoon.net (8.12.4/8.12.4) with ESMTP id g62JCdoo071989 for ; Tue, 2 Jul 2002 15:12:39 -0400 (EDT) (mail-from fant@pobox.com) X-Authentication-Warning: net.bluemoon.net: fantom owned process doing -bs Date: Tue, 2 Jul 2002 15:12:39 -0400 (EDT) From: Andrew Fant X-X-Sender: fantom@net.bluemoon.net To: CHEMISTRY@ccl.net Subject: Of Linux Databases and Xeon Desktops Message-ID: <20020702150012.C70254-100000@net.bluemoon.net> MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hello All, I looking for pointers and advice on two separate questions. Firstly, does anyone have any suggestions about a program that will run under linux that has similar functionality to Isis/base? I have a small (.LT. 1000) set of compounds that I would like to store a 2d structure for, in addition to some scalar and string data. This would just be running stand-alone for me, so I don't need a multiuser RDBMS, and I am not enough of a code-jockey to write a database backend that can talk to cactvs. Secondly, is anyone using the new dual 2GHz Xeon workstations that are coming out from the big PC vendors? I am looking at a new dual processor linux desktop for myself, and it appears that the Intel party line is to discourage P4s from being used in dual processor systems. At least, none of the major vendors seem to sell Dual P4 configurations. This is not a problem, but I have heard mixed opinions about the use of Xeons in desktop systems. I would appreciate any feedback, including just a hand in the air saying that you are using it and don't regret it. Thanks in Advance, Andy Andrew Fant | This | "If I could walk THAT way... Molecular Geek | Space | I wouldn't need the talcum powder!" fant@pobox.com | For | G. Marx (apropos of Aerosmith) Boston, MA USA | Hire | http://www.pharmawulf.com From chemistry-request@server.ccl.net Tue Jul 2 13:59:13 2002 Received: from mail2.fullerton.edu ([137.151.1.10]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g62HxCx04718 for ; Tue, 2 Jul 2002 13:59:13 -0400 Received: from viruswall1 (viruswall1.Fullerton.EDU [137.151.2.93]) by mail2.fullerton.edu (8.11.6/8.10.1) with SMTP id g62Hx8c10421 for ; Tue, 2 Jul 2002 10:59:10 -0700 (PDT) Received: FROM e2k2.AD.FULLERTON.EDU BY viruswall1 ; Tue Jul 02 10:59:06 2002 -0700 X-MimeOLE: Produced By Microsoft Exchange V6.0.5762.3 content-class: urn:content-classes:message MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Subject: Autodock / Autotools 7 atom type limit? Date: Tue, 2 Jul 2002 10:58:47 -0700 Message-ID: <4E4792C2A56F9242A6E1807025B2693E663A66@e2k2.AD.FULLERTON.EDU> X-MS-Has-Attach: X-MS-TNEF-Correlator: Thread-Topic: Autodock / Autotools 7 atom type limit? Thread-Index: AcIh8h0F+vEuzXv4Qn6PWdLRvuXHTA== From: "Herron, Steven" To: Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id g62HxEx04719 Dear CCLers:, I keep getting this error in autodock: 7 atom types declared in "", S_line "CANOHFc"; maximum allowed is 6. My small molecule compound has some Fluorine atoms, which increases my ligand atom types above 6. With this ligand, autodock always crashes with the above error. Any suggestions on how I can use autodock to dock this ligand? Steven Herron sherron@fullerton.edu From chemistry-request@server.ccl.net Wed Jul 3 02:56:01 2002 Received: from web12804.mail.yahoo.com ([216.136.174.39]) by server.ccl.net (8.11.6/8.11.0) with SMTP id g636u0x31750 for ; Wed, 3 Jul 2002 02:56:00 -0400 Message-ID: <20020703065559.62662.qmail@web12804.mail.yahoo.com> Received: from [64.94.101.217] by web12804.mail.yahoo.com via HTTP; Tue, 02 Jul 2002 23:55:59 PDT Date: Tue, 2 Jul 2002 23:55:59 -0700 (PDT) From: amor san juan Subject: Re: CCL:Autodock tools under LINUX (success) To: "Garrett M. Morris" , chemistry@ccl.net In-Reply-To: MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Hello Dr. Morris: This is about ADT (latest edition) in linux.It works well in my RedHat7 linux here yet Im experiencing some problem. For the 3ptb-ben distribution file, ADT can visualize both the docked ligand and protein. I tried my sample that contains 109 residues and showed no problem i.e. docked ligand and protein can be viewed in ADT.HOwever, when i used >500 residues no A, C, N grid maps generated and only H, e, and O maps were created (using autogrid3) that resulted to inability to view the docked ligand-protein to ADT. Hoping you will give me attention regarding this concern. Thanks in advance, Amor --- "Garrett M. Morris" wrote: > > > Hi Carlos, > > I read your post on the CCL about AutoDockTools on > Linux. I'm happy > you figured out what your problem was with your > Operating System. > Have you actually tried using AutoDockTools? > > On Tue, 2 Jul 2002, Dr. Carlos F. Marcos wrote: > > > > > Hi, everybody. I've sent a message a couple of > days ago regarding > > a problem trying to run AutoDockTools under Linux. > Thanks so much > > to all that have answered my question. I could > successfully solve > > the problem just by