From chemistry-request@server.ccl.net Mon Jan 6 03:22:41 2003 Received: from smtp.netcologne.de ([194.8.194.112]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h068Me009677 for ; Mon, 6 Jan 2003 03:22:41 -0500 Received: from lapsigma (unknown [194.8.222.60]) by smtp.netcologne.de (Postfix) with ESMTP id 2DCE186781; Mon, 6 Jan 2003 09:22:38 +0100 (MET) From: =?iso-8859-1?Q?Holger_Clau=DFen?= To: "'Alan Leo'" , Subject: RE: FLEXX error message from ligand MOL2 read Date: Mon, 6 Jan 2003 09:22:32 +0100 Message-ID: <005401c2b55c$c5dd2b60$2700000a@lapsigma> MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" X-Priority: 3 (Normal) X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook, Build 10.0.4024 Importance: Normal In-Reply-To: <031e01c2b279$5d1bb8c0$e3cae88c@pak3> X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2800.1106 Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id h068Mf009680 Dear Alan, 1.) There is currently no FlexX specific newsgroup. However, please feel free to send any comment and question to flexx-info@biosolveit.de. 2.) The error message indicates in fact an error in the mol2 file. There may by plenty of reasons, so that I cannot say much without the file. Perhaps, you can send it to me, so that I can look to it. 3.) Ligand structures should always be minimized before docking. You can use any external force field for minimizing the ligands e.g. the Tripos force filed with comes with Sybyl. Please, note that the newes FlexX version is able to minimize ligands upon loading, if the flag AUTOMINIZISE in the config.dat is set to 1. Regards, Holger Claussen -- H.Claußen, BioSolveIT GmbH, An der Ziegelei 75, 53757 St. Augustin, Germany H.Claussen@biosolveit.de, www.biosolveit.de, Tel/Fax: +49 2241 973 66 60/88 > -----Original Message----- > From: Computational Chemistry List [mailto:chemistry-request@ccl.net] On > Behalf Of Alan Leo > Sent: Thursday, January 02, 2003 5:09 PM > To: chemistry@ccl.net > Subject: CCL:FLEXX error message from ligand MOL2 read > > Hi, All: > > I am using FLEXX evalution now, but when I input the ligand minimization > mol2 file, > the following error messgae is appeared: > _____________________________________________ > FLEXX> lig > FLEXX/LIGAND> read TSB_min > >> DATA ERROR: No molecules found. > [occured in line 126 of file TSB_min] > Segmentation fault (core dumped) > _____________________________________________ > > I have three question: > 1. I don't know if there is any newsgroup related to FLEXX except chemweb > newsgroup. > > 2. The error message above point out the error of my sybyl mol2 file > error, > or maybe it > is because of other reasons. > > 3. Should I minimize the ligand structure before I generate the > *_min.mol2 > file? Which software > I should use? > > Don't peng me, I am a newbie. :) Your help is much appreciated.. > > Best, > Alan > > > > > -= 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 > > > From chemistry-request@server.ccl.net Sun Jan 5 04:50:58 2003 Received: from hal.netbox.cz ([212.96.166.1]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h059ov015473 for ; Sun, 5 Jan 2003 04:50:57 -0500 Received: from lubos (r10s01p08.home.nbox.cz [212.96.184.72]) by hal.netbox.cz (Postfix) with SMTP id 3C632171D2A; Sun, 5 Jan 2003 10:50:56 +0100 (CET) Message-ID: <003b01c2b49f$71414d60$d200a8c0@mshome.net> Reply-To: "Lubos Vrbka" From: "Lubos Vrbka" To: "Rongjian Sa" Cc: References: <007201c2b3c4$82b754d0$cf137fca@pc26> Subject: Re: CCL:How to analysis the TRAJECTORY file of CPMD Date: Sun, 5 Jan 2003 10:47:20 +0100 Organization: NCBR MIME-Version: 1.0 Content-Type: multipart/related; type="multipart/alternative"; boundary="----=_NextPart_000_0037_01C2B4A7.D2AA27E0" 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_0037_01C2B4A7.D2AA27E0 Content-Type: multipart/alternative; boundary="----=_NextPart_001_0038_01C2B4A7.D2B1C900" ------=_NextPart_001_0038_01C2B4A7.D2B1C900 Content-Type: text/plain; charset="gb2312" Content-Transfer-Encoding: quoted-printable hi, >I want to know how to analysis the TRAJECTORY file of CPMD. And I = wander if you can give me some advice on this >scheme. From CPMD mail = list, I have know there is a program that can convert the TRAJECTORY = into other format. >Then some other program such as the GopenMol can = give a graphic result for it. So I want to know where I can find this = >program. And any help of you will be greatly appreciated! you can find gopenmol on the following address: = http://www.csc.fi/gopenmol/ i can't help you with the analysis software for cpmd (i don't use it) - = probably you could try search on google... hth, _@_: ################################################# Lubos Vrbka National Centre for Biomolecular Research Masaryk university, Brno, Czech Republic shnek@chemi.muni.cz http://www.chemi.muni.cz/~shnek tel. +420 5 4112 9508 ################################################# ------=_NextPart_001_0038_01C2B4A7.D2B1C900 Content-Type: text/html; charset="gb2312" Content-Transfer-Encoding: quoted-printable
hi,
 
>I want to=20 know how to analysis the TRAJECTORY file of CPMD. And I wander if you = can give=20 me some advice on this >scheme. From CPMD mail list, I have = know  there=20 is a program that can convert the TRAJECTORY into other format. >Then = some=20 other program such as the GopenMol can give a graphic result for it. So = I want=20 to know where I can find this >program. And any help of you will be = greatly=20 appreciated!
you can find gopenmol on the following = address:=20 http://www.csc.fi/gopenmol/
i can't help you with the analysis = software for=20 cpmd (i don't use it) - probably you could try search on=20 google...
 
hth,
_@_:
 
#################################################
Lubos=20 Vrbka
National Centre for Biomolecular Research
Masaryk = university, Brno,=20 Czech Republic
 
shnek@chemi.muni.cz
http://www.chemi.muni.cz/~shnek<= /A>
tel.=20 +420 5 4112=20 9508
#################################################
 
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------=_NextPart_000_0037_01C2B4A7.D2AA27E0-- From chemistry-request@server.ccl.net Mon Jan 6 10:21:24 2003 Received: from wn1.sci.kun.nl ([131.174.8.1]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h06FLN000597 for ; Mon, 6 Jan 2003 10:21:24 -0500 Received: from ac12.sci.kun.nl by wn1.sci.kun.nl via ac12.sci.kun.nl [131.174.179.19] with ESMTP for id h06FLN5v009455 (8.12.5/3.57); Mon, 6 Jan 2003 16:21:23 +0100 (MET) From: "E.L. Willighagen" Received: by ac12.sci.kun.nl via egonw@localhost for chemistry@ccl.net id h06FLNWp011267 (8.12.5/1.3); Mon, 6 Jan 2003 16:21:23 +0100 (MET) Date: Mon, 6 Jan 2003 16:21:23 +0100 (MET) Message-Id: <200301061521.h06FLNWp011267@ac12.sci.kun.nl> To: chemistry@ccl.net Subject: QSAR data set with experimental spectra Hi all, Today I've browsed the internet for QSAR data sets of compounds with experimental IR/NMR/mass spectra. I've found a few small data sets with 'simple' compounds for which I could look up the spectra, but these are actually not large enough. Are there large (>100 compounds) data sets with associated biological activities with the IR/NMR/mass spectra available? Looking forward to hear your ideas and suggestions, kind regards, Egon Willighagen From chemistry-request@server.ccl.net Mon Jan 6 05:28:28 2003 Received: from lipid.biocomp.unibo.it ([137.204.193.11]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h06ASP025403 for ; Mon, 6 Jan 2003 05:28:28 -0500 Received: by lipid.biocomp.unibo.it (Postfix, from userid 514) id 0DECF27A7C; Mon, 6 Jan 2003 11:33:41 +0100 (CET) Received: from localhost (localhost [127.0.0.1]) by lipid.biocomp.unibo.it (Postfix) with ESMTP id F05BE2EAED for ; Mon, 6 Jan 2003 11:33:41 +0100 (CET) Date: Mon, 6 Jan 2003 11:33:41 +0100 (CET) From: Ivan Rossi To: CompChem Mailing List Subject: ANN: ESF school on structural genomics Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII http://www.biocomp.unibo.it/school/html2003/ We are pleased to announce the: Bologna Winter School on Biotechnology 2003 HOT TOPICS IN STRUCTURAL GENOMICS 9-15 February 2003, Bologna - Italy http://www.biocomp.unibo.it/school/html2003/ email : school2003@biocomp.unibo.it The main topic will be the state of the art of protein structure prediction after CASP 5 (Critical Assessment of Techniques for Protein Structure Prediction, Asilomar, December 2002). Focus will be on comparative modelling, low homology protein modelling, new fold recognition, ab initio structure prediction, protein-protein and protein-DNA interaction, prediction of protein function and structure prediction of membrane proteins. LECTURERS Pierre Baldi University of California Irvine, CA, USA Nir Ben-Tal Tel Aviv University Tel Aviv, IL Soren Brunak Technical University of Denmark Lyngby, DK Chris Bystroff Rensselaer Polytechnic Institute Troy, NY, USA Rita Casadio University of Bologna Bologna, IT Manuela Helmer-Citterich University "Tor Vergata" Roma, IT Joel Janin LEBS, CNRS Gif sur Ivette, FR Sue Jones EBI Hinxton, UK David T. Jones University College London, UK Arthur M. Lesk University of Cambridge Cambridge, UK John Moult University of Maryland Rockville, MD, USA Anna Tramontano University "La Sapienza" Roma IT Alfonso Valencia National Center of Biotechnology Cantoblanco, ES Gunnar von Hejine University of Stockholm Stockholm, SE Stephen White University of California Irvine, USA For Application send a short C.V. to school2003@biocomp.unibo.it. You will be notified by e-mail of acceptance. Deadline for application is December 30, 2002 The School is partially granted by the European Science Foundation (Integrated Approaches for Functional Genomics programme) FOR LIVING EXPENSES AN OFFER IS AVAILABLE: a package of 500 EURO that covers lunches, coffee breaks and social dinner. TWO OFFERS FOR THE ACCOMODATION AT THE ERASMUS COLLEGE, IN DOWNTOWN BOLOGNA, ARE ALSO AVAILABLE: 160 EURO per person for a double room (6 nights) 260 EURO per person for a single room, if available (6 nights). Dues will be payed upon acceptance with modalities to be specified. University of Bologna CIRB, INTERDEPARTMENTAL CENTER FOR BIOTECHNOLOGY CORSO DI LAUREA IN BIOTECNOLOGIE European Science Foundation Consorzio Interuniversitario Biotecnologie Consiglio Nazionale per le Ricerche Marino Golinelli Foundation O.N.L.U.S. Organisation: AIRBBC Associazione Italiana per la Ricerca in Biofisica e Biologia Computazionale From chemistry-request@server.ccl.net Mon Jan 6 10:52:30 2003 Received: from ccl.net ([192.148.249.4]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h06FqU001854 for ; Mon, 6 Jan 2003 10:52:30 -0500 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 h06FqUj23156; Mon, 6 Jan 2003 10:52:30 -0500 (EST) Date: Mon, 6 Jan 2003 10:52:30 -0500 (EST) From: Jan Labanowski To: chemistry@ccl.net, mel@asdn.net Subject: 03.05.18 4th Int Conf Intelligent Process. and Manuf of Materials Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII ---------- Forwarded message ---------- Date: Tue, 7 Jan 2003 00:21:54 +0900 From: Hiroshi Mizuseki Reply-To: ipmm@imr.edu To: ipmm@imr.edu Subject: IPMM'03 --> Dear all, The IPMM'03 conference (The 4th International Conference on Intelligent Processing and Manufacturing of Materials) will be held in Sendai, Japan, May 18-23, 2003. To know more about IPMM'03, please visit the website http://www-lab.imr.tohoku.ac.jp/~ipmm/ where you will find useful information. *** IMPORTANT *** Extension of Abstract Submission Deadline: January, 10th. Please be informed that the deadline for abstract submission has been extended to 10 January 2003. --- Planned Sessions I. Focus Sessions: Nanotechnology Molecular Electronics - molecular wires, switches, and circuits - simulation Carbon-based New Materials - Fullerenes, Carbon Nanotubes, and other structures - Applications Clusters (other than carbon) - silicon, metal, and other clusters - applications Advanced Silicon Technology - Si/SiO2 interface - surface chemistry Atomic-level Measurement and Manipulation - STM, AFM, and X-Rays Micro-Electronic Machines Nano-Sensors and Instruments Biomaterials - Protein Engineering - DNA as an Element of Molecular Engineering - Mechanisms Next-Generation Computing Systems - Quantum and DNA Computing II. Standard Sessions: Intelligent Processing and Manufacturing Simulation Modeling - new materials and property prediction - materials processing and product manufacturing - supervisory and process control Agent-based Modeling - holonic systems and intelligent manufacturing - Swarm Intelligence and Artificial Life - optimization versus incremental improvements - local vs. global decision-making Software and "Soft" wear - Fuzzy Logic, Neural Networks, Evolutionary Programming, and Chaos Theory - Intelligent User Interfaces Robotics and Machines - mini- and micro-machines - telerobotic applications - remote communication systems (outer space and underground applications) Processes for the 21st Century - raw materials production systems (mining and processing) - metals production and forming - finishing and final-shape processes The Philosophy of Intelligence in New Materials and Processes - Nature of intelligence - Transhumanism and the Machine Age --- If you have any question regarding the IPMM'03 conference, please feel free to contact me. We much look forward to hearing from you soon. Best Regards, Hiroshi Mizuseki (ipmm@imr.edu) (on behalf of the local organizing committee) http://www-lab.imr.tohoku.ac.jp/~mizuseki/nanowire.html PS. If you have already submitted an abstract please disregard this message From chemistry-request@server.ccl.net Mon Jan 6 11:01:18 2003 Received: from sandmail01.sd.accelrys.com ([209.120.169.30]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h06G1I002465 for ; Mon, 6 Jan 2003 11:01:18 -0500 To: chminf-l@listserv.indiana.edu, chemistry@server.ccl.net, qsar_society@accelrys.com Subject: Call for Posters at Accelrys World MIME-Version: 1.0 X-Mailer: Lotus Notes Release 5.0.9a January 7, 2002 Message-ID: From: osman@accelrys.com Date: Mon, 6 Jan 2003 08:01:16 -0800 X-MIMETrack: Serialize by Router on sandmail01/Server/Accelrys(Release 5.0.9 |November 16, 2001) at 01/06/2003 08:01:18 AM, Serialize complete at 01/06/2003 08:01:18 AM Content-Type: multipart/alternative; boundary="=_alternative 0057D5DE88256CA6_=" This is a multipart message in MIME format. --=_alternative 0057D5DE88256CA6_= Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable CALL FOR POSTERS --- Accelrys World 2003 Scientific software and IT event, located at Hotel del Coronado, San=20 Diego, California during February 24-26, 2003=20 (http://www.accelrys.com/accelrysworld/). The details of the agenda is at = http://www.accelrys.com/accelrysworld/agenda.html . The conference is now = open for poster submissions.=20 Please use the following form to submit posters (with 150 word abstracts): = http://www.accelrys.com/accelrysworld/poster=5Fsubmission.php .=20 The deadline for submitting posters is January 24th.=20 Cheers...osman Osman F. G=FCner, Ph.D. Executive Director Cheminformatics and Rational Drug Design Accelrys Inc., 858-799-5341 osman@accelrys.com, http://www.accelrys.com --=_alternative 0057D5DE88256CA6_= Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable
CALL FOR POSTERS ---  Accelrys = World 2003

Scientific software and IT event, lo= cated at Hotel del Coronado, San Diego, California during February 24-26, 2= 003 (http://www.accelrys.com/accelrysworld/).  The details of the agen= da is at http://www.accelrys.com/accelrysworld/agenda.html .  The conf= erence is now open for poster submissions.  

Please use the following form to sub= mit posters (with 150 word abstracts): http://www.accelrys.com/accelrysworl= d/poster=5Fsubmission.php .  

The deadline for submitting posters = is January 24th.  

Cheers...osman

Osman F. G=FCner, Ph.D.
