From chemistry-request@server.ccl.net Fri May 11 06:27:00 2001 Received: from mailrelay1.lrz-muenchen.de ([129.187.254.101]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f4BAQxI32342 for ; Fri, 11 May 2001 06:26:59 -0400 Received: from sun1.lrz-muenchen.de by mailrelay1.lrz-muenchen.de with ESMTP for chemistry@ccl.net; Fri, 11 May 2001 12:26:58 +0200 Received: from localhost (ui22204@localhost) by sun1.lrz-muenchen.de (8.8.8+Sun/8.8.8) with ESMTP id MAA21750 for ; Fri, 11 May 2001 12:26:56 +0200 (MET DST) X-Authentication-Warning: sun1.lrz-muenchen.de: ui22204 owned process doing -bs Date: Fri, 11 May 2001 12:26:56 +0200 (MET DST) From: Eugene Leitl X-X-Sender: To: Subject: Re: CCL:FYI: Current SPECfp landscape... (fwd) Message-Id: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII ---------- Forwarded message ---------- Date: Fri, 11 May 2001 06:22:40 -0400 From: Bob Drzyzgula To: Eugene Leitl Cc: Beowulf@beowulf.org Subject: Re: CCL:FYI: Current SPECfp landscape... (fwd) Eugene, Thanks. This well confirms the price in my table; A 256MB RDRAM RIMM costs around $200. To add three more of these to the $800 256MB configuration at JNCS (all the pricing was based on 1GB configurations) would raise the total price to $1,400, which is what I had used for a 1.7GHz P4 system. --Bob On Fri, May 11, 2001 at 10:39:47AM +0200, Eugene Leitl wrote: > ---------- Forwarded message ---------- > Date: Thu, 10 May 2001 15:35:38 +0100 > From: jmmckel@attglobal.net > To: Eugene Leitl > Cc: chemistry@ccl.net > Subject: Re: CCL:FYI: Current SPECfp landscape... (fwd) > > FYI: > > An Intel/P4/1.7GHZ with 256 MByte Rambus memory, high quality fan, tested is $799 [case and P4 power supply add > $99] can be had from a quality source, WWW.JNCS.COM. I've been using them for years. > > John McKelvey > > Eugene Leitl wrote: > > > ---------- Forwarded message ---------- > > Date: Thu, 10 May 2001 10:04:01 -0400 > > From: Bob Drzyzgula > > To: beowulf@beowulf.org > > Subject: Re: FYI: Current SPECfp landscape... > > > > Wes Bauske was kind enough to point out that > > I could do the Pentium 4 system a bit more > > cheaply. I'd missed the fact that Pentium 4 > > boards are available with 4 RIMM slots, so one > > can use 256MB RIMMs, which are available at about > > half the price per MB over the 512MB modules. > > Thus, it should be possible to do a 1.5GHz Pentium > > 4 system for a core (CPU+MB+Memory) cost of around > > $1300 or so. A 1.7GHz system would cost around > > $100 more than that. Updated tables below. Also, > > I added SPECfp2000/K$. Fascinating how the Pentium 4 > > comes out second in each one of these tables... > > > > Thanks, Wes. > > > > --Bob > > > > Sorted in declining order of SPECfp2000: > > > > Sfp/ > > Processor MHz L2 Si Sfp core $ K$ Notes > > ------------------------- ---- ----- --- --- ------ --- ---------- > > Alpha (21264) 833 8192 533 644 9,000 72 (UP2000+, est) > > Pentium 4 1700 256 586 608 1,400 434 (D850GB, RDRAM) > > PA-8700 750 N/A 603 581 14,000 42 (HP J6700, 2304KB L1) > > AMD Athlon (Thunderbird) 1330 256 539 445 2,000 223 (GA7DX, DDR SDRAM) > > UltraSPARC III 750 8192 395 421 8,500 50 (Ocelot) > > AMD Athlon (Thunderbird) 1300 256 491 374 520 719 (A7V, PC133 SDRAM) > > Pentium III (Coppermine) 1000 256 428 314 1,900 165 (VC820, RDRAM) > > UltraSPARC II 480 8192 234 291 10,000 29 (AXdp) > > > > Sorted in declining order of SPECint2000: > > > > Sfp/ > > Processor MHz L2 Si Sfp core $ K$ Notes > > ------------------------- ---- ----- --- --- ------ --- ---------- > > PA-8700 750 N/A 603 581 14,000 42 (HP J6700, 2304KB L1) > > Pentium 4 1700 256 586 608 1,400 434 (D850GB, RDRAM) > > AMD Athlon (Thunderbird) 1330 256 539 445 2,000 223 (GA7DX, DDR SDRAM) > > Alpha (21264) 833 8192 533 644 9,000 72 (UP2000+, est) > > AMD Athlon (Thunderbird) 1300 256 491 374 520 719 (A7V, PC133 SDRAM) > > Pentium III (Coppermine) 1000 256 428 314 1,900 165 (VC820, RDRAM) > > UltraSPARC III 750 8192 395 421 8,500 50 (Ocelot) > > UltraSPARC II 480 8192 234 291 10,000 29 (AXdp) > > > > Sorted in order of increasing cost: > > > > Sfp/ > > Processor MHz L2 Si Sfp core $ K$ Notes > > ------------------------- ---- ----- --- --- ------ --- ---------- > > AMD Athlon (Thunderbird) 1300 256 491 374 520 719 (A7V, PC133 