From chemistry-request@server.ccl.net Wed Nov 21 01:53:17 2001 Received: from mail.kemi.dtu.dk ([130.225.67.150]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id fAL6rGB12220 for ; Wed, 21 Nov 2001 01:53:16 -0500 Received: from [192.38.70.75] (pon.ok.dtu.dk [192.38.70.75]) by mail.kemi.dtu.dk (8.11.6/8.11.4) with ESMTP id fAL6r2k07665; Wed, 21 Nov 2001 07:53:03 +0100 Mime-Version: 1.0 X-Sender: pon@mail.kemi.dtu.dk Message-Id: In-Reply-To: <20011120170502.65197.qmail@web12905.mail.yahoo.com> References: <20011120170502.65197.qmail@web12905.mail.yahoo.com> Date: Wed, 21 Nov 2001 07:53:30 +0100 To: Meike Reinhold From: Per-Ola Norrby Subject: Re: CCL:B3LYP s B3P86 Cc: chemistry@ccl.net Content-Type: text/plain; charset="us-ascii" ; format="flowed" >Dear CClers, > >I am looking for papers discussing the comparison of B3LYP vs B3P86 >in transition metal systems >(first or second row only). I am especially interested in their >ability to calulate structural >data accurately. Any hints would be appreciated, >Meike reinhold > >===== >Meike Reinhold >Chemistry Department >University of York >UK A good source would be "Computational Organometallic Chemistry", edited by Tom Cundari, avaliable from Marcel-Dekker. Specifically, chapter 4 by Diedenhofen, Wagener, and Frenking, does exactly the comparison you're asking for. You can find the book at this link: http://www.dekker.com/servlet/product/productid/0478-9 Best, Per-Ola -- ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ Per-Ola Norrby, Assoc. Professor, http://compchem.dfh.dk/PeO/ Technical University of Denmark, Dept. of Chem., Org. Chem. Building 201, Kemitorvet, DK-2800 Kgs. Lyngby, Denmark Email: pon@kemi.dtu.dk tel +45-45252123, fax +45-45933968 From chemistry-request@server.ccl.net Wed Nov 21 00:00:36 2001 Received: from epimetheus.hosting4u.net ([209.15.2.70]) by server.ccl.net (8.11.6/8.11.0) with SMTP id fAL50ZB10738 for ; Wed, 21 Nov 2001 00:00:36 -0500 Received: (qmail 18146 invoked from network); 21 Nov 2001 05:00:24 -0000 Received: from zeus.hosting4u.net (HELO proinformatix.com) (209.15.2.56) by mail-gate.hosting4u.net with SMTP; 21 Nov 2001 05:00:24 -0000 Received: from yersina ([210.50.61.30]) by proinformatix.com ; Tue, 20 Nov 2001 23:00:22 -0600 Reply-To: From: "Sergio Manzetti" To: "Chemistry Discussion G" Subject: 3D structure phylogenia Date: Wed, 21 Nov 2001 15:05:22 -0800 Message-ID: <000901c172e1$01a122b0$2793b583@yersina> MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit X-Priority: 3 (Normal) X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook, Build 10.0.2627 Importance: Normal X-MimeOLE: Produced By Microsoft MimeOLE V5.00.2919.6700 Hi everyone, I wonder if any of you knows about a interactive 3D engine that classifies an uploaded 3D structure and outputs a phylogenetic tree based on RMSD and fold similarities? Cheers Sergio ________________________________________________________________________ _______________________________ Sergio Manzetti Research Scholar Centre of Molecular Biotechnology/ Supercomputer Facility Queensland University of Technology 2 George St. BRISBANE 4000 