From chemistry-request@server.ccl.net Mon Feb 18 17:08:29 2002 Received: from rwcrmhc54.attbi.com ([216.148.227.87]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g1IM8TZ09280 for ; Mon, 18 Feb 2002 17:08:29 -0500 Received: from C1353359A ([12.228.114.158]) by rwcrmhc54.attbi.com (InterMail vM.4.01.03.27 201-229-121-127-20010626) with SMTP id <20020218220804.JVRV1214.rwcrmhc54.attbi.com@C1353359A>; Mon, 18 Feb 2002 22:08:04 +0000 Reply-To: From: "Mark Thompson" To: "Per-Ola Norrby" , Subject: RE: MOLDEN display Date: Mon, 18 Feb 2002 14:08:22 -0800 Message-ID: <000901c1b8c8$c765ebc0$0300a8c0@attbi.com> MIME-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: 7bit X-Priority: 3 (Normal) X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook IMO, Build 9.0.2416 (9.0.2911.0) X-MimeOLE: Produced By Microsoft MimeOLE V5.50.4807.1700 Importance: Normal In-Reply-To: Dear Per-Ola, If you have access to a Windows-based computer, ArgusLab has terrific capabilities for generating surfaces from any data that can be put into a simple Gaussian cube file format. You can download a trial version at www.arguslab.com Cheers, Mark ================================= Mark Thompson, Ph.D. Planaria Software Seattle, WA. http://www.arguslab.com ================================= > -----Original Message----- > From: Computational Chemistry List [mailto:chemistry-request@ccl.net]On > Behalf Of Per-Ola Norrby > Sent: Monday, February 18, 2002 5:48 AM > To: chemistry@ccl.net > Subject: CCL:MOLDEN display > > > Dear CCL:ers, > > I want to visualize orbitals in a molden file. Currently, > I'm using molden for this (logically...), but for the size of system > I'm currently looking at (ca 300 basis functions), drawing one > 3D-orbital on screen requires ca 5 minutes (I'm working on an SGI > O2). Any tips on a faster program which is able to read molden > files? Alternatively, any fast orbital display program and a > conversion utility? I have access to Spartan (an old version) and > Molekel, if someone happens to have a way to convert my molden-file > (molden -> mkl would be ideal). I also have Molecule on a Macintosh, > and a couple of Linux machines, if you have any tips for those. > Please, send no suggestions about Windows programs to me, I have no > such machines, and will not get any. > > Best regards, > > Per-Ola Norrby > -- > > ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ > 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 > > -= This is automatically added to each message by mailing script =- > CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- > To Admins > MAILSERV@ccl.net -- HELP CHEMISTRY or HELP SEARCH > CHEMISTRY-SEARCH@ccl.net -- archive search | Gopher: > gopher.ccl.net 70 > Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: > jkl@ccl.net > > > > > > From chemistry-request@server.ccl.net Tue Feb 19 08:06:31 2002 Received: from hotmail.com ([64.4.37.184]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g1JD6VZ32567 for ; Tue, 19 Feb 2002 08:06:31 -0500 Received: from mail pickup service by hotmail.com with Microsoft SMTPSVC; Tue, 19 Feb 2002 05:06:05 -0800 Received: from 133.11.92.210 by pv2fd.pav2.hotmail.msn.com with HTTP; Tue, 19 Feb 2002 13:06:05 GMT X-Originating-IP: [133.11.92.210] From: "tianxiao young" To: CHEMISTRY@ccl.net Subject: imaginary mode code Date: Tue, 19 Feb 2002 13:06:05 +0000 Mime-Version: 1.0 Content-Type: text/plain; format=flowed Message-ID: X-OriginalArrivalTime: 19 Feb 2002 13:06:05.0803 (UTC) FILETIME=[30A4A3B0:01C1B946] Dear all, I am trying to plot the imaginary mode of the transition state using the output file of Gaussian 98. Could you please recommend any code or reference? Thank you very much in advance. Yours, txyoung _________________________________________________________________ Join the world’s largest e-mail service with MSN Hotmail. http://www.hotmail.com From chemistry-request@server.ccl.net Tue Feb 19 06:04:13 2002 Received: from orionl0.ccf.auth.gr ([155.207.199.31]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g1JB4CZ30053 for ; Tue, 19 Feb 2002 06:04:12 -0500 Received: from chem011 (chem011.chem.auth.gr [155.207.64.94]) by orionl0.ccf.auth.gr (8.11.6/8.11.4/8.11.4) with SMTP id g1JB3gb23066 for ; Tue, 19 Feb 2002 13:03:42 +0200 (EET) Organization: Message-ID: <004a01c1b934$b3104370$5e40cf9b@chem.auth.gr> From: "temper" To: Subject: MP2 opt Date: Tue, 19 Feb 2002 13:00:52 +0200 MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_0045_01C1B945.75E8AF30" 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 X-Virus-Scanned: by mail.auth.gr, virus data file v4185 created Feb 06 2002 This is a multi-part message in MIME format. ------=_NextPart_000_0045_01C1B945.75E8AF30 Content-Type: text/plain; charset="iso-8859-7" Content-Transfer-Encoding: quoted-printable I've been trying to do a geometry optimization using MP2/6-311++(d,p) = (210 basis functions) with GAUSSIAN 98W A.11 but I can't. WHY?(I have an ATHLON 1.6+GHz with 512 MB memory and 30+ GB hard disk). The operating system is WINDOWS 2000. I defined memory and hard disk: %m=3D180MB ------------------------------------------------- #p mp2/6-311++(d,p) opt scf=3Ddirect maxdisk=3D7000MB ------------------------------------------------- The error from the output is shown below: (Enter C:\G98W\l906.exe) Frozen-core derivative calculation, NFC=3D 10 NFV=3D 0. FulOut=3DF Deriv=3DT AODrv=3DT MMem=3D 3 MDisk=3D 18 MDiskD=3D 18 W3Min=3D 1270080 MinDsk=3D 1759100 NBas6D=3D 216 NBas2D=3D 23697 NTT=3D 23436 LenExt=3D 21464976 MDV=3D 23464976 MDiskM=3D 1380 NBas2p=3D 23300 Disk-based method using ON**2 memory for 18 occupieds at a time. Estimated scratch disk usage=3D 333638376 words. IMap=3D 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 IMap=3D 21 22 23 24 25 26 27 28 Actual scratch disk usage=3D 333205784 words. JobTyp=3D1 Pass 1: I=3D 11 to 28. writwa Can anyone give me an advice? Thanks in advance. Postgraduate (Ph.D) Student Vasilios I. Teberekidis Laboratory of Applied Quantum Chemistry=20 Aristotle University of Thessaloniki (Greece) Tel.:(+30 31) 99 78 20 +30937 66 18 18 E-mail: temper@chem.auth.gr www: http://users.auth.gr/temper ------=_NextPart_000_0045_01C1B945.75E8AF30 Content-Type: text/html; charset="iso-8859-7" Content-Transfer-Encoding: quoted-printable
I've been trying to do a = geometry=20 optimization using MP2/6-311++(d,p) (210 basis=20 functions)
 with GAUSSIAN 98W A.11 = but I=20 can't.
WHY?(I have an ATHLON 1.6+GHz = with 512 MB=20 memory and 30+ GB hard disk).
The operating system is = WINDOWS=20 2000.
I defined memory and = hard=20 disk:
 
%m=3D180MB
-------------------------------------------------
#p mp2/6-311++(d,p) opt = scf=3Ddirect=20 maxdisk=3D7000MB
-------------------------------------------------

The error from the output is shown=20 below:
(Enter=20 C:\G98W\l906.exe)
Frozen-core derivative = calculation,=20 NFC=3D 10 NFV=3D 0.
FulOut=3DF Deriv=3DT=20 AODrv=3DT
MMem=3D 3 MDisk=3D 18 = MDiskD=3D=20 18
W3Min=3D 1270080 = MinDsk=3D 1759100=20 NBas6D=3D 216
NBas2D=3D 23697 NTT=3D = 23436 LenExt=3D=20 21464976
MDV=3D 23464976 MDiskM=3D = 1380 NBas2p=3D=20 23300
Disk-based method using = ON**2 memory=20 for 18 occupieds at a time.
Estimated scratch disk = usage=3D=20 333638376 words.
IMap=3D 1 2 3 4 5 6 7 8 9 = 10 11 12 13=20 14 15 16 17 18 19 20
IMap=3D 21 22 23 24 25 26 = 27=20 28
Actual scratch disk = usage=3D 333205784=20 words.
JobTyp=3D1 Pass 1: I=3D = 11 to=20 28.
writwa
 
Can anyone give me an advice? = Thanks in=20 advance.