installing in my system the > necessary OpenGL > > graphic libraries, which come in a packet called > Mesa. On the othe > > hand, Chris wrote that he found the autodock tools > "quite bad and > > highly unstable". Can anyone suggest an > alternative to do flexible > > docking under Linux? Have a nice day > > I was curious to know who "Chris" is, your reply to > CCL did not > explain who he was or which version of AutoDockTools > he had used and > on which platform. We have never heard from Chris > about his > experiences, and we would love to hear from him, in > particular what > gave him the impression that ADT was "quite bad and > highly unstable". > > We have a large number of people using AutoDockTools > quite happily > here at Scripps and elsewhere around the world. Any > feedback is > always welcome, so that we can make future releases > better. > > Furthermore, I would appreciate you making a > distinction in your > discussions in public fora like the CCL, between > "AutoDock" and > "AutoDockTools" (ADT). > > AutoDock is a standalone computational package, that > does not have, > and does not require a GUI to run. It is very > stable and well tested. > AutoDock has been distributed to more than 1600 > sites around the world > in the last decade, and there are more than 300 > publications in the > literature citing its successful use. AutoDock is > under active > development, and its popularity is continuing to > grow. > > AutoDockTools is a Graphical User Interface (GUI) > and is relatively > new, having been distributed in just the last couple > of years. It is > still evolving and being developed, chiefly by Ruth > Huey, and builds > upon the terrific Python Molecule Viewer (PMV) > developed by Michel > Sanner, also here at Scripps. The ADT GUI helps to > make AutoDock > easier to use. > > AutoDockTools is *not* required to run AutoDock. > Even if you cannot > get AutoDockTools to run on your particular flavour > of operating > system, AutoDock will still run without problems, > and you can still > carry out flexible docking. The User Guide > distributed with AutoDock > explains in great detail how to do this. > > I hope this clears up any misconceptions, and I look > forward to > hearing from you about your posting and experiences, > > > Best wishes, > > Garrett > > ___ > Dr Garrett M. Morris, MA, DPhil > The Scripps Research Institute, tel: (858) > 784-2292 > Dept. Molecular Biology, MB-5, fax: (858) > 784-2860 > 10550 North Torrey Pines Road, email: > garrett@scripps.edu > La Jolla, CA 92037-1000, USA. > www.scripps.edu/pub/olson-web/gmm > > > > -= This is automatically added to each message by > mailing script =- > CHEMISTRY@ccl.net -- To Everybody | > CHEMISTRY-REQUEST@ccl.net -- To Admins > Ftp: ftp.ccl.net | WWW: > http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net > > > > > __________________________________________________ Do You Yahoo!? Sign up for SBC Yahoo! Dial - First Month Free http://sbc.yahoo.com From chemistry-request@server.ccl.net Tue Jul 2 17:48:03 2002 Received: from gate-sl1.mdli.com ([208.200.221.3]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g62Lm2x11150 for ; Tue, 2 Jul 2002 17:48:02 -0400 Received: (from smap@localhost) by gate-sl1.mdli.com (8.8.8/8.8.8) id OAA17935; Tue, 2 Jul 2002 14:47:50 -0700 (PDT) Received: from puffin.mdli.com(172.16.1.12) by gate-sl1 via smap (V2.1) id xma017931; Tue, 2 Jul 02 14:47:47 -0700 Received: from exch-sl02.mdli.com by puffin.mdli.com (980427.SGI.8.8.8/BCH1.0) id OAA01943; Tue, 2 Jul 2002 14:47:46 -0700 (PDT) Received: by exch-sl02.mdli.com with Internet Mail Service (5.5.2653.19) id ; Tue, 2 Jul 2002 14:47:45 -0700 Message-ID: From: Bob Snyder To: "'List Server, ACSMEDI'" , "'List Server, CCL'" , "'List Server, CHMINF'" , "'List Server, ISISFORUM-L'" , "'List Server, CHMINF'" , "'List Server, MOL-DIVERSITY'" , "'List Server, STS-L'" Subject: CINF Agenda for ACS 224th National Meeting, Boston, MA Date: Tue, 2 Jul 2002 14:47:45 -0700 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2653.19) Content-Type: multipart/alternative; boundary="----_=_NextPart_001_01C22212.195BD680" This message is in MIME format. Since your mail reader does not understand this format, some or all of this message may not be legible. ------_=_NextPart_001_01C22212.195BD680 Content-Type: text/plain To view the CINF program for the upcoming ACS National Meeting in Boston see the CINF web site at: http://www.lib.uchicago.edu/cinf/acs_upcoming.html Bob Snyder CINF Program Chair ------------------------------------- Robert W. Snyder, Ph.D. Director Database Marketing MDL Information Systems email: bobs@mdl.com telephone: +1-510-357-2222, ext. 1162 cell phone: +1-510-816-5112 text msg: 5108165112@mobile.att.net Never stop searching. ------_=_NextPart_001_01C22212.195BD680 Content-Type: text/html Message
To view the CINF program for the upcoming ACS National Meeting in Boston see the CINF web site at:
 