QLD AUSTRALIA email: s.manzetti@student.qut.edu.au Tlf: +61 7 3864 1434 www: http://www.life.sci.qut.edu.au/html/research/cmgenetics.html www2: http://www.its.qut.edu.au/hpc/ From chemistry-request@server.ccl.net Wed Nov 21 02:51:19 2001 Received: from beta.ceti.etat-ge.ch ([160.53.239.114]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id fAL7pIB13259 for ; Wed, 21 Nov 2001 02:51:18 -0500 Received: by beta.etat-ge.ch with Internet Mail Service (5.5.2653.19) id <4T6YDMP2>; Wed, 21 Nov 2001 08:51:02 +0100 Message-ID: From: "De Vito David (DIP)" To: "'chemistry@ccl.net'" Subject: Geometry optimisation problem Date: Wed, 21 Nov 2001 08:50:58 +0100 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2653.19) Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id fAL7pJB13260 > Hello ! > > I'm trying to optimize an octahedrical iridium +3 hexaaquo complex with > BP86 functional (ADF2000) with and without relativistic effects (IV basis > set), but the geometry doesn't convege. Some time ago I made the same > optimization with HF methods and I found stable structure... > > Can somebody give me some good advices ? I think that the MO occupation > isn't stable during SCF cycle and this lead to structural convergence > problems... > > > Best regards at all from Switzerland. > > > D. De Vito > > > ******************************************************************** > > D. De Vito > Enseignant de Chimie et d'Informatique, Adjoint au Bureau de Gestion > Collège Rousseau > 16A, Avenue du Bouchet > Case Postale 216 > 1211 Genève 28 > Suisse > +4122 / 733.71.30 (Collège) > +4122 / 733.71.82 (Fax) > > http://lcta.unige.ch/~devito (Page personnelle) > http://wwwedu.ge.ch/po/rousseau (Site officiel du Collège) > > ******************************************************************** > From chemistry-request@server.ccl.net Wed Nov 21 14:49:45 2001 Received: from sas.asc.hpc.mil ([129.48.244.126]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id fALJniB06553 for ; Wed, 21 Nov 2001 14:49:45 -0500 Received: from asc.hpc.mil (wk32.asc.hpc.mil [129.48.245.32]) by sas.asc.hpc.mil (8.11.6/8.11.6) with ESMTP id fALJnXX1204921 for ; Wed, 21 Nov 2001 14:49:33 -0500 (EST) Sender: duanx@asc.hpc.mil Message-ID: <3BFC04E0.F9A581B5@asc.hpc.mil> Date: Wed, 21 Nov 2001 14:47:44 -0500 From: XIAOFENG FRANK DUAN Organization: CSC X-Mailer: Mozilla 4.78 [en] (X11; U; IRIX 6.5 IP22) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net Subject: Convert MOs between G98/Jaguar and GAMESS Content-Type: multipart/alternative; boundary="------------B396FBB9C6E3CFC6EDEEDBB8" --------------B396FBB9C6E3CFC6EDEEDBB8 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi, all! I'd like to convert MOs from G98/Jaguar calculations to GAMESS's $vec format. Does any one know where to find a program or scripts to do so? Thanks! -- Xiaofeng Frank Duan, Ph.D | Phone: 937-904-8307 Sr. Application Analysit | Fax: 937-255-2288 ASC MSRC | Email: duanx@asc.hpc.mil Wright-Patterson AFB | URL: www.asc.hpc.mil --------------B396FBB9C6E3CFC6EDEEDBB8 Content-Type: text/html; charset=us-ascii Content-Transfer-Encoding: 7bit Hi, all!

