From chemistry-request@ccl.net Wed May 21 06:12:38 2003 Received: from cuces.unisi.it (cuces.unisi.it [193.205.4.2]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h4LACbbc028634 for ; Wed, 21 May 2003 06:12:38 -0400 Received: from CONVERSION-DAEMON.cuces.unisi.it by cuces.unisi.it (PMDF V6.1-1 #30546) id <01KW5IKBOX1S0002J5(at)cuces.unisi.it> for chemistry(at)ccl.net; Wed, 21 May 2003 12:12:24 +0100 (MET) Received: from unisi.it (ccmaol10.chim.unisi.it [172.16.29.96]) by cuces.unisi.it (PMDF V6.1-1 #30546) with ESMTPA id <01KW5IIU7TCY0003MM(at)cuces.unisi.it> for chemistry(at)ccl.net; Wed, 21 May 2003 12:08:16 +0100 (MET) Date: Wed, 21 May 2003 11:59:34 +0200 From: "Nicolas Ferre'" Subject: CCL: Molecular orbital visualization Sender: ferre(at)unisi.it To: chemistry(at)ccl.net Message-id: <3ECB4E06.D825B9B6(at)unisi.it> Organization: Universita` di Siena MIME-version: 1.0 X-Mailer: Mozilla 4.78iC-CCK-MCD [en_US] (X11; U; AIX 5.1) Content-type: text/plain; charset=us-ascii Content-transfer-encoding: 7bit X-Accept-Language: en Dear all, I'm looking for a unix program able to visualize (in 3D) molecular orbitals according to the following requirements: 1) handling large molecular systems 2) zooming on a subset of atoms 3) discarding a subset of atoms I don't need any powerful graphics stuff (OpenGL), this is only in order to setup QM/MM calculations using CASSCF for the QM part. Unfortunately, even if Molden has a zooming capability while displaying 3D MOs, the result is very ugly (at least on my ibm box) and meaningless. Thanks. Nicolas -- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Nicolas FERRE' (PhD) phone/fax : +39-0577-234278 Dipartimento di Chimica Universita` di Siena mailto:ferre*at*unisi.it via Aldo Moro 53100 SIENA (Italia) http://ccmaol1.chim.unisi.it/ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ From chemistry-request@ccl.net Wed May 21 08:44:21 2003 Received: from soul.helsinki.fi (soul.helsinki.fi [128.214.3.1]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h4LCiJbc032192 for ; Wed, 21 May 2003 08:44:20 -0400 Received: from localhost (mpjohans@localhost) by soul.helsinki.fi (8.9.3p2/8.9.3) with ESMTP id PAA317690 for ; Wed, 21 May 2003 15:44:14 +0300 (EEST) X-Authentication-Warning: soul.helsinki.fi: mpjohans owned process doing -bs Date: Wed, 21 May 2003 15:44:14 +0300 (EEST) From: Mikael Johansson X-X-Sender: mpjohans)at(soul.helsinki.fi To: chemistry)at(ccl.net Subject: CCL: pdm97 or other general ESP-fitting programs Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hello All! Does anyone know what became of the pdm97 ESP-fitting program, written by the now late D.E. Williams? Is it available anywhere? Alternatively, does anyone have recommendations of other programs capable of fitting ESP charges? Ideally, one with a Turbomole interface :-) Have a nice day, Mikael J. http://www.helsinki.fi/~mpjohans/ From chemistry-request@ccl.net Wed May 21 07:51:43 2003 Received: from celebris04.cetem.gov.br (correio.cetem.gov.br [200.20.105.10]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h4LBpgbc030856 for ; Wed, 21 May 2003 07:51:43 -0400 Received: by correio.cetem.gov.br with Internet Mail Service (5.5.2653.19) id ; Wed, 21 May 2003 08:53:14 -0300 Message-ID: <216FE3CA3D4DD611AE2600105AD16BDFD56B34)at(correio.cetem.gov.br> From: Ian Hovell To: =?iso-8859-1?Q?Chemistry_=28Correio_eletr=F4nico=29?