 
 
Postgraduate (Ph.D) = Student
Vasilios=20 I. Teberekidis
Laboratory of Applied Quantum Chemistry
Aristotle=20 University of Thessaloniki (Greece)
Tel.:(+30 31) 99 78=20 20
        +30937 66 18 = 18
E-mail: temper@chem.auth.gr
www: http://users.auth.gr/temper
------=_NextPart_000_0045_01C1B945.75E8AF30-- From chemistry-request@server.ccl.net Tue Feb 19 09:29:02 2002 Received: from postoffice.mail.cornell.edu ([132.236.56.7]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g1JET2Z02066 for ; Tue, 19 Feb 2002 09:29:02 -0500 Received: from cornell.edu ([128.84.182.122]) by postoffice.mail.cornell.edu (8.9.3/8.9.3) with ESMTP id JAA07013 for ; Tue, 19 Feb 2002 09:28:41 -0500 (EST) Sender: richard@cornell.edu Message-ID: <3C726119.7F88130A@cornell.edu> Date: Tue, 19 Feb 2002 09:28:41 -0500 From: Richard Gillilan X-Mailer: Mozilla 4.77 [en] (X11; U; Linux 2.4.16 i686) X-Accept-Language: en MIME-Version: 1.0 CC: chemistry@ccl.net Subject: CCL: Beamtime available at Cornell References: <01080610031300.07943@lcta1> <200108071245.OAA02595@chinon.cnrs-orleans.fr> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Sorry, this is not strictly a comp chem item, but there may be readers here who work in both fields, but are unaware that our resource is available: Thanks! Richard Gillilan MacCHESS, Cornell -- Protein Crystallography at MacCHESS -- MacCHESS, the macromolecular structure facility at the Cornell High-Energy Synchrotron Source, offers high-brightness x-ray beamtime to general academic and industrial users worldwide through a fast and simple application process. Cornell is within a day's drive of most of the Northeast as far South as the Baltimore-Washington area. Experienced staff scientists are on duty to help you and your students get the most out of your crystals. We are expanding and new users are welcome. Special experimental setups are also possible, contact the staff for details. Can't travel? Send us your crystals. We'll send you data with no collaborative/publishing obligation. o one-page, online express-mode applications for beamtime o small friendly academic environment o Ph.D. staff scientists on duty to help you o no collaborative publishing obligations o new Quantum 210 4Kx4K CCD detector with a 1 second chip readout! o BL-2 Containment for virus work o unique dual Quantum-4 CCD detector for large unit cells/high resolution (*) o 60-processor supercomputer for structure solving o support for FireWire disks, DVD (*), tape backup o multi-terabyte RAID storage o high-speed networking (gigabit internal, 100Mb out) o fast turnaround FedEX Crystallography (*) Contact MacCHESS for availability Visit our website: http://www.macchess.cornell.edu From chemistry-request@server.ccl.net Tue Feb 19 08:29:18 2002 Received: from signe.teokem.lu.se ([130.235.29.71]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g1JDTHZ00566 for ; Tue, 19 Feb 2002 08:29:17 -0500 Received: from teokem.lu.se (loke.teokem.lu.se [130.235.29.92]) by signe.teokem.lu.se (SGI-8.9.3/8.9.3) with ESMTP id OAA83015 for ; Tue, 19 Feb 2002 14:28:31 +0100 (CET) Sender: ulf@signe.teokem.lu.se Message-ID: <3C72541C.6EA3D3CD@teokem.lu.se> Date: Tue, 19 Feb 2002 14:33:16 +0100 From: Ulf Ryde Organization: Lund university X-Mailer: Mozilla 4.78 [en] (X11; U; Linux 2.4.8-26mdkenterprise i686) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net Subject: Quantum Bioinorganic Chemistry Conference Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit Conference announcement: QBIC-2 Orenas castle, Sweden July 27-29, 2002 http://www.teokem.lu.se/~ulf/Qbic The 2nd international conference on Quantum Bioinorganic Chemistry is now open for registration. QBIC-2, will take place Saturday July 27 (10.00) to Monday July 29, 2002 (~16.00). The conference will be held at Orenas castle, at the coast of Oresund, 40 km northwest of Lund in Sweden. . The scientific program will cover the use of quantum chemical methods to study problems of interest in biological inorganic chemistry. It will be a small and informal meeting with a maximum of 70 participants. The scientific program will consist of 19 lectures and a poster exhibition