 
Bob Snyder
CINF Program Chair
 

-------------------------------------
 
Robert W. Snyder, Ph.D.
Director Database Marketing
MDL Information Systems

email:      bobs@mdl.com
telephone:  +1-510-357-2222,  ext. 1162
cell phone: +1-510-816-5112
text msg:   5108165112@mobile.att.net
 
Never stop searching.
 
------_=_NextPart_001_01C22212.195BD680-- From chemistry-request@server.ccl.net Wed Jul 3 10:09:38 2002 Received: from lauca.usach.cl ([158.170.64.28]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g63E9cx08213 for ; Wed, 3 Jul 2002 10:09:38 -0400 Received: from localhost (fgonzale@localhost) by lauca.usach.cl (8.11.6/8.11.6) with ESMTP id g63E5Nu15642 for ; Wed, 3 Jul 2002 10:05:23 -0400 Date: Wed, 3 Jul 2002 10:05:23 -0400 (CLT) From: Fdo Danilo Gonzalez Nilo To: Subject: Metal-Protein in AutoDock Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi all!, I'm working with AutoDock using a proteina with Mn+2 in the active site. So, I need to add the parameters of Mn+2. In this way,... Some body know any good reference (web sites, papers, etc.) where is explain the procedure to add new parameters in autodock?. I will summarise the answars. Thanks a lot! Danilo Gonzalez N. University of Santiago de Chile Faculty of Chemistry and Biology, Biochemistry Lab. Casilla 40, Correo 33, Santiago, Chile Fono: (562) 681 1542 Anexo:814 E-mail : fgonzale@lauca.usach.cl Fax : (562) 681 2108 ************************************************************************** From chemistry-request@server.ccl.net Wed Jul 3 13:27:44 2002 Received: from hsc.usf.edu ([131.247.67.157]) by server.ccl.net (8.11.6/8.11.0) with SMTP id g63HRiS13402 for ; Wed, 3 Jul 2002 13:27:44 -0400 Received: through eSafe SMTP Relay 1022858817; Wed Jul 03 13:21:52 2002 Received: from mindless.com (out.moffitt.usf.edu [131.247.182.200]) by hsc.usf.edu (8.9.3+Sun/8.9.3) with ESMTP id NAA04588 for ; Wed, 3 Jul 2002 13:27:42 -0400 (EDT) Message-ID: <3D2333D6.63722813@mindless.com> Date: Wed, 03 Jul 2002 13:26:46 -0400 From: David Smith X-Mailer: Mozilla 4.78 [en] (Win95; U) X-Accept-Language: en MIME-Version: 1.0 To: CCL Subject: moleuclar dynamics freeware Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hello CCl'ers, Im just curious if any one knows of any free software that can relax a ligand and or a ligand protein complex using any type of in situ protocol, preferably applicable to linux or windows. Thanks, David Smith From chemistry-request@server.ccl.net Wed Jul 3 08:40:10 2002 Received: from guppy.vub.ac.be ([134.184.129.2]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g63Ce9x06640 for ; Wed, 3 Jul 2002 08:40:09 -0400 Received: from mach.vub.ac.be (mach.vub.ac.be [134.184.129.3]) by guppy.vub.ac.be (8.9.1b+Sun/3.17.1.ap (guppy)) id OAA28201; Wed, 3 Jul 2002 14:38:12 +0200 (MET DST) for Received: from algcpc7.vub.ac.be ([134.184.24.76]) by mach.vub.ac.be (8.9.3/3.13.3.ap (mach)) id OAA04374; Wed, 3 Jul 2002 14:40:03 +0200 (MET DST) for Message-Id: <5.1.1.6.0.20020704144001.00a54888@pop.vub.ac.be> X-Sender: dft2003@pop.vub.ac.be X-Mailer: QUALCOMM Windows Eudora Version 5.1.1 Date: Thu, 04 Jul 2002 14:41:48 +0200 To: chemistry@ccl.net From: DFT 2003 Subject: 10th International Conference on the Applications of Density Functional Theory in Chemistry and Physics Mime-Version: 1.0 Content-Type: multipart/alternative; boundary="=====================_21155199==.ALT" --=====================_21155199==.ALT Content-Type: text/plain; charset="iso-8859-1"; format=flowed Content-Transfer-Encoding: quoted-printable Dear Colleagues, With this message I have the honour and pleasure to announce that the 10th= =20 International Conference on the Applications of Density Functional Theory=20 in Chemistry and Physics will take place in Brussels, at the Vrije=20 Universiteit Brussel, from September 5 tot September 12, 2003. Please find below the members of the Scientific Committee, the Organizing=20 Committee and the complete list of invited speakers (all confirmed) Scientific Committee : E. Baerends (Amsterdam) A. Bencini (Florence) J. Garcia De La Vega (Madrid) P. Geerlings (Brussels, Chairman) A. Goursot (Montpellier) E. Gross (W=FCrzburg) N. Handy (Cambridge) R. Nalewajski (Cracow) D. Salahub (Ottawa) K. Schwarz (Vienna) A. Theophilou (Athens) J. Weber (Geneva) Organizing Committee : P. Geerlings (Brussels =96 VUB) F. De Proft (Brussels =96 VUB) C. Van Alsenoy (Antwerp =96 UA) L. Vanquickenborne (Louvain =96 KUL) R. Schoonheydt (Louvain =96 KUL) M. Waroquier (Ghent =96 RUG) W. Mortier (Machelen =96 EXXON Mobil) J. Li=E9vin (Brussels =96 ULB) X. Gonze (Louvain =96 UCL) J.M. Andr=E9 (Namur - FUNDP) J. Delhalle (Namur =96 FUNDP) J.L. Br=E9das (Mons =96 UMH/Tucson-Univ. Arizona) Invited Speakers : P. Ayers Duke University, North Carolina, USA P. Blaha Technische Universit=E4t Wien, Austria S. Burt National Cancer Insitute, SAIC, Frederick, USA R. Car Princeton University , Princeton, USA M. Casida Universit=E9 Joseph Fourier, Grenoble, France J. Cioslowski Florida State University, USA P. Coppens University at Buffalo, New York, USA J. Dobson Griffith University, Queensland, Australia M. Ernzerhof Universit=E9 de Montr=E9al, Montr=E9al, Canada W. Kohn* University of California, Santa Barbara, USA D. Langreth Rutgers University, New Jersey, USA C. Lecomte Universit=E9 Henri Poincar=E9, Nancy, France N. March ** Oxford University/ University of Antwerp, Belgium J. Mintmire Oklahoma State University, Stillwater, USA R. Parr*** University of North Carolina, Chapel Hill, USA J. Perdew Tulane University, New Orleans, USA J. Sauer H=FCmboldt Universit=E4t zu Berlin, Germany M. Scheffler Fritz Haber Institut, Berlin, Germany P. Senet Universit=E9 de Bourgogne, Dijon, France M. Sprik University of Cambridge, UK R. Van Leeuwen Rijksuniversiteit Groningen, Groningen, The Netherlands T. Wesolowski University of Geneva, Geneva, Switzerland W. Yang Duke University, North Carolina, USA T. Ziegler University of Calgary, Alberta, Canada _____________________________ *Special lecture ** Concluding remarks *** Chairman of the first session Further information on the Congress is available on our website=20 http://www.vub.ac.be/dft2003, opened today. The registration will be started around October 15, 2002. If you are interested in attending in this congress please complete the=20 pre-registration form at the website. Please excuse us if this message reaches you via different channels. Hoping to meet you in Brussels in September 2003, with very best regards, Paul Geerlings Chair of the Scientific and Organizing Committee --=====================_21155199==.ALT Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Dear Colleagues,