= Subject: CCL: Scipcm job fails to complete Date: Wed, 21 May 2003 08:53:10 -0300 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 h4LBphbc030857 Dear CCLers, Below is an edited output from a failed gaussian job. It fails stating: ShPair-CalcS2-2 allocation failure: I have been unable to find any reference to this in the manual. Can any body shed any light on this problem TIA Ian %mem=10MW %nproc=1 Will use up to 1 processors via shared memory. Default route: MaxDisk=2000MB ------------------------------------------ # rhf/3-21g* scrf=scipcm geom=connectivity ------------------------------------------ 1/38=1,57=2/1; 2/17=6,18=5,40=1/2; 3/5=5,7=1,11=1,25=1,30=1/1,2,3; 4/7=1/1; 5/5=2,32=1,38=4,40=1000/2; 6/7=2,8=2,9=2,10=2,28=1/1; 99/5=1,9=1/99; ----------------------------------- Solvated Solutes: hydroxyquinaldine ----------------------------------- Symbolic Z-matrix: Charge = 0 Multiplicity = 1 C C 1 1.3604 C 2 1.42079 1 119.7042 C 3 1.40232 2 118.70315 1 0.34555 0 C 4 1.41382 3 120.51752 2 -0.18059 0 C 5 1.35698 4 119.39375 3 0.01308 0 H 1 1.07087 2 119.8106 3 179.80729 0 N 3 1.36706 2 119.24129 1 -179.8798 0 C 4 1.42029 3 117.18863 2 179.53833 0 H 5 1.07213 4 119.27995 3 179.97652 0 H 6 1.07187 5 120.4652 4 -179.87495 0 C 9 1.351 4 119.63294 3 -0.08886 0 C 8 1.30384 3 119.65922 2 -179.2798 0 H 9 1.07275 4 119.13639 3 -179.92619 0 H 12 1.07142 9 121.24498 4 -179.79238 0 O 2 1.36814 1 123.62778 6 179.62457 0 H 16 0.96618 2 113.32298 1 -0.66918 0 C 13 1.51008 8 120.08982 3 179.47196 0 H 18 1.08504 13 110.04764 8 -121.81192 0 H 18 1.07866 13 110.46305 8 -1.29531 0 H 18 1.08544 13 110.22502 8 119.45484 0 ---------------------------Cut out put---------------------------- Projected INDO Guess. Warning! Cutoffs for single-point calculations used. Requested convergence on RMS density matrix=1.00D-04 within 64 cycles. Requested convergence on MAX density matrix=1.00D-02. Requested convergence on energy=5.00D-05. ShPair-CalcS2-2 allocation failure: iend,mxcore= 166464 137127 Error termination via Lnk1e in C:\G98W\l502.exe. Job cpu time: 0 days 0 hours 13 minutes 28.0 seconds. File lengths (MBytes): RWF= 14 Int= 0 D2E= 0 Chk= 1 Scr= 1 Ian Hovell - Ph.D. NUCLEO DE MODELAGEM MOLECULAR-NMM Centro de Tecnologia Mineral - CETEM Ministerio da Cijncia e da Tecnologia- MCT Avenida Ipj, No 900 - Cidade Universitaria Ilha do Fundco Rio de Janeiro RJ Brasil CEP 21941-590 tel 00 55 (xx) 3865 - 7216 Fax 00 55 (xx) 22602837 ou 2290-4286 e-mail hovell)at(cetem.gov.br From chemistry-request@ccl.net Wed May 21 11:06:11 2003 Received: from admin.cnrs-orleans.fr (admin.cnrs-orleans.fr [163.9.1.2]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h4LF6Abc004490 for ; Wed, 21 May 2003 11:06:10 -0400 Received: from chinon (chinon.cnrs-orleans.fr [163.9.6.107]) by admin.cnrs-orleans.fr (8.12.9/jtpda-5.4) with ESMTP id h4LF4OOX017601 ; Wed, 21 May 2003 17:04:24 +0200 (MET DST) Content-Type: text/plain; charset="iso-8859-1" From: Konrad Hinsen To: Mikael Johansson , CHEMISTRY!at!ccl.net Subject: CCL: Re: pdm97 or other general ESP-fitting programs Date: Wed, 21 May 2003 17:04:23 +0200 User-Agent: KMail/1.4.3 References: In-Reply-To: MIME-Version: 1.0 Message-Id: <200305211704.23122.hinsen@cnrs-orleans.fr> X-MailScanner: Found to be clean Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id h4LF6Bbc004491 > Alternatively, does anyone have recommendations of other programs capable > of fitting ESP charges? Ideally, one with a Turbomole interface :-) There is an ESP charge fitting module in the Molecular Modelling Toolkit: http://dirac.cnrs-orleans.fr/MMTK/ It uses a numerically stable solver based on singular-value decomposition, and permits sum and symmetry constraints. No Turbomole interface, but very probably it would only take a handful of Python code lines to implement one, assuming that the data formats are known. -- ------------------------------------------------------------------------------- Konrad Hinsen | E-Mail: hinsen&at&cnrs-orleans.fr Centre de Biophysique Moleculaire (CNRS) | Tel.: +33-2.38.25.56.24 Rue Charles Sadron | Fax: +33-2.38.63.15.17 45071 