Executive Director
Cheminformatics and Rational Drug Design
Accelrys Inc.,  858-799-5341
osman@accelrys.com, http://www.accelrys.com --=_alternative 0057D5DE88256CA6_=-- From chemistry-request@server.ccl.net Mon Jan 6 12:57:18 2003 Received: from facepe.dqf.ufpe.br ([150.161.5.2]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h06HvDD05949 for ; Mon, 6 Jan 2003 12:57:17 -0500 Received: from dqf.ufpe.br ([150.161.5.23]) by facepe.dqf.ufpe.br (8.12.6/8.12.6) with ESMTP id h06FZQm7000130 for ; Mon, 6 Jan 2003 13:35:27 -0200 (BRST) (envelope-from mozart.pimentel@dqf.ufpe.br) Message-ID: <3E19B63C.9030108@dqf.ufpe.br> Date: Mon, 06 Jan 2003 15:00:44 -0200 From: Mozart Pimentel User-Agent: Mozilla/5.0 (X11; U; Linux i686; en-US; rv:1.0.1) Gecko/20020830 X-Accept-Language: en-us, en MIME-Version: 1.0 To: chemistry@ccl.net Subject: Problem with NBO 5.0 on nwchem 4.1 Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 8bit I'm trying to run a NBO job in nwchem 4.1, the molecule in question has 100 atoms, wich was over the limit of atoms suppoted by oldier versions of NBO, but the NBO 5.0 is meant to support, by default, 200 atoms and 2000 basis functions. As i'm using STO-3G as basis, i thought the job would run easily, but it always ends up with the message: Error in SR CONVRT ------------------------------------------------------------------------ nbo: Call to NBHALT 0 ------------------------------------------------------------------------ ------------------------------------------------------------------------ current input line : 113: task nbo ------------------------------------------------------------------------ 0:0:nbo: Call to NBHALT:: 0 0: ARMCI aborting 0 (0). the keywords of NBO task were $NBO FNHO $END so, all analysis were performed, but no NHO matrix was printed out, only the above message. Another thing, i've ran a job with less atoms, and it worked fine. Does anyone know what's happening here? Thanks a lot, Mozart. Mozart Pimentel Departamento de Química Fundamental Universidade Federal de Pernambuco - Brazil. mozart.pimentel@dqf.ufpe.br From chemistry-request@server.ccl.net Mon Jan 6 13:02:05 2003 Received: from web12001.mail.yahoo.com ([216.136.172.207]) by server.ccl.net (8.11.6/8.11.0) with SMTP id h06I25D06093 for ; Mon, 6 Jan 2003 13:02:05 -0500 Message-ID: <20030106180204.65412.qmail@web12001.mail.yahoo.com> Received: from [152.3.169.5] by web12001.mail.yahoo.com via HTTP; Mon, 06 Jan 2003 10:02:04 PST Date: Mon, 6 Jan 2003 10:02:04 -0800 (PST) From: Jianping Lin Subject: HOW to output specific part in Gaussian 98 To: chemistry@ccl.net MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Hi all, I am trying to using Gaussian 98 to get the atomic charges for my system. Because the system is a little bit large, I just want to output the atomic charges part and don't need the interatomic angles part. How can I do this? Thanks very much Jianping lin Department of Chemistry Duke University __________________________________________________ Do you Yahoo!? Yahoo! Mail Plus - Powerful. Affordable. Sign up now. http://mailplus.yahoo.com From chemistry-request@server.ccl.net Mon Jan 6 14:24:06 2003 Received: from antivirus2.its.rochester.edu ([128.151.57.53]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h06JO5D08558 for ; Mon, 6 Jan 2003 14:24:05 -0500 Received: from antivirus2.its.rochester.edu (localhost [127.0.0.1]) by antivirus2.its.rochester.edu (8.12.4/8.12.4) with ESMTP id h06JO58a026720 for ; Mon, 6 Jan 2003 14:24:05 -0500 (EST) Received: from mail.rochester.edu (mail1.ats.rochester.edu [128.151.224.31]) by antivirus2.its.rochester.edu (8.12.4/8.12.4) with SMTP id h06JO5Dj026717 for ; Mon, 6 Jan 2003 14:24:05 -0500 (EST) Received: from frenkel.chem.rochester.edu (frenkel.chem.rochester.edu [128.151.195.84]) by mail.rochester.edu (8.12.4/8.12.1) with ESMTP id h06JNvDa022908 for ; Mon, 6 Jan 2003 14:23:57 -0500 (EST) Content-Type: text/plain; charset="us-ascii" From: wei Reply-To: weiz@mail.rochester.edu Organization: university of