With this message I have the honour and pleasure to announce that the 10th International Conference on the Applications of Density Functional Theory in Chemistry and Physics will take place in Brussels, at the Vrije Universiteit Brussel, from September 5 tot September 12, 2003.
Please find below the members of the Scientific Committee, the Organizing Committee and the complete list of invited speakers (all confirmed)

Scientific Committee :
E. Baerends (Amsterdam)
A. Bencini (Florence)
J. Garcia De La Vega (Madrid)
P. Geerlings (Brussels, Chairman)
A. Goursot (Montpellier)
E. Gross (W=FCrzburg)
N. Handy (Cambridge)
R. Nalewajski (Cracow)
D. Salahub (Ottawa)
K. Schwarz (Vienna)
A. Theophilou (Athens)
J. Weber (Geneva)

Organizing Committee :
P. Geerlings (Brussels =96 VUB)
F. De Proft (Brussels =96 VUB)
C. Van Alsenoy (Antwerp =96 UA)
L. Vanquickenborne (Louvain =96 KUL)
R. Schoonheydt (Louvain =96 KUL)
M. Waroquier (Ghent =96 RUG)
W. Mortier (Machelen =96 EXXON Mobil)
J. Li=E9vin (Brussels =96 ULB)
X. Gonze (Louvain =96 UCL)
J.M. Andr=E9 (Namur - FUNDP)
J. Delhalle (Namur =96 FUNDP)
J.L. Br=E9das (Mons =96 UMH/Tucson-Univ. Arizona)

Invited Speakers :
P. Ayers Duke University, North Carolina, USA
P. Blaha Technische Universit=E4t Wien, Austria
S. Burt National Cancer Insitute, SAIC, Frederick, USA
R. Car Princeton University , Princeton, USA
M. Casida Universit=E9 Joseph Fourier, Grenoble, France
J. Cioslowski Florida State University, USA
P. Coppens University at Buffalo, New York, USA
J. Dobson Griffith University, Queensland, Australia
M. Ernzerhof Universit=E9 de Montr=E9al, Montr=E9al, Canada
W. Kohn* University of California, Santa Barbara, USA
D. Langreth Rutgers University, New Jersey, USA
C. Lecomte Universit=E9 Henri Poincar=E9, Nancy, France
N. March ** Oxford University/ University of Antwerp, Belgium
J. Mintmire Oklahoma State University, Stillwater, USA
R. Parr*** University of North Carolina, Chapel Hill, USA
J. Perdew Tulane University, New Orleans, USA
J. Sauer H=FCmboldt Universit=E4t zu Berlin, Germany
M. Scheffler Fritz Haber Institut, Berlin, Germany
P. Senet Universit=E9 de Bourgogne, Dijon, France
M. Sprik University of Cambridge, UK
R. Van Leeuwen Rijksuniversiteit Groningen, Groningen, The Netherlands
T. Wesolowski University of Geneva, Geneva, Switzerland
W. Yang Duke University, North Carolina, USA
T. Ziegler University of Calgary, Alberta, Canada

_____________________________
*Special lecture
** Concluding remarks
*** Chairman of the first session


Further information on the Congress is available on our website http://www.vub.ac.be/dft2003, opened today.

The registration will be started around October 15, 2002.
If you are interested in attending in this congress please complete the pre-registration form at the website.
Please excuse us if this message reaches you via different=20 channels.
Hoping to meet you in Brussels in September 2003,