Orleans Cedex 2 | Deutsch/Esperanto/English/ France | Nederlands/Francais ------------------------------------------------------------------------------- From chemistry-request@ccl.net Wed May 21 12:57:02 2003 Received: from ccl.net (pagergate.ccl.net [192.148.249.4]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h4LGv2bc007267 for ; Wed, 21 May 2003 12:57:02 -0400 Received: from krakow.ccl.net (krakow.ccl.net [192.148.249.195]) by ccl.net (8.11.6+Sun/8.11.6/OSC 2.1) with ESMTP id h4LGv1t03403; Wed, 21 May 2003 12:57:01 -0400 (EDT) Date: Wed, 21 May 2003 12:57:00 -0400 (EDT) From: Jan Labanowski To: MicroElectronics:at:AtomicScaleDesign.net cc: chemistry:at:ccl.net, Jan Labanowski , gusev:at:us.ibm.com Subject: Call for papers, MRS Fall 2003 Symposium: Fundamentals of Novel Oxide/Semiconductor Interfaces, Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=X-UNKNOWN Content-Transfer-Encoding: 8BIT ************************************************************************** MRS Symposium E: Fundamentals of Novel Oxide/Semiconductor Interfaces December 1-5, 2003 , Boston MA DEADLINE for on-line abstract submission: June 19, 2003 (see http://mrsfall2003.abstractcentral.com/) Symposium Organizers Cammy Abernathy (U. Florida), Evgeni Gusev (IBM T.J. Watson Res. Center), Darrell Schlom (Penn State Univ.), Susanne Stemmer (UCSB) The interfaces between oxides and semiconductors are important to a number of emerging technologies and are becoming all the more critical as devices scale into the nanometer regime. Concurrent with advances in incorporating new gate dielectrics in traditional Si technology, a considerable number of other applications for novel oxide/semiconductor interfaces are currently being considered. These include ferroelectric/semiconductor interfaces for novel sensors and oxide/compound semiconductor interfaces for field-effect transistors. Numerous research efforts are focused on understanding and exploiting the properties of novel oxide/semiconductor interfaces that fulfill the stringent requirements for these and other applications. The goal of this symposium is to bring together researchers involved with novel oxide/semiconductor interfaces, including, but not limited to, traditional Si-based devices. Of particular interest for this symposium are contributions on fundamental growth studies, atomic scale structural characterization, simulation and modeling of interfaces, and novel physical characterization methods of defects. Papers are anticipated in the following areas: 7 Epitaxial growth of oxides on semiconductors (including SiGe, SiC, Ge, Si, GaAs, GaN) and semiconductors on oxides 7 Growth and physical characterization of alternative gate dielectrics for Si-based devices 7 Fundamental growth studies of amorphous and polycrystalline metal oxides 7 Atomic and electronic structure calculations of semiconductor/oxide interfaces 7 Experimental and theoretical studies of interfaces and defects 7 New developments in physical characterization methods for ultrathin oxides and interfaces 7 Novel heterostructures 7 Novel devices incorporating semiconductor/oxide interfaces 7 Chemical stability of oxide/semiconductor interfaces 7 Piezoelectric/semiconductor integration including MEMS 7 Ferroelectric/semiconductor integration including FRAMs 7 Modeling of growth and interfaces 7 Oxynitrides in combination with alternative high-k oxides Invited speakers (partial list) include: Israel Baumvol (UFRGS, Brazil), Peter Bloechl (Clausthal Univ. of Technology, Germany),Matt Copel (IBM T.J. Watson Res. Center), Brent Gila (Univ. of Florida), Supratik Guha (IBM T.J. Watson Res. Center), Yong Liang (Motorola), T.P. Ma (Yale Univ.), Gerd Norga(IBM Z|rich, Switzerland), Jasprit Singh (Univ. of