during the whole meeting. Invited speakers Margareta Blomberg, Stockholm university, Sweden Paulo Carloni, SISSA, Trieste, Italy Tim Clark, University Erlangen-Nürnberg, Germany Robert. J. Deeth, Warwick university, UK Richard A. Friesner, Columbia University, USA Michael B. Hall, Texas A&M University, USA Pawel M. Kozlowski, University of Louisville, Kentucky, USA Feliu Maseras, University Autonoma Barcelona, Spain: Kenneth M. Merz, Pennsylvania State University, USA Keiji Morokuma, Emory University, USA Frank Neese, Max Planck Institute, Mulheim, Germany Lou Noodleman, Scripps Research Institute, USA Michele Parrinello, Max Planck Institute, Stuttgart, Germany Carme Rovira, University of Barcelona, Spain Sason Shaik, The Hebrew University, Jerusalem, Israel Edward. I. Solomon, Stanford University, USA Arieh Warshel, University of Southern California, USA Kazundari Yoshizawa, Kyoto University, Japan Registration opens: February, 19 Registration closes: May, 31. Abstract submission: June, 16 Registration to QBIC-2 should be done online at http://www.teokem.lu.se/~ulf/Qbic/register.html. Please note that the registration will not be valid before the receipt of the conference fee. The conference is strictly limited to 70 participants. They will be selected based on the date of payment. 60 people have shown their interest by pre-registration. Conference fee 600 SEK (Swedish kronor, very roughly 60$) Full board and lodging at Orenas castle, two nights: 2970 SEK single room; 2540 SEK double room. Coffee, lunch, and dinner at Orenas castle the three conference days: 1345 SEK Youth hostel at Landskrona (10 km; shuttle bus will be available morning and evening) 2 nights: 400 SEK. Maximum 7 people. Payment must be made by bank transfer following the information in http://www.teokem.lu.se/~ulf/Qbic. QBIC-2 is an official satellite conference of the 6th European Conference on Biological Inorganic Chemistry, EUROBIC-6, to be held in Lund, Sweden, and Copenhagen, Denmark, July 30 to August 3, 2002. It follows immediately after the 35th International Conference on Coordination Chemistry, ICCC 35 in Heidelberg, July 21-26, 2002. The sixth World Congress of Theoretically Oriented Chemists, WATOC-6, is held in Lugano, Switzerland, August, 4-9, 2002. Organising committee Ulf Ryde, Lund (Ulf.Ryde@teokem.lu.se) Bjorn O. Roos, Lund Per. E. M. Siegbahn, Stockholm Lars Hemmingsen, Copenhagen From chemistry-request@server.ccl.net Tue Feb 19 12:01:55 2002 Received: from outmail-1.caramail.com ([213.193.12.65]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g1JH1sZ05295 for ; Tue, 19 Feb 2002 12:01:54 -0500 Date: Tue, 19 Feb 2002 12:01:54 -0500 Received: from lycos.co.uk (newwww-9.caramail.com [213.193.12.19]) by outmail-1.caramail.com (8.8.8/8.8.8) with SMTP id SAA10248 for chemistry@ccl.net; Tue, 19 Feb 2002 18:01:30 +0100 (MET) Posted-Date: Tue, 19 Feb 2002 18:01:30 +0100 (MET) From: JOSE Drive To: chemistry@ccl.net Message-ID: <1014138090022590@lycos.co.uk> X-Mailer: Caramail - www.caramail.com X-Originating-IP: [213.1.45.14] Mime-Version: 1.0 Subject: Re:Autodock Content-Type: multipart/mixed; boundary="=_NextPart_Caramail_0225901014138090_ID" 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_Caramail_0225901014138090_ID Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Dear CClers, I am trying to compile autodock on an IBM PC compatable computer running Linux Mandrake 7.2. I seem to have problems compiling the makefile. I have changed the necessary parameters in the program for my computer configuration but find certain line numbers have problems. some have corrected this in some cases by including a return in the statement but others problems are not so easy. Has anybody else in the users group compiled autodock on a Pc running Linux and if successful which Linux operating system did you use. Many Thanks Claudius D'Silva ______________________________________________________ Free Email - http://www.lycos.co.uk Get your domain for =A39.90 - http://lycos.uk.domainnames.com/default.asp?caller=3Dlycos_ef Win a widescreen TV - http://sundayleague.lycos.co.uk --=_NextPart_Caramail_0225901014138090_ID--