with very best regards,


Paul Geerlings
Chair of the Scientific and Organizing Committee





--=====================_21155199==.ALT-- From chemistry-request@server.ccl.net Wed Jul 3 13:22:17 2002 Received: from postoffice.mail.cornell.edu ([132.236.56.7]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g63HMHS13330 for ; Wed, 3 Jul 2002 13:22:17 -0400 Received: from cornell.edu (sweet1.foodsci.cornell.edu [132.236.147.65]) by postoffice.mail.cornell.edu (8.9.3/8.9.3) with ESMTP id NAA19276; Wed, 3 Jul 2002 13:22:12 -0400 (EDT) Sender: dwood@cornell.edu Message-ID: <3D2325C7.6A13D882@cornell.edu> Date: Wed, 03 Jul 2002 12:26:47 -0400 From: "Dr. Richard L. Wood" X-Mailer: Mozilla 4.75C-SGI [en] (X11; I; IRIX 6.5 IP32) X-Accept-Language: en MIME-Version: 1.0 To: "chemistry@ccl.net" Subject: CHARMM help Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi all I have a 27 amino acid peptide, which when fully extended (i.e., all phi and psi angles are 180 degrees) is 83.825 Angstroms long. Is there a way using CHARMM (without varying angles), that I can build this molecule so that the two atoms that are at the ends are closer together and all the other atoms have "appropriate" coordinates? In other words, I would like the first atom, an HT1 of a glycine to be at 0,0,0 and the farthest atom away, an OT1 of a proline, to be at 0,0,75, say, (so in some way seeding these two atoms), and then have CHARMM build the coordinates for the other atoms. Any help will be greatly appreciated. Thank you, Richard -- Richard L. Wood, Ph. D. Physical/Computational Chemist Post-doctoral Associate Department of Food Science 120 Stocking Hall Cornell University, Ithaca, NY 14853 From chemistry-request@server.ccl.net Wed Jul 3 14:30:59 2002 Received: from cliff.st-andrews.ac.uk (root@[138.251.140.9]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g63IUwS14756 for ; Wed, 3 Jul 2002 14:30:58 -0400 Received: from edge.st-andrews.ac.uk (sdjp@edge [138.251.140.2]) by cliff.st-andrews.ac.uk (8.9.1a/8.9.1) with ESMTP id TAA14316 for ; Wed, 3 Jul 2002 19:30:57 +0100 (BST) Received: from localhost (sdjp@localhost) by edge.st-andrews.ac.uk (8.9.1a/8.9.1) with SMTP id TAA19691 for ; Wed, 3 Jul 2002 19:30:57 +0100 (BST) Date: Wed, 3 Jul 2002 19:30:56 +0100 (BST) From: Stuart Purdie X-Sender: sdjp@st-and.ac.uk To: chemistry@ccl.net Subject: Molecular B3LYP gaps Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear CCLers We've been using the B3LYP hybrid functional for solid state calculations (as implemented in Crystal98), and we've found a material where is appears to give incorrect band gaps. To date, we've only found one report of this in the literature, namely for FeS2 (J Muscat et al, ChemPhysLett 342 p397-401 (2001)). However, given that B3LYP was 'conditioned' on data for molecular systems, we were wondering if anyone was aware of a case where it gets the HOMO-LUMO gap incorrect for a molecular system, and what the nature of the molecular orbitals are that straddle the gap. I'll post a summary of responses. Stuart Purdie PhD student University of St Andrews School of Chemistry Purdie Building St Andrews KY16 9SS +44 (0)1334 463899 From chemistry-request@server.ccl.net Wed Jul 3 17:41:56 2002 Received: from lauca.usach.cl ([158.170.64.28]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g63LfsS18823 for ; Wed, 3 Jul 2002 17:41:55 -0400 Received: from localhost (fgonzale@localhost) by lauca.usach.cl (8.11.6/8.11.6) with ESMTP id g63Lbl504956 for ; Wed, 3 Jul 2002 17:37:47 -0400 Date: Wed, 3 Jul 2002 17:37:47 -0400 (CLT) From: Fdo Danilo Gonzalez Nilo To: Subject: CHARMm with LAM-MPI Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi all, We are testing CHARMm in cluster enviroment with LAM-MPI. Any body know some program to check all CPU in cluster? (some thing like "top" command ) Thanks a lot, Danilo Gonzalez N. University of Santiago de Chile Faculty of Chemistry and Biology, Computational Chemistry Lab. Casilla 40, Correo 33, Santiago, Chile Fono: (562) 681 1542 Anexo:799 E-mail : fgonzale@lauca.usach.cl Fax : (562) 681 2108 ************************************************************************** From chemistry-request@server.ccl.net Wed Jul 3 22:38:37 2002 Received: from master.cluster ([64.162.84.26]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g642cbS05119 for ; Wed, 3 Jul 2002 22:38:37 -0400 Received: from uclink.berkeley.edu (huskie.cluster [192.168.123.8]) by