I'd like to convert MOs from G98/Jaguar calculations to GAMESS's $vec format. Does any one know where to find a program or scripts to do so?

Thanks! 

-- 
 Xiaofeng Frank Duan, Ph.D | Phone: 937-904-8307
 Sr. Application Analysit  | Fax:   937-255-2288
 ASC MSRC                  | Email: duanx@asc.hpc.mil
 Wright-Patterson AFB      | URL:   www.asc.hpc.mil
  --------------B396FBB9C6E3CFC6EDEEDBB8-- From chemistry-request@server.ccl.net Wed Nov 21 08:57:53 2001 Received: from hive.niaid.nih.gov ([137.187.152.55]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id fALDvqB24771 for ; Wed, 21 Nov 2001 08:57:52 -0500 Received: by hive.niaid.nih.gov with Internet Mail Service (5.5.2653.19) id ; Wed, 21 Nov 2001 08:57:36 -0500 Message-ID: <7B9BE47109ACD211B96700104B23575305D58F95@hive.niaid.nih.gov> From: Cynthia Cotter To: Cc: Cynthia Cotter Subject: RFP NIH-NIAID-DAIT-02-16, Availability Announcement Date: Wed, 21 Nov 2001 08:57:01 -0500 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2653.19) Content-Type: multipart/alternative; boundary="----_=_NextPart_001_01C17294.64F441A0" 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_01C17294.64F441A0 Content-Type: text/plain; charset="iso-8859-1" Ladies and Gentlemen: You are hereby informed of the availability of Request for Proposal (RFP) NIH-NIAID-DAIT-02-16, "Bioinformatics Integration Support Contract." This RFP has been released electronically and may be accessed by way of the NIAID Contract Management Branch (CMB) Home Page - see below for access instructions. NIAID/CMB Home Page (via the WWW): Use http://www.niaid.nih.gov/contract/ to access the NIAID/CMB Home Page. Once at the NIAID/CMB Home Page, click on the "Current RFPs" link and then click on "RFP-NIH-NIAID-DAIT-02-16". If you have any questions or difficulties obtaining the RFP, please contact me by phone or email. Cyndie Cotter Contracting Officer Contract Management Branch National Institute of Allergy and Infectious Diseases, NIH 6700-B Rockledge Drive MSC 7612, Room 2109 TEL: 301-402-0641 FAX: 301-402-0972 EMAIL: cc41w@nih.gov http://www.niaid.nih.gov/contract/archive/RFP02-16.pdf Cyndie ------_=_NextPart_001_01C17294.64F441A0 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable RFP NIH-NIAID-DAIT-02-16, Availability Announcement

Ladies and Gentlemen:

You are hereby informed of the = availability of Request for Proposal (RFP) NIH-NIAID-DAIT-02-16, = "Bioinformatics Integration = Support Contract."  This = RFP has been released electronically and may be accessed by way of the = NIAID Contract Management Branch (CMB) Home Page - see below for access = instructions.

      NIAID/CMB Home Page (via the = WWW):  Use = http://www.niaid.nih.gov/contract/ to access the NIAID/CMB Home Page.  Once = at the NIAID/CMB Home Page, click on the "Current RFPs" = link and then click on "RFP-NIH-NIAID-DAIT-02-16".

If you have any questions or = difficulties obtaining the RFP, please contact me by phone or = email.

Cyndie = Cotter
Contracting Officer
Contract Management = Branch
National Institute of Allergy = and
 Infectious Diseases, = NIH
6700-B Rockledge Drive
MSC 7612, Room 2109
TEL:  301-402-0641
FAX:  = 301-402-0972
EMAIL:  cc41w@nih.gov