SDRAM) > > Pentium 4 1700 256 586 608 1,400 434 (D850GB, RDRAM) > > Pentium III (Coppermine) 1000 256 428 314 1,900 165 (VC820, RDRAM) > > AMD Athlon (Thunderbird) 1330 256 539 445 2,000 223 (GA7DX, DDR SDRAM) > > UltraSPARC III 750 8192 395 421 8,500 50 (Ocelot) > > Alpha (21264) 833 8192 533 644 9,000 72 (UP2000+, est) > > UltraSPARC II 480 8192 234 291 10,000 29 (AXdp) > > PA-8700 750 N/A 603 581 14,000 42 (HP J6700, 2304KB L1) > > > > Sorted in declining order of SPECfp2000/K$ > > Sfp/ > > Processor MHz L2 Si Sfp core $ K$ Notes > > ------------------------- ---- ----- --- --- ------ --- ---------- > > AMD Athlon (Thunderbird) 1300 256 491 374 520 719 (A7V, PC133 SDRAM) > > Pentium 4 1700 256 586 608 1,400 434 (D850GB, RDRAM) > > AMD Athlon (Thunderbird) 1330 256 539 445 2,000 223 (GA7DX, DDR SDRAM) > > Pentium III (Coppermine) 1000 256 428 314 1,900 165 (VC820, RDRAM) > > Alpha (21264) 833 8192 533 644 9,000 72 (UP2000+, est) > > UltraSPARC III 750 8192 395 421 8,500 50 (Ocelot) > > PA-8700 750 N/A 603 581 14,000 42 (HP J6700, 2304KB L1) > > UltraSPARC II 480 8192 234 291 10,000 29 (AXdp) > > > > _______________________________________________ > > Beowulf mailing list, Beowulf@beowulf.org > > To change your subscription (digest mode or unsubscribe) visit http://www.beowulf.org/mailman/listinfo/beowulf > > > > -= 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 > > > > _______________________________________________ > Beowulf mailing list, Beowulf@beowulf.org > To change your subscription (digest mode or unsubscribe) visit http://www.beowulf.org/mailman/listinfo/beowulf _______________________________________________ Beowulf mailing list, Beowulf@beowulf.org To change your subscription (digest mode or unsubscribe) visit http://www.beowulf.org/mailman/listinfo/beowulf From chemistry-request@server.ccl.net Fri May 11 10:20:20 2001 Received: from fluorid.ethz.ch ([129.132.126.40]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f4BEKJI03617 for ; Fri, 11 May 2001 10:20:19 -0400 Received: from igc.phys.chem.ethz.ch (fluorid [129.132.126.40]) by fluorid.ethz.ch (8.8.8/8.8.8) with ESMTP id QAA23510 for ; Fri, 11 May 2001 16:17:40 +0200 (CEST) Sender: portmann@igc.phys.chem.ethz.ch Message-ID: <3AFBF483.B6621CCA@igc.phys.chem.ethz.ch> Date: Fri, 11 May 2001 16:17:39 +0200 From: Stefan Portmann X-Mailer: Mozilla 4.61 [en] (X11; I; IRIX 6.3 IP32) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net Subject: Abstract Management System Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear Colleagues I'm a co-organizer of WATOC'02 (The World Association of Theoretically Oriented Chemists; http://www.watoc02.ch) taking place in Lugano Switzerland in August 2002. I'm currently evaluating an electronic abstract submitting and management system for the congress. Can you tell me, what you are using for your conference? I'm interested in both, commercial and self made solutions. Thanks for your input Stefan -- Dr. Stefan Portmann Laboratory of Physical Chemistry ETH-Zurich Universitaetsstr. 65 CH-8092 Zurich Switzerland Phone: +41 (0) 1 632 57 82 Fax: +41 (0) 1 632 16 15 e-mail: portmann@igc.phys.chem.ethz.ch WWW: http://igc.ethz.ch/portmann/ From chemistry-request@server.ccl.net Fri May 11 10:58:27 2001 Received: from unomail.unomaha.edu ([137.48.1.6]) by server.ccl.net (8.11.0/8.11.0) with SMTP id f4BEwRI03930 for ; Fri, 11 May 2001 10:58:27 -0400 Received: by unomail.unomaha.edu(Lotus SMTP MTA v4.6.4 (830.2 3-23-1999)) id 86256A49.00521E4E ; Fri, 11 May 2001 09:56:57 -0500 X-Lotus-FromDomain: UNIVERSITY OF NEBRASKA From: Guangping_Li/CAS/UNO/UNEBR@unomail.unomaha.edu To: chemistry@ccl.net Message-ID: <86256A49.00521C91.00@unomail.unomaha.edu> Date: Fri, 11 May 2001 09:56:51 -0500 Subject: normal inquiry Mime-Version: 1.0 Content-type: text/plain; charset=us-ascii Content-Disposition: inline Dear friends: Does anyone know of any software which can be used to extract the amino sequence of a peptide from a PDB (protein data bank) file? I'm looking for several experimental peptide PDB files for demonstration too, and these peptides better have 10-20 amino residues. Thanks for your help. Jim From chemistry-request@server.ccl.net Fri May 11 10:11:01 2001 Received: from popserver.healthtech.com ([140.239