master.cluster (8.11.6/8.11.6) with ESMTP id g642cVf09167; Wed, 3 Jul 2002 19:38:31 -0700 Message-ID: <3D23B462.5070508@uclink.berkeley.edu> Date: Wed, 03 Jul 2002 19:35:14 -0700 From: "David E. Konerding" User-Agent: Mozilla/5.0 (Windows; U; Windows NT 5.0; en-US; rv:1.0.0) Gecko/20020530 X-Accept-Language: en-us, en MIME-Version: 1.0 To: Fdo Danilo Gonzalez Nilo CC: chemistry@ccl.net Subject: Re: CCL:CHARMm with LAM-MPI References: Content-Type: text/plain; charset=us-ascii; format=flowed Content-Transfer-Encoding: 7bit Fdo Danilo Gonzalez Nilo wrote: >Hi all, > >We are testing CHARMm in cluster enviroment with LAM-MPI. >Any body know some program to check all CPU in cluster? (some thing like >"top" command ) > >Thanks a lot, > >Danilo Gonzalez N. > > > What sort of status check do you want? Is your goal to find a set of free CPUs on which to run CHARMm? In that, the best solution is one which actually ensures that the machines are free, rather than using some ad-hoc mechanism such as load (which is inaccurate due to disk-waits, and time smoothing). Queuing systems such as OpenPBS, Maui, and Sun Grid Engine are designed to do this and they do it fairly well, as long as users respect the queue system (there's nothing quite so bad as a user who knows the queue policy and insists on logging into a node manually to run their job, which typically screws up any scaling you hoped to get using MPI). An alternative, which is easy to set up and works well in many situations is the gexec/gstat/gmond combo of programs > from ganglia.sourceforge.net. The "gstat" command quickly tells you the state of nodes, and the gexec command can make it quite easy to generate an MPICH mpi host list file (presumably also useful with LAM/MPI). CLUSTER INFORMATION Name: unspecified Hosts: 13 Gexec Hosts: 12 Dead Hosts: 0 Localtime: Wed Jul 3 19:36:45 2002 CLUSTER HOSTS Hostname LOAD CPU Gexec CPUs (Procs/Total) [ 1, 5, 15min] [ User, Nice, System, Idle] client09.hanalei 2 ( 0/ 38) [ 0.00, 0.02, 0.51] [ 0.0, 0.0, 0.0, 100.0] ON client15.hanalei 2 ( 2/ 38) [ 0.00, 0.00, 0.00] [ 0.0, 0.0, 0.0, 100.0] ON client10.hanalei 2 ( 1/ 42) [ 0.96, 1.12, 1.94] [ 50.0, 0.0, 0.0, 50.0] ON client11.hanalei 2 ( 1/ 41) [ 0.98, 0.97, 0.99] [ 49.8, 0.0, 0.1, 50.1] ON client14.hanalei 2 ( 1/ 41) [ 0.99, 0.97, 0.98] [ 49.3, 0.0, 0.1, 50.6] ON client07.hanalei 2 ( 1/ 41) [ 1.00, 1.00, 1.00] [ 49.2, 0.0, 0.5, 50.3] ON client13.hanalei 2 ( 3/ 44) [ 1.02, 1.00, 1.03] [ 32.7, 0.0, 16.7, 50.6] ON client12.hanalei 2 ( 3/ 44) [ 1.97, 1.99, 2.00] [ 99.4, 0.0, 0.0, 0.0] ON workstation7.hanalei 1 ( 0/ 53) [ 0.99, 0.97, 0.91] [ 0.0, 0.0, 0.0, 100.0] ON client08.hanalei 2 ( 2/ 48) [ 2.04, 2.03, 2.06] [ 58.4, 0.0, 38.4, 2.9] ON client01.hanalei 2 ( 2/ 45) [ 2.05, 2.02, 2.01] [ 97.9, 0.0, 0.2, 1.3] ON client02.hanalei 2 ( 2/ 44) [ 2.12, 2.03, 2.00] [ 96.9, 0.0, 0.6, 2.7] ON From chemistry-request@server.ccl.net Wed Jul 3 23:03:43 2002 Received: from smtp1.dti.ne.jp ([202.216.228.36]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g6433hS05437 for ; Wed, 3 Jul 2002 23:03:43 -0400 Received: from b159504364 (PPP351.fukuoka-ip.dti.ne.jp [211.132.93.101]) by smtp1.dti.ne.jp (3.07) with SMTP id g6433cmg018645 for ; Thu, 4 Jul 2002 12:03:41 +0900 (JST) Message-ID: <000b01c22307$679d4ae0$655d84d3@b159504364> From: "Telkuni" To: Subject: Role of electron correlation in hydrogen bonds -Summary Date: Thu, 4 Jul 2002 12:03:42 +0900 MIME-Version: 1.0 Content-Type: text/plain; charset="Windows-1252" Content-Transfer-Encoding: 7bit X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 5.50.4133.2400 X-MimeOLE: Produced By Microsoft MimeOLE V5.50.4133.2400 Hello CCLers, A few days ago, I posted a question of electron correlation effect in hydrogen bonds: > Dear CCLers, > > I have a question of the role of electron correlation in > hydrogen bonds. I hope to hear your opinion. > > I think there are small correlation effects in hydrogen > bonds, because: > > 1) There is no electron between bonding atoms, so > correlation effect is very small. > > 2) The hydrogen bonds are made of electronic static > potential(by coulomb force). So there is electronic effect > rather than quantum effect. Here is the summary of replies. From them, I think one should consider the electron correlation in hydrogen bonds. I found very good paper which is describing about electron correlation effect on DNA base pairs. J.Sponer et.al "Structures and Energies of Hydrogen-Bonded