rochester To: chemistry@ccl.net Subject: question about parallel running of charmm Date: Mon, 6 Jan 2003 14:20:38 -0500 User-Agent: KMail/1.4.1 MIME-Version: 1.0 Message-Id: <200301061420.38890.weiz@mail.rochester.edu> Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id h06JO6D08559 Hi, all: I want to do a parallel running of charmm on a beowulf cluster with 16 nodes. the queing system is openpbs, I attached the job file, machine file and charmm input file at the end. after I type "qsub job", the job seems to be running well, while I type "pbsnodes -a | less", it gave out following output: ********************************** node008 state = free np = 2 properties = p8 ntype = cluster jobs = 0/5501.pauli node009 state = free np = 2 properties = p8 ntype = cluster jobs = 0/5501.pauli node010 state = free np = 2 properties = p8 ntype = cluster jobs = 0/5501.pauli node011 state = free np = 2 properties = p8 ntype = cluster jobs = 0/5501.pauli node012 state = free np = 2 properties = p8 ntype = cluster jobs = 0/5501.pauli node013 state = free np = 2 properties = p8 ntype = cluster jobs = 0/5501.pauli node014 state = free np = 2 properties = p8 ntype = cluster jobs = 0/5501.pauli node015 state = free np = 2 properties = p8 ntype = cluster jobs = 0/5501.pauli *********************************************** however,when I go to every single machine to check the status, I found that this work is only running on node015. Can anybody give me some hint for what is going on here, is this the right way to run charmm parallelly? regards wei zhuang attachment: 1)job file: (gpcharmm is a parallel version executable of charmm ) ************************************ #PBS -l ncpus=8 #PBS -N BCL #PBS -q feed #PBS -l nodes=8:p8 #PBS -l cput=100:00:00,mem=512mb # cd $PBS_O_WORKDIR cp $PBS_NODEFILE tmpfile /usr/local/bin/creator tmpfile macfile /usr/local/bin/gpcharmm rm tmpfile /usr/local/bin/gpcharmm -p4pg macfile < xxxx.inp >xxxx.out ************************************************ 2)machine file: ******************************************* node015 0 node014 1 /usr/local/bin/gpcharmm node013 1 /usr/local/bin/gpcharmm node012 1 /usr/local/bin/gpcharmm node011 1 /usr/local/bin/gpcharmm node010 1 /usr/local/bin/gpcharmm node009 1 /usr/local/bin/gpcharmm node008 1 /usr/local/bin/gpcharmm *******************************************8 3)input file: ******************************************* * This is the input file for the modelling and simulation of * ANTAMANIDE in chloroform * !==================================================== ! define data directory and output directory !===================================================== set 0 /home/shiva/data !input data directory set 9 /home/shiva/scratch ! scratch directory set cutoff 10.0 bomblev -2 open read form unit 43 name @0xxx.rtf read rtf card unit 43 close unit 43 open read form unit 2 name @0xxx.prm read parameter card unit 2 close unit 2 !======================================================= !Generate PSF !======================================================== ...................................... !======================================== ! Write out formatted PSF !======================================== OPEN UNIT 33 CARD WRITE NAME /home/shiva/xxx.psf WRITE PSF CARD UNIT 33 CLOSE UNIT 33 !===================================== ! Read the coordinate file !==================================== OPEN UNIT 37 CARD READ NAME /home/shiva/crd/xxx.pdb READ COOR pdb UNIT 37 CLOSE UNIT 37 COOR PRINT !MINIMIZE THE STRUCTURE NBONDS CUTNb 12.0 CTOFnb 10.0 CTONnb 8.0 ! impose periodic boundary conditions: set L 30 crystal define cubic @L @L @L 90.0 90.0 90.0 crystal build noper 0 cutoff 14.0 image byres XCEN 0.0 YCEN 0.0 ZCEN 0.0 select segid SOLV end update inbfrq 10 imgfrq 10 mini abnr nstep 100000 nprint 200 open write card unit 11 name @0xxx.pdb write coor pdb card unit 11 close unit 11 OPEN UNIT 38 CARD WRITE NAME @0.crd WRITE COOR CARD UNIT 38 CLOSE UNIT 38 stop *********************************************************8888 From