Michigan), Andre Stesmans (Univ. Leuven, Belgium), Akira Toriumi (Univ. of Tokyo, Japan), David Vanderbilt (Rutgers Univ.), and John Williams (Auburn Univ.) Depending on the number of submitted abstract, we anticipate to have a three day Symposium from Dec. 1 (Mon.) to Dec. 3. (Wedn), 2003. As usual, the fall MRS meeting will be held in Boston, MA. The MRS Fall meeting program and submission information can be found at: http://www.mrs.org/meetings/fall2003/. From chemistry-request@ccl.net Wed May 21 13:00:07 2003 Received: from ccl.net (pagergate.ccl.net [192.148.249.4]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h4LH07bc007418 for ; Wed, 21 May 2003 13:00:07 -0400 Received: from krakow.ccl.net (krakow.ccl.net [192.148.249.195]) by ccl.net (8.11.6+Sun/8.11.6/OSC 2.1) with ESMTP id h4LH06t03718; Wed, 21 May 2003 13:00:06 -0400 (EDT) Date: Wed, 21 May 2003 13:00:05 -0400 (EDT) From: Jan Labanowski To: chemistry:at:ccl.net, jkl:at:ccl.net cc: ancarauta:at:uol.com.br Subject: Periodic system (fwd) Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII ---------- Forwarded message ---------- Return-Path: Date: Wed, 21 May 2003 13:52:56 -0300 Message-Id: Subject: Periodic system From: "ancarauta" To: jkl:at:ccl.net Hi. I'm calculating a periodic system but the solvent molecules are blowing up the box. Does anybodry help me? Thanks a lot. Alexandre Carauta --- UOL, o melhor da Internet http://www.uol.com.br/ From chemistry-request@ccl.net Wed May 21 15:29:27 2003 Received: from mxout2.cac.washington.edu (mxout2.cac.washington.edu [140.142.33.4]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h4LJTRbc011577 for ; Wed, 21 May 2003 15:29:27 -0400 Received: from smtp.washington.edu (smtp.washington.edu [140.142.32.139]) by mxout2.cac.washington.edu (8.12.1+UW03.04/8.12.1+UW02.12) with ESMTP id h4LJTGg9012519 for ; Wed, 21 May 2003 12:29:16 -0700 Received: from gonaou ([128.95.128.116]) (authenticated bits=0) by smtp.washington.edu (8.12.1+UW03.04/8.12.1+UW02.12) with ESMTP id h4LJTGPx022202 (version=TLSv1/SSLv3 cipher=RC4-MD5 bits=128 verify=NOT) for ; Wed, 21 May 2003 12:29:16 -0700 Message-ID: <008e01c31fcf$47b80740$74805f80@gonaou> From: "Carsten Detering" To: Subject: CCL:dock5, phdock and chemgrid Date: Wed, 21 May 2003 21:29:21 +0200 Organization: University of Washington MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 6.00.2800.1158 X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2800.1165 Hi all, I wonder if anyone of you has successfully used the chemgrid feature in Dock5? I tried to use it, but I get an error like fmt: read unexpected character apparent state: internal I/O last format: (10X,F8.2,5X,F8.2,5X,F5.3) lately reading sequential formatted internal IO Aborted I created an INCHEM file as described in the README file, and made sure that the ';' are in the correct place. Anybody got an idea what could be the problem here?? My second question is, if anybody used the phDock feature in Dock. THis is mentioned several papers (Pharmacophore-based Molecular Docking to account for Ligand Flexibility, Proteins, 51 (2003) 172-188, among others), and is implemented in Dock4, but it is not mentioned in the manual. Could anybody tell me how to invoke it? I will report all helpful answers. Thanks a lot in advance, Carsten ------------------------------------- Carsten Detering University of Washington Department of Chemistry Seattle, WA 98195 From chemistry-request@ccl.net Wed May 21 15:53:34 2003 Received: from ultra.chem.ucsb.edu (ultra.chem.ucsb.edu [128.111.114.119]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h4LJrYbc012188 for ; Wed, 21 May 2003 15:53:34 -0400 Received: from localhost (localhost [127.0.0.1]) by ultra.chem.ucsb.edu (Postfix) with ESMTP id 