DNA Base Pairs. A Nonempirical Study with Inclusion of Electron Correlation " J. Phys. Chem., 100, p1965 (1996) * Thank you very much Prof. Bagatur'yants, Dr. CHIU, Dr. Bowlus, Dr. Kress, Dr. Lewars and Dr. Hultin. ////// Replies ///////////////////////////////// 1) from Alexander Bagatur'yants ------------------------ Dear Dr. Telkuni, Both statements are not quite correct: > 1) There isn't no electron between bonding atoms, so > correlation effect is very small. Of course, there are electrons between bonding atoms, e.g., in the case of O...H-O bonds (most typical case), there are elctrons of the O lone pair. > 2) The hydrogen bonds are made of electronic static > potential(by coulomb force). So there is electronic effect > rather than quantum effect. Both effects cannot be separated. In principle, it can be stated that ALL chemical interactions are due to Coulomb forces (see Hellmann--Feynman theorem and DFT). Next, of course electron correlation effects should be important in H-bond description, as these are important at all in the description of intermolecular forces (van der Waals component, etc.). Best regards, Prof. Alexander Bagatur'yants Photochemistry Center, Russian Academy of Science ul. Novatorov 7a, Moscow, 117421 Russia Phone: (007-095)-936-2588 Fax: (007-095)-936-1255 E-mail: sasha@photonics.ru Home page: http://www.photonics.ru/eng/bagat/bagat.htm 2) from Wing Lok Abe Kurtz CHIU ------------------------ Hi Telkuni, I only partially agree you. In some cases, you are right. However, there are a lot of cases, your interpretation may not be right. For example, covalent character can be found between the hydrogen bonds of the DNA or RNA base pairs. You can find the J-coupling between them. Using the NBO analysis, you also can find the electron transfer in it. Therefore, it is important to include the electron correlation on hydrogen bonds. Cheers, Kurtz Dr. Wing Lok Abe Kurtz CHIU MRSC Department of Chemistry, The Chinese University of Hong Kong. Hong Kong SAR, China 3) from Stephen Bowlus ------------------------ Hydrogen bonds are more than simple coulombic forces. While the strength of the hydrogen bond can be approximated in this way (as is done by several forcefields), it's directionality is poorly described. And coulombic forces may introduce spurious "hydrogen bonds:" consider the case of a bond to an oxygen, compared to that of a similarly charged sulfur. sb 4) from Jim Kress ------------------------ Look at: http://www.kressworks.com/Research/Quantum_Chemistry/Potential_Energy_Surfac es/water_dimer/water_dimer_results.html 25% of the binding energy in the water dimer hydrogen bond appears to be > from electron correlation effects. Jim 5) from E. Lewars ------------------------ You could find some systems (H2O dimer, NH3 dimer, H2O...NH3, CH3COOH diemer, etc) for which geometries and H-bond energies are known, and do calculations on them at the HF and at the MP2 levels, using 6h3 6-31G* basis or bigger, and compare the results. Note that high-quality H-bond energies apparently requite BSSE correction, either using the counterpoise method, or a very big basis set. (A series of your own calculations like this would be satisfying, but I am sure there are several published papers on HF vs. MP2 for H-bonding.) E. Lewars 6) from Philip G. Hultin ------------------------ I don't have the specific answer to your question on CCL, but I should point out that recent experimental work has clearly shown that there is a significant "covalent" component to the H-bond interaction - i.e. it is not entirely Coulombic. A couple of years ago NMR work by (I think) Ad Bax et al. demonstrated J-coupling through a hydrogen bond. Since J-coupling is mediated by electrons in bonds, this was clear evidence that there is electron sharing going on. I am afraid that I don't have the exact reference, and I suspect that there are newer updates on this topic. So, I think you should not rule out "quantum" effects in modeling H-bonding. Dr. Philip G. Hultin Associate Department Head and Associate Professor of Chemistry University of Manitoba Winnipeg, MB, Canada R3T 2N2 (vox) 204-474-9814 (fax) 204-474-7608 mailto:hultin@cc.umanitoba.ca http://www.umanitoba.ca/chemistry/ /////////// End of the Replies ------------------------------------------------ Telkuni Tsuru Kyushyu Electronic Technology and Research telkuni@venus.dti.ne.jp ------------------------------------------------