ANTONIO LAVECCHIA, PhD
Computational Chemistry
Dept of Pharmaceutical Chemistry
University of Naples
Via D. Montesano, 49
80131 NAPOLI
E-Mail: lavecchi@unina.it
Phone: ++39 081 678613/619
Fax: ++39 081 678644 --=====================_85920650==_.ALT-- From chemistry-request@server.ccl.net Wed Jan 8 20:29:00 2003 Received: from mercury.sunesis.com ([64.240.200.4]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h091SxD25509 for ; Wed, 8 Jan 2003 20:29:00 -0500 X-MimeOLE: Produced By Microsoft Exchange V6.0.6249.0 Content-Class: urn:content-classes:message MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Subject: Fast PyMOL (and other 3D progs.) on OSX Date: Wed, 8 Jan 2003 17:28:56 -0800 Message-ID: X-MS-Has-Attach: X-MS-TNEF-Correlator: Thread-Topic: Fast PyMOL (and other 3D progs.) on OSX thread-index: AcK3fnm2Cp6SHhEGS5qGO8vicQQYRg== From: "DeLano, Warren" To: Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id h091T0D25510 Good news for OSX users -- the Mac can finally do fast OpenGL graphics under X11! With OSX 10.2.3, the public X11 beta, and Fink, you can now install a complete version of PyMOL on a Mac without compromising performance. The same should be true for most of your other favorite X11/OpenGL graphics programs. You can find two sets of instructions on how to do this linked from the PyMOL home page. http://pymol.sf.net Cheers, Warren From chemistry-request@server.ccl.net Wed Jan 8 16:10:34 2003 Received: from sirene.rz.uni-duesseldorf.de ([134.99.128.2]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h08LAXD20332 for ; Wed, 8 Jan 2003 16:10:33 -0500 Received: from conversion-daemon by neptun.rz.uni-duesseldorf.de (Sun Internet Mail Server sims.4.0.2001.07.26.11.50.p9) id <0H8E00E01YTIUU@neptun.rz.uni-duesseldorf.de> for chemistry@ccl.net; Wed, 8 Jan 2003 22:10:31 +0100 (MET) Received: from mail.rz.uni-duesseldorf.de (mail.rz.uni-duesseldorf.de [134.99.128.30]) by neptun.rz.uni-duesseldorf.de (Sun Internet Mail Server sims.4.0.2001.07.26.11.50.p9) with ESMTP id <0H8E00CC3YTID9@neptun.rz.uni-duesseldorf.de> for chemistry@ccl.net; Wed, 08 Jan 2003 22:10:30 +0100 (MET) Date: Wed, 08 Jan 2003 22:10:30 +0100 (MET) From: konietz@uni-duesseldorf.de Subject: Ref. for 6-31+G(d) in G98 for As In-reply-to: <3DFB0249.9B752263@ioc.ac.ru> X-Sender: konietz@neptun To: chemistry@ccl.net Message-id: MIME-version: 1.0 Content-type: TEXT/PLAIN; charset=US-ASCII Content-transfer-encoding: 7BIT Dear Listmembers, can anyone point me to the reference to the 6-31+g(d) basis set for arsenic used in Gaussian98. The EMSL Gaussian Basis Set Order Form says that 6-31+G(d) is not available for As. Also the Gaussian homepage tells me that it is not available for As. This basis set does not look like a typical 6-31g kind of basis. Thanks in advance, Stefan. From chemistry-request@server.ccl.net Thu Jan 9 08:04:49 2003 Received: from cholla.wustl.edu ([128.252.62.53]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h09D4mD23811 for ; Thu, 9 Jan 2003 08:04:48 -0500 Received: (from baker@localhost) by cholla.wustl.edu (8.11.6/8.11.6) id h09D4iP31060; Thu, 9 Jan 2003 07:04:44 -0600 Date: Thu, 9 Jan 2003 07:04:44 -0600 From: "Nathan A. Baker" To: jz7@duke.edu Cc: CHEMISTRY@ccl.net Subject: Re: CCL:electrostatics potential plot Message-ID: <20030109070444.I29205@cholla.wustl.edu> Reply-To: Nathan Baker References: <018601c2b46e$158f99d0$eabf1098@CONCORDIA> Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Disposition: inline User-Agent: Mutt/1.2.5.1i In-Reply-To: <018601c2b46e$158f99d0$eabf1098@CONCORDIA>; from jz7@duke.edu on Sat, Jan 04, 2003 at 10:54:02PM -0500 Organization: Washington University in St. Louis X-URL: http://www.biochem.wustl.edu/~baker There are several programs available; I'd recommend OpenDX (http://www.opendx.org) or VMD (http://www.ks.uiuc.edu/Research/vmd). The APBS software package (http://agave.wustl.edu/apbs) has routines to convert UHBD data to formats compatible with those programs. Hope this helps, Nathan jz7@duke.edu (01-04-2003 22:54:02-0500): >Dear all, > >Happy New year! > >I use UHBD to calculate the electrostatics potential of a protein-DNA >complex. The result is a list of many many potentials. But How can I >view the result as a 3-D plot with different colors to represent high >and low potentials? (Maybe free software.) > >Thanks a lot! > > >-= 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 > > > > End of message from jz7@duke.edu. -- Nathan A. Baker, Assistant Professor Washington University in St. Louis School of Medicine Dept. of Biochemistry and Molecular Biophysics Center for Computational Biology 700 S. Euclid Ave., Campus Box 8036, St. Louis, MO 63110 Phone: (314) 362-2040, Fax: (314) 362-0234 URL: http://www.biochem.wustl.edu/~baker From chemistry-request@server.ccl.net Thu Jan 9 08:02:50 2003 Received: from cholla.wustl.edu ([128.252.62.53]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h09D2oD23738 for ; Thu, 9 Jan 2003 08:02:50 -0500 Received: (from baker@localhost) by cholla.wustl.edu (8.11.6/8.11.6) id h09D2dM30986; Thu, 9 Jan 2003 07:02:39 -0600 Date: Thu, 9 Jan 2003 07:02:39 -0600 From: "Nathan A. Baker" To: Wibke Sudholt Cc: Damian A Scherlis Perel , CHEMISTRY@ccl.net, "Michael J. Holst" Subject: Re: CCL:code to solve Poisson-Boltzmann Message-ID: <20030109070239.H29205@cholla.wustl.edu> Reply-To: Nathan Baker References: Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Disposition: inline User-Agent: Mutt/1.2.5.1i In-Reply-To: ; from wibke@sdsc.edu on Thu, Dec 26, 2002 at 05:58:44PM -0800 Organization: Washington University in St. Louis X-URL: http://www.biochem.wustl.edu/~baker Hi All -- APBS uses Mike Holst's PMG/MG multigrid software package for numerical solution of the PBE. Additionally, Mike's original software pacakge is available from his web site (http://scicomp.ucsd.edu/~mholst/codes/pmg/index.html). Have fun! -- Nathan Wibke Sudholt (12-26-2002 17:58:44-0800): >Hello, > >perhaps you may take a look at APBS: > >http://agave.wustl.edu/apbs/ > >I hope this helps, > >Wibke Sudholt >University of California, San Diego >wibke@sdsc.edu > > >-----Original Message----- >From: Computational Chemistry List [mailto:chemistry-request@ccl.net]On >Behalf Of Damian A Scherlis Perel >Sent: Thursday, December 26, 2002 4:50 PM >To: chemistry@ccl.net >Subject: CCL:code to solve Poisson-Boltzmann > > > > Dear all, > > I am interested in a subroutine or package to solve > numerically in a grid elliptic partial differential > equations (in particular the Poisson-Boltzmann equation). > I have been trying with the multigrid code of Michael > Holst released in 1995, but it shows serious inaccuracies > in R3 for the kind of trial potentials I used to test it. > Is anyone aware of some other code suitable for this? > > Many thanks, and happy holidays, > > ------------------------ > Damian Scherlis > Department of Materials Science & Engineering > Massachusetts Institute of Technology > damians@mit.edu > 617 253 6026 > > > > > > > > > >-= 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 > > > > End of message from Wibke Sudholt. -- Nathan A. Baker, Assistant Professor Washington University in St. Louis School of Medicine Dept. of Biochemistry and Molecular Biophysics Center for Computational Biology 700 S. Euclid Ave., Campus Box 8036, St. Louis, MO 63110 Phone: (314) 362-2040, Fax: (314) 362-0234 URL: http://www.biochem.wustl.edu/~baker From chemistry-request@server.ccl.net Thu Jan 9 09:58:22 2003 Received: from mr4.wpafb.af.mil ([198.97.67.52]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h09EwMD27366 for ; Thu, 9 Jan 2003 09:58:22 -0500 Received: from mr4.wpafb.af.mil (root@localhost) by mr4.wpafb.af.mil with ESMTP id h09EwIl11188 for ; Thu, 9 Jan 2003 09:58:18 -0500 (EST) Received: from mvs2.wpafb.af.mil (mvs2.wpafb.af.mil [198.97.67.123]) by mr4.wpafb.af.mil with ESMTP id h09EwIQ11184 for ; Thu, 9 Jan 2003 09:58:18 -0500 (EST) Received: from mvs2.wpafb.af.mil (localhost [127.0.0.1]) by mvs2.wpafb.af.mil (8.11.6/8.11.6) with ESMTP id h09EwHb20256 for ; Thu, 9 Jan 2003 09:58:17 -0500 (EST) Received: from fszhtv02.wpafb.af.mil (fszhtv02.wpafb.af.mil [129.48.28.35]) by mvs2.wpafb.af.mil (8.11.6/8.11.6) with ESMTP id h09EwHa20248 for ; Thu, 9 Jan 2003 09:58:17 -0500 (EST) Received: by fszhtv02 with Internet Mail Service (5.5.2653.19) id ; Thu, 9 Jan 2003 09:52:59 -0500 Message-ID: <53A10F824E50D511820800508BDF3F22078BB006@fszhtv12.wpafb.af.mil> From: Trohalaki Steven Contr AFRL/MLPJ To: "'chemistry@CCL.net'" Subject: seconding letters for Jan Date: Thu, 9 Jan 2003 09:52:48 -0500 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2653.19) Content-Type: text/plain; charset="iso-8859-1" Dear CCLers, I am nominating Jan Labanowski for ACS's Patterson-Crane Award (see http://membership.acs.org/C/Colu/welcome.html) and I am in need of seconding letters. There is no limit and the Chair of the awards committee says that the more supporting material the better so I'd be obliged if you would send me email with a statement on what CCL means to you and how it's helped your career. Sincerely, Steve Trohalaki Visiting Scientist Air Force Research Lab steven.trohalaki@wpafb.af.mil From chemistry-request@server.ccl.net Thu Jan 9 11:22:06 2003 Received: from chemcomp.com ([209.226.194.164]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h09GM3D31323 for ; Thu, 9 Jan 2003 11:22:06 -0500 Received: from chemcomp.ca (smtp.chemcomp.com [209.226.194.167]) by chemcomp.com (8.9.3/8.9.3) with ESMTP id LAA14399 for ; Thu, 9 Jan 2003 11:21:56 -0500 Received: from BHPC ([209.226.194.162]) (authenticated) by chemcomp.ca (8.11.6/8.11.6) with ESMTP id h09FHOH24233 for ; Thu, 9 Jan 2003 10:17:25 -0500 Message-ID: <000801c2b7fb$38d3e3c0$a00101c0@chemcomp.com> From: "Katie Rodgers" To: Subject: CCG Congratulates the Ten Winners of the Spring 2003 CCG Excellence Awards Date: Thu, 9 Jan 2003 11:21:53 -0500 Organization: Chemical Computing Group Inc. MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_0005_01C2B7D1.4FA55B80" 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 This is a multi-part message in MIME format. ------=_NextPart_000_0005_01C2B7D1.4FA55B80 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable MONTREAL, January 9, 2003 - Today Chemical Computing Group (CCG) = together with the American Chemical Society's (ACS) Division of = Computers in Chemistry (COMP) announced the latest winners of the CCG = Excellence Awards to be presented at the Spring 2003 ACS National = Meeting in New Orleans. Due to the overwhelming response, CCG has = increased its sponsorship of the contest from five award winners to ten. = The awards will be presented on Tuesday, March 25 at the Computers in = Chemistry poster session, which begins at 6pm =20 The contest was created to stimulate graduate student participation at = ACS National Meetings in COMP division poster sessions and symposia and = has been effective in doing so. "The growth in response to this contest = since its inception is very gratifying. Not only did we double the = number of awards presented, but the submissions received multiplied = substantially. The contest is intended to encourage interaction between = scientists and the competing students, which is beneficial to these = future computational chemists. CCG will continue to work with COMP to = help facilitate this exchange of information," said Pamela Newton, = Director of Sales and Marketing at CCG. =20 =20 Winners were chosen based upon the quality and significance of the = research presented as well as the strength of the supporting materials. = The COMP executive committee had a difficult task of judging, as = competition was fierce due to the quantity and quality of entries. The = following winners will receive a one-year software license for CCG's MOE = -The Molecular Operating Environment and reimbursement for travel costs = to attend an ACS meeting to present their research: =20 AIKENS, Christine (Ms.) Department of Chemistry, Iowa State University Molecular Electronic Structure and Magnetic Properties of = Y2Ti(?-X)2TiY2(X,Y=3DH,F,Cl,Br) Isomers Advisor - Mark S. Gordon, Department of Chemistry, Iowa State University =20 BUCHETE, Nicolae-Viorel (Mr.) Department of Chemistry, Boston University The Effect of Relative Side Chain Orientations on the Ability of = Statistical Potentials to Identify Native-Like Structures of Proteins Advisor - John E. Straub, Boston University =20 CUI, Guanglei (Mr.) Department of Chemistry, SUNY at Stony Brook The Complicated Folding of a Simple Peptide Studied by Multiple Folding = Simulations and Replica Exchange Approach Advisor - Carlos Simmerling, Department of Chemistry, SUNY at Stony = Brook =20 DONG, Haitao (Mr.) Department of Chemistry and Biochemistry, The University of Oklahoma Quasiharmonic Vibrations of Water, Water Clusters, and Liquid Water from = Principal Component Analysis of Quantum or QM/MM Trajectories Advisor - Ralph A. Wheeler, Department of Chemistry and Biochemistry, = The University of Oklahoma =20 IVANOV, Ivaylo N. (Mr.) Center for Molecular Modeling and Department of Chemistry, University of = Pennsylvania Relative pKs from First Principles Molecular Dynamics: The Case of = Histidine Deprotonation Advisor - Michael L. Klein, Director and Hepburn Professor of Physical = Science, University of Pennsylvania =20 KATT, William B. (Mr.) Department of Chemistry, Rensselaer Polytechnic Institute Optimization of Molecular Properties Through Structural Mutation and = Virtual Screening with QSAR Models Advisor - Curt M. Breneman, Department of Chemistry, Rensselaer = Polytechnic Institute =20 KORMOS, Bethany (Ms.) Department of Chemistry, University of Minnesota Utilizing Density Functional Theory to Study Nucleophilic Substitution = Reactions: Optimization of an Adiabatic Connection Method and its = Application Advisor - Christopher J. Cramer, Department of Chemistry, University of = Minnesota =20 STROCKBINE, Bentley (Mr.) Department of Pharmacological Sciences, Stony Brook University Advances in Structure Prediction Techniques Advisor - Carlos Simmerling, Department of Chemistry, SUNY at Stony = Brook =20 WU, Min (Ms.) Department of Chemistry, New York University Structural Studies of an Environmental Carcinogen within a Y Family = Bypass DNA Polymerase Advisor - Suse Broyde, Department of Biology, New York University =20 ZHOU, Zhigang (Mr.) Department of Chemistry, Duquesne University Resistant Effect Exploring of HIV-1 RT Mutation by Molecular Dynamics Advisor - Jeffrey D. Madura, Department of Chemistry and Biochemistry, = Duquesne University =20 Applications for the next round will be accepted soon. Previous winners = are welcome to enter. An application must be submitted to the Treasurer = of the COMP. Then an abstract must be submitted through the ACS OASYS = system for online paper submissions prior to the deadline. Visit = http://membership.acs.org/C/COMP/CCG/ccg.html for further information. =20 Chemical Computing Group Inc. is a leading provider of computational = applications aimed at the drug discovery and design marketplace. CCG's = flagship product is the award winning Molecular Operating Environment = (MOE), which offers visualization, simulation, and methodology = development in one package. MOE provides an integrated suite of = powerful, yet intuitive chemistry software tools for HTS, Structure = Based Design, Molecular modeling and Protein and Homology modeling as = well as an embedded programming language for the rapid prototyping of = scientific methods. Biologists, medicinal chemists, and computational = chemists use MOE in pharmaceutical companies, biotechnology companies, = and universities worldwide. =20 CCG is based in Montreal, Canada, with offices in L=F6rrach, Germany and = Cambridge, UK. For more information, please visit our website = http://www.chemcomp.com. Send E-mail inquiries to info@chemcomp.com. ------=_NextPart_000_0005_01C2B7D1.4FA55B80 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable

MONTREAL,=20 January 9, 2003 - Today = Chemical=20 Computing Group (CCG) together with the American Chemical Society=92s = (ACS)=20 Division of Computers in Chemistry (COMP) announced the latest winners = of the=20 CCG Excellence Awards to be presented at the Spring 2003 ACS National = Meeting in=20 New Orleans. Due to the=20 overwhelming response, CCG has increased its sponsorship of the contest = from=20 five award winners to ten. = The=20 awards will be presented on Tuesday, March 25 at the Computers in = Chemistry=20 poster session, which begins at 6pm

The=20 contest was created to stimulate graduate student participation at ACS = National=20 Meetings in COMP division poster sessions and symposia and has been = effective in=20 doing so. =93The growth = in response=20 to this contest since its inception is very gratifying. Not only did we double the = number of=20 awards presented, but the submissions received multiplied = substantially. The contest is intended to = encourage=20 interaction between scientists and the competing students, which is = beneficial=20 to these future computational chemists. =20 CCG will continue to work with COMP to help facilitate this = exchange of=20 information,=94 said Pamela Newton, Director of Sales and = Marketing=20 at CCG. =

Winners=20 were chosen based upon the quality and significance of the research = presented as=20 well as the strength of the supporting materials. The COMP executive committee = had a=20 difficult task of judging, as competition was fierce due to the quantity = and=20 quality of entries. The = following=20 winners will receive a one-year software license for CCG=92s MOE = =96The=20 Molecular Operating Environment and reimbursement for travel costs to = attend an=20 ACS meeting to present their research:

AIKENS, Christine = (Ms.)

Department of Chemistry, = Iowa State=20 University

Molecular=20 Electronic Structure and Magnetic Properties of = Y2Ti(?-X)2TiY2(X,Y=3DH,F,Cl,Br)=20 Isomers

Advisor - Mark S. Gordon, = Department=20 of Chemistry, Iowa State University

BUCHETE, = Nicolae-Viorel=20 (Mr.)

Department of Chemistry, = Boston=20 University

The = Effect of=20 Relative Side Chain Orientations on the Ability of Statistical = Potentials to=20 Identify Native-Like Structures of Proteins

Advisor - John E. Straub, = Boston=20 University

CUI, Guanglei=20 (Mr.)

Department of Chemistry, = SUNY at=20 Stony Brook

The = Complicated=20 Folding of a Simple Peptide Studied by Multiple Folding Simulations and = Replica=20 Exchange Approach

Advisor - Carlos = Simmerling,=20 Department of Chemistry, SUNY at Stony Brook

DONG, Haitao=20 (Mr.)

Department of Chemistry = and=20 Biochemistry, The University of Oklahoma

Quasiharmonic=20 Vibrations of Water, Water Clusters, and Liquid Water from Principal = Component=20 Analysis of Quantum or QM/MM Trajectories

Advisor - Ralph A. = Wheeler,=20 Department of Chemistry and Biochemistry, The

University of=20 Oklahoma

IVANOV, Ivaylo N.=20 (Mr.)

Center for Molecular = Modeling and=20 Department of Chemistry, University of = Pennsylvania

Relative pKs=20 > from First Principles Molecular Dynamics: =20 The Case of Histidine Deprotonation

Advisor - Michael L. = Klein, Director=20 and Hepburn Professor of Physical Science,

University of=20 Pennsylvania

KATT, William B.=20 (Mr.)

Department of Chemistry, = Rensselaer=20 Polytechnic Institute

Optimization of=20 Molecular Properties Through Structural Mutation and Virtual Screening = with QSAR=20 Models

Advisor - Curt M. = Breneman,=20 Department of Chemistry, Rensselaer Polytechnic = Institute

KORMOS, Bethany=20 (Ms.)

Department of Chemistry, = University=20 of Minnesota

Utilizing=20 Density Functional Theory to Study Nucleophilic Substitution = Reactions: Optimization of an Adiabatic = Connection=20 Method and its Application

Advisor - Christopher J. = Cramer,=20 Department of Chemistry, University of Minnesota

STROCKBINE, = Bentley=20 (Mr.)

Department of = Pharmacological=20 Sciences, Stony Brook University

Advances in = Structure=20 Prediction Techniques

Advisor - Carlos = Simmerling,=20 Department of Chemistry, SUNY at Stony Brook

WU, Min=20 (Ms.)

Department of Chemistry, = New York=20 University

Structural=20 Studies of an Environmental Carcinogen within a Y Family Bypass DNA=20 Polymerase

Advisor - Suse Broyde, = Department of=20 Biology, New York University

ZHOU, Zhigang=20 (Mr.)

Department of Chemistry, = Duquesne=20 University

Resistant = Effect=20 Exploring of HIV-1 RT Mutation by Molecular Dynamics

Advisor - Jeffrey D. = Madura,=20 Department of Chemistry and Biochemistry, Duquesne

University

Applications for the next round will be accepted soon. Previous winners are welcome = to=20 enter. An application = must be=20 submitted to the Treasurer of the COMP. =20 Then an abstract must be submitted through the ACS OASYS system = for=20 online paper submissions prior to the deadline. Visit http://membership.acs.org/C/COMP/CCG/ccg.html for=20 further information.

Chemical=20 Computing Group Inc. is a leading provider of computational applications = aimed=20 at the drug discovery and design marketplace. CCG=92s flagship product is = the award=20 winning Molecular Operating Environment (MOE), which offers=20 visualization, simulation, and methodology development in one = package. MOE provides an = integrated suite=20 of powerful, yet intuitive chemistry software tools for HTS, Structure = Based=20 Design, Molecular modeling and Protein and Homology modeling as well = as an embedded programming language for the = rapid=20 prototyping of scientific methods. =20 Biologists, medicinal chemists, and computational chemists use = MOE=20 in pharmaceutical companies, biotechnology companies, and universities=20 worldwide.

CCG is=20 based in Montreal, Canada, with offices in L=F6rrach, Germany and = Cambridge,=20 UK. For more information, = please=20 visit our website http://www.chemcomp.com. Send E-mail inquiries to info@chemcomp.com.