chemistry-request@server.ccl.net Mon Jan 6 16:05:14 2003 Received: from mail2.uklinux.net ([80.84.72.32]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h06L5ED11348 for ; Mon, 6 Jan 2003 16:05:14 -0500 Received: from [10.0.0.5] (host217-43-58-42.range217-43.btcentralplus.com [217.43.58.42]) by mail2.uklinux.net (Postfix) with ESMTP id A601F409FBC; Mon, 6 Jan 2003 21:05:12 +0000 (UTC) Date: Mon, 6 Jan 2003 21:02:11 +0000 (GMT) From: X-X-Sender: To: Damian A Scherlis Perel Cc: Subject: Re: CCL:G98 in parallel in a dual Xeon In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII On Sun, 5 Jan 2003, Damian A Scherlis Perel wrote: > shmget failed.: Invalid argument Hint: SystemV IPC missing from kernel (providing you are using Linux). Try the "ipcs" command. If it fails, that can be the problem. Szilva From chemistry-request@server.ccl.net Mon Jan 6 18:30:07 2003 Received: from wilson.acpub.duke.edu ([152.3.233.69]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h06NU7D15646 for ; Mon, 6 Jan 2003 18:30:07 -0500 Received: from CONCORDIA (concordia.lib.duke.edu [152.16.191.233]) by wilson.acpub.duke.edu (8.12.4/8.12.4/Duke-5.0.0) with SMTP id h06NU69M021227; Mon, 6 Jan 2003 18:30:06 -0500 (EST) X-Originating-IP: 152.3.169.5 X-Mailer: MyDuke.com X-Originator-Info: jz7@acpub From: To: Subject: UHBD output file Date: Mon, 6 Jan 2003 18:24:57 -0500 Message-ID: <018301c2b5da$d3865790$eabf1098@CONCORDIA> MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit Thread-Index: AcK12tODx9Hg69SGQ7CelJ7QkI1cPA== Content-Class: urn:content-classes:message X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2800.1106 Dear All, What is the command for UHBD to generate a ".phi" file (including the electrostatics potentials). I need this file in gOpenMol to plot the 3- D isopotential contour. Or do you know what kind of potential file UHBD can generate that gOpenMol can read. Thanks a lot! From chemistry-request@server.ccl.net Mon Jan 6 21:34:02 2003 Received: from api_lab_bdc.achillion.com ([64.51.60.221]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h072Y2D20246 for ; Mon, 6 Jan 2003 21:34:02 -0500 Received: by api_lab_bdc.achillion.com with Internet Mail Service (5.5.2653.19) id ; Mon, 6 Jan 2003 21:32:16 -0500 Message-ID: From: Ken Torikoshi To: "'chemistry@ccl.net'" Subject: Alternative DBs for WDI and MDDR? Date: Mon, 6 Jan 2003 21:31:18 -0500 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2653.19) Content-Type: text/plain; charset="iso-8859-1" Hi All, We are looking for any (free if possible) alternative databases for WDI and MDDR for our computational analysis. Does anyone have any information. Please let us know. We will summarize the results. Thank you. -- Ken From chemistry-request@server.ccl.net Mon Jan 6 18:59:04 2003 Received: from relay.pnl.gov ([130.20.128.34]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h06Nx4D16401 for ; Mon, 6 Jan 2003 18:59:04 -0500 Received: from vscan2.pnl.gov ([130.20.64.141]) by pnl.gov (PMDF V5.2-33 #42505) with SMTP id <01KQX58BC8BY8WWN9A@pnl.gov> for chemistry@ccl.net; Mon, 6 Jan 2003 15:59:00 PST Received: from 130.20.251.27 by vscan2.pnl.gov (InterScan E-Mail VirusWall NT) ; Mon, 06 Jan 2003 15:59:00 -0800 Received: by pnlmse02.pnl.gov with Internet Mail Service (5.5.2653.19) id ; Mon, 06 Jan 2003 15:59:00 -0800 Date: Mon, 06 Jan 2003 15:58:55 -0800 From: "Windus, Theresa L" Subject: RE: Problem with NBO 5.0 on nwchem 4.1 To: "'Mozart Pimentel'" , chemistry@ccl.net Message-id: 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 h06Nx4D16402 Hi Mozart, It is difficult to give you an answer without more information. If you could send your input and output files to nwchem-support@emsl.pnl.gov, we can take a look at it. Regards, Theresa Windus -----Original Message----- From: Mozart Pimentel [mailto:mozart.pimentel@dqf.ufpe.br] Sent: Monday, January 06, 2003 9:01 AM To: chemistry@ccl.net Subject: CCL:Problem with NBO 5.0 on nwchem 4.1 I'm trying to run a NBO job in nwchem 4.1, the molecule in question