0EC8550354; Wed, 21 May 2003 12:53:33 -0700 (PDT) Received: from ultra.chem.ucsb.edu ([127.0.0.1]) by localhost (ultra [127.0.0.1]) (amavisd-new, port 10024) with ESMTP id 15404-07; Wed, 21 May 2003 12:53:32 -0700 (PDT) Received: by ultra.chem.ucsb.edu (Postfix, from userid 3016) id 8AD6150353; Wed, 21 May 2003 12:53:31 -0700 (PDT) Received: from localhost (localhost [127.0.0.1]) by ultra.chem.ucsb.edu (Postfix) with ESMTP id 3F0481707D0; Wed, 21 May 2003 12:53:31 -0700 (PDT) Date: Wed, 21 May 2003 12:53:31 -0700 (PDT) From: John Bushnell To: Ian Hovell Cc: =?iso-8859-1?Q?Chemistry_=28Correio_eletr=F4nico=29?= Subject: Re: CCL:Scipcm job fails to complete In-Reply-To: <216FE3CA3D4DD611AE2600105AD16BDFD56B34*at*correio.cetem.gov.br> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-Virus-Scanned: by amavisd-new Looks like you don't have enough memory. Try increasing your %mem assignment and see if that helps. (10MW is 80MB by the way, so you likely can increase this on a newer PC.) - John On Wed, 21 May 2003, Ian Hovell wrote: > Dear CCLers, > Below is an edited output from a failed gaussian job. > It fails stating: ShPair-CalcS2-2 allocation failure: > I have been unable to find any reference to this in the manual. > Can any body shed any light on this problem > TIA > Ian > %mem=10MW > %nproc=1 > Will use up to 1 processors via shared memory. > Default route: MaxDisk=2000MB > ------------------------------------------ > # rhf/3-21g* scrf=scipcm geom=connectivity > ------------------------------------------ -snip- > ShPair-CalcS2-2 allocation failure: iend,mxcore= 166464 137127 > Error termination via Lnk1e in C:\G98W\l502.exe. From chemistry-request@ccl.net Wed May 21 20:29:04 2003 Received: from lac.chem.nagoya-u.ac.jp (lac.chem.nagoya-u.ac.jp [133.6.84.199]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h4M0T3bc020010 for ; Wed, 21 May 2003 20:29:04 -0400 Received: from lac2.chem.nagoya-u.ac.jp (lac2.chem.nagoya-u.ac.jp [133.6.84.36]) by lac.chem.nagoya-u.ac.jp (Postfix) with ESMTP id E19E4D9DC5 for ; Thu, 22 May 2003 09:29:01 +0900 (JST) From: Hannes Loeffler Organization: Nagoya University To: chemistry..at..ccl.net Subject: CCL: shifting coordinates with CHARMM Date: Thu, 22 May 2003 09:29:35 +0900 User-Agent: KMail/1.5 MIME-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: 7bit Content-Disposition: inline Message-Id: <200305220929.35135.hloeffler..at..lac.chem.nagoya-u.ac.jp> Hi, is it possible to re-center coordinates with CHARMM? Some viewing programs are not aware of PBCs and during a simulation the system of interest may diffuse to the edges of the box. It might be useful, therefore, to shift an atom (or maybe an arbritary point in space) to the center of the box. TIA, Hannes. From chemistry-request@ccl.net Wed May 21 17:52:53 2003 Received: from shrek1.uol.com.br (shrek1.uol.com.br [200.221.29.16]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h4LLqrbc016636 for ; Wed, 21 May 2003 17:52:53 -0400 Received: from uol.com.br (unknown [172.26.5.201]) by shrek1.uol.com.br (Postfix) with ESMTP id 29F3A25042; Wed, 21 May 2003 18:52:48 -0300 (BRT) Date: Wed, 21 May 2003 18:52:48 -0300 Message-Id: Subject: periodic system MIME-Version: 1.0 Content-Type: text/plain;charset="iso-8859-1" From: "ancarauta" To: jkl:at:ccl.net Cc: CHEMISTRY:at:ccl.net X-XaM3-API-Version: 2.4 R4 ( B5 ) X-SenderIP: 200.157.150.4 Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id h4LLqrbc016639 Hi. > I'm calculating a periodic system but the solvent > molecules are blowing up the box. Does anybodry help me? > > Thanks a lot. > > Alexandre Carauta PS.: I'm using the CERIUS program and the density is ok. Thanks a lot in advance. Alexandre Carauta --- UOL, o melhor da Internet http://www.uol.com.br/