http://www.niaid.nih.gov/contract/archive/RFP02-16.pdf=
Cyndie=20

------_=_NextPart_001_01C17294.64F441A0-- From chemistry-request@server.ccl.net Wed Nov 21 18:08:10 2001 Received: from femail18.sdc1.sfba.home.com ([24.0.95.145]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id fALN89B10327 for ; Wed, 21 Nov 2001 18:08:10 -0500 Received: from C1353359A ([65.4.172.51]) by femail18.sdc1.sfba.home.com (InterMail vM.4.01.03.20 201-229-121-120-20010223) with SMTP id <20011121230758.SNOM1435.femail18.sdc1.sfba.home.com@C1353359A>; Wed, 21 Nov 2001 15:07:58 -0800 Message-ID: <000f01c172e0$ba402010$33ac0441@sttln1.wa.home.com> Reply-To: "Mark A. Thompson" From: "Mark A. Thompson" To: Cc: , Subject: ArgusLab 3.0 beta release available Date: Wed, 21 Nov 2001 15:03:26 -0800 MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_000C_01C1729D.ABD54FC0" X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 5.50.4807.1700 X-MimeOLE: Produced By Microsoft MimeOLE V5.50.4807.1700 This is a multi-part message in MIME format. ------=_NextPart_000_000C_01C1729D.ABD54FC0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable **************************************** ArgusLab 3.0 beta release is now available **************************************** We are excited to announce the release of the beta version of ArgusLab = 3.0 ArgusLab is used by thousands of researchers and academics around the = world. ArgusLab delivers state-of-the-art graphics and computational methods = and is known as one of the easiest, most intuitive, molecular modeling = programs currently available. Please visit http://www.planaria-software.com to download a copy. New Features ----------------- Extensive support for Surfaces: simple, difference, mapped, and mapped = difference. Incredibly easy-to-use Surface construction and editing tool. Render surfaces in opaque, translucent, mesh, and dot Generate grid files for surfaces: orbitals, electron density, = electrostatic potential, and spin density. Import Gaussian cube files for surfaces. Read molecule structure from Gaussian .log files Clipping plane for surfaces. Automatic assignment of atomic hybridization. Automatic assignment of force field atom type. Automatic ring finder and aromatic ring display. Improved interface to the SCRF solvent model. Printing. Charge equilibration charges for the UFF force field. Extensive support of Undo/Redo for all user-input to the graphics = window. Space filling rendermode added. Apply rendermode options to subsets of atoms and bonds. Apply automatic hybrid, ffatom type, and ring finding to subsets of = atoms Apply geometry optimization updates to subsets of atoms. Set background color Lots of bug fixes from ArgusLab 2.0 Greatly enhance HTML help system with tutorials. ************************ Full list of 3.0 features ************************ Interactive 3D Molecule Builder with: =20 -------------------------------------------- Interactive 3D manipulator Fragment Library Beautify Geometry Automatically Add/Hide/Delete Hydrogens Cut/Copy/Paste Supports complete Undo/Redo for all user input actions Render modes: wireframe, ball & cylinder, cylinder, and space filling Geometry Monitors Periodic table tool for selecting new or modifying existing atoms Set background color Clipping planes for surfaces Apply render modes to selected subsets of atoms and bonds Render Surfaces as opaque, mesh, dot, and translucent Automatic assignment of atom hybridization and bond orders Support for automatically finding rings and assigning aromatic rings Automatic assignment of force field atom types =20 Calculation Types =20 --------------------- Single-Point Energies Optimize Geometries Electronic Excitation Spectra Improved interface to Self Consistent Reaction Field (SCRF) Solvent = Model =20 Properties ------------ Generate Surfaces: simple, difference, mapped, and mapped difference = using any grid data Calculate grid data for surfaces: orbitals, electron density, = electrostatic potential, spin density Import Gaussian cube files for use in rendering surfaces Ground and excited state dipole moments Transition moments Ground and excited state Mulliken and ZDO charges Rotary strengths for excited states Molecular Mechanics ------------------------- Universal Force Field (UFF) for the entire periodic table Calculates Charge-Equilibration charges from the Rappe' & Goddard model Quantum Mechanics ----------------------- =20 Extended Huckel with parameters for the entire periodic table (supports = fractional orbital occupations) MNDO, AM1, and PM3 semi-empirical Hamiltonians ZINDO semi-empirical Hamiltonian for excited states Restricted and Unrestricted Hartree-Fock SCF Enhanced ZINDO parameters stored in a user-modifiable external file Heats of formation for MNDO, AM1, and PM3 =20 Miscellaneous Printing -------------------------- File Types: supports XYZ, PDB, ArgusLab XML, and Gaussian .log file = formats HTML Help No size limitations for number of atoms Multi-threaded architecture allows multiple molecules opened = simultaneously and running calculations Runs on Windows 98, Win ME, Windows NT 4.0, Windows 2000, and Windows XP =20 ------=_NextPart_000_000C_01C1729D.ABD54FC0 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable
 
****************************************
  ArgusLab 3.0 beta = release is now=20 available
****************************************
We are excited to announce = the release of=20 the beta version of ArgusLab 3.0
ArgusLab is used by thousands = of=20 researchers and academics around the world.
ArgusLab delivers = state-of-the-art=20 graphics and computational methods and is known as one of the easiest, = most=20 intuitive, molecular modeling programs currently available.
 