has 100 atoms, wich was over the limit of atoms suppoted by oldier versions of NBO, but the NBO 5.0 is meant to support, by default, 200 atoms and 2000 basis functions. As i'm using STO-3G as basis, i thought the job would run easily, but it always ends up with the message: Error in SR CONVRT ------------------------------------------------------------------------ nbo: Call to NBHALT 0 ------------------------------------------------------------------------ ------------------------------------------------------------------------ current input line : 113: task nbo ------------------------------------------------------------------------ 0:0:nbo: Call to NBHALT:: 0 0: ARMCI aborting 0 (0). the keywords of NBO task were $NBO FNHO $END so, all analysis were performed, but no NHO matrix was printed out, only the above message. Another thing, i've ran a job with less atoms, and it worked fine. Does anyone know what's happening here? Thanks a lot, Mozart. Mozart Pimentel Departamento de Química Fundamental Universidade Federal de Pernambuco - Brazil. mozart.pimentel@dqf.ufpe.br -= 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 From chemistry-request@server.ccl.net Mon Jan 6 16:38:12 2003 Received: from ameiurus.usu.edu ([129.123.1.197]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h06LcBD12470 for ; Mon, 6 Jan 2003 16:38:12 -0500 Received: from pc3 (pc3.chem.usu.edu [129.123.3.37]) by ameiurus.usu.edu (8.11.6/8.11.6) with SMTP id h06LVNo03551; Mon, 6 Jan 2003 14:31:23 -0700 Reply-To: From: "Tapas Kar" To: "Jianping Lin" , Subject: RE: HOW to output specific part in Gaussian 98 Date: Mon, 6 Jan 2003 14:28:41 -0700 Message-ID: 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 IMO, Build 9.0.2416 (9.0.2911.0) X-MIMEOLE: Produced By Microsoft MimeOLE V6.00.2800.1106 Importance: Normal In-Reply-To: <20030106180204.65412.qmail@web12001.mail.yahoo.com> X-MailScanner: Found to be clean Use Geom=noangle in Route card. *********************************************** "We owe a lot to the Indians, who taught us how to count, without which no worthwhile scientific discovery could have been made." - Albert Einstein - ---------------------------------------------------------------------------- ---- Tapas Kar, Ph. D Department of Chemistry & Biochemistry Utah State University Logan, UT 84322-0300 Tel: 435-797-7230 Fax: 435-797-3390 Email: tapaskar@cc.usu.edu Web: http://www.chem.usu.edu/faculty/Tapas/index.html -----Original Message----- From: Computational Chemistry List [mailto:chemistry-request@ccl.net]On Behalf Of Jianping Lin Sent: Monday, January 06, 2003 11:02 AM To: chemistry@ccl.net Subject: CCL:HOW to output specific part in Gaussian 98 Hi all, I am trying to using Gaussian 98 to get the atomic charges for my system. Because the system is a little bit large, I just want to output the atomic charges part and don't need the interatomic angles part. How can I do this? Thanks very much Jianping lin Department of Chemistry Duke University __________________________________________________ Do you Yahoo!? Yahoo! Mail Plus - Powerful. Affordable. Sign up now. http://mailplus.yahoo.com -= 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 From chemistry-request@server.ccl.net Mon Jan 6 21:40:32 2003 Received: from api_lab_bdc.achillion.com ([64.51.60.221]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h072eWD20422 for ; Mon, 6 Jan 2003 21:40:32 -0500 Received: by api_lab_bdc.achillion.com with Internet Mail Service (5.5.2653.19) id ; Mon, 6 Jan 2003 21:38:46 -0500 Message-ID: From: Ken Torikoshi To: "'chemistry@ccl.net'" Subject: Compound catalog in the sdf format Date: Mon, 6 Jan 2003 21:38:18 -0500 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2653.19) Content-Type: text/plain; charset="iso-8859-1" Hi All. We are categorizing various format of vender catalogs for computational research. Currently we are focusing SD-format, and if you have any information, please let us know. We will summarize the results. Thank you. -- Ken ktorikoshi@achillion.com