Please visit http://www.planaria-software.co= m =20 to download a copy.
 
New Features
-----------------
 
Extensive support for = Surfaces: simple,=20 difference, mapped, and mapped difference.
Incredibly easy-to-use = Surface=20 construction and editing tool.
Render surfaces in opaque, = translucent,=20 mesh, and dot
Generate grid files for = surfaces:=20 orbitals, electron density, electrostatic potential, and spin=20 density.
Import Gaussian cube files = for=20 surfaces.
Read molecule structure from = Gaussian=20 .log files
Clipping plane for = surfaces.
Automatic assignment of = atomic=20 hybridization.
Automatic assignment of force = field atom=20 type.
Automatic ring finder and = aromatic ring=20 display.
Improved interface to the = SCRF solvent=20 model.
Printing.
Charge equilibration charges = for the UFF=20 force field.
Extensive support of = Undo/Redo for all=20 user-input to the graphics window.
Space filling rendermode=20 added.
Apply rendermode options to = subsets of=20 atoms and bonds.
Apply automatic hybrid, = ffatom type, and=20 ring finding to subsets of atoms
Apply geometry optimization = updates to=20 subsets of atoms.
Set background = color
Lots of bug fixes from = ArgusLab=20 2.0
Greatly enhance HTML help = system with=20 tutorials.
 
 
************************
Full list of 3.0 = features
************************
 
Interactive 3D Molecule = Builder=20 with: 
--------------------------------------------
Interactive 3D = manipulator
Fragment=20 Library
Beautify Geometry
Automatically Add/Hide/Delete=20 Hydrogens
Cut/Copy/Paste
Supports complete Undo/Redo for all user = input=20 actions
Render modes: wireframe, ball & cylinder, cylinder, and = space=20 filling
Geometry Monitors
Periodic table tool for selecting new or = modifying existing atoms
Set background color
Clipping planes for=20 surfaces
Apply render modes to selected subsets of atoms and = bonds
Render=20 Surfaces as opaque, mesh, dot, and translucent
Automatic assignment = of atom=20 hybridization and bond orders
Support for automatically finding rings = and=20 assigning aromatic rings
Automatic assignment of force field atom=20 types
 
 Calculation = Types =20
---------------------
Single-Point = Energies
Optimize=20 Geometries
Electronic Excitation Spectra
Improved interface to = Self=20 Consistent Reaction Field (SCRF) Solvent Model
 
Properties
------------
Generate Surfaces: simple, = difference,=20 mapped, and mapped difference using any grid data
Calculate grid data = for=20 surfaces: orbitals, electron density, electrostatic potential, spin=20 density
Import Gaussian cube files for use in rendering = surfaces
Ground=20 and excited state dipole moments
Transition moments
Ground and = excited=20 state Mulliken and ZDO charges
Rotary strengths for excited=20 states
Molecular = Mechanics
-------------------------
Universal Force Field (UFF) = for the=20 entire periodic table
Calculates Charge-Equilibration charges from = the Rappe'=20 & Goddard model
Quantum = Mechanics
-----------------------  =
Extended Huckel with = parameters for the=20 entire periodic table (supports fractional orbital occupations)
MNDO, = AM1,=20 and PM3 semi-empirical Hamiltonians
ZINDO semi-empirical Hamiltonian = for=20 excited states
Restricted and=20 Unrestricted Hartree-Fock SCF
Enhanced ZINDO parameters stored in a=20 user-modifiable external file
Heats of formation for MNDO, AM1, and=20 PM3
 
Miscellaneous  = Printing
--------------------------
File Types:=20 supports XYZ, PDB, ArgusLab XML, and Gaussian .log file formats
HTML=20 Help
No size limitations for number of atoms
Multi-threaded = architecture=20 allows multiple molecules opened simultaneously and running = calculations
Runs=20 on Windows 98, Win ME, Windows NT 4.0, Windows 2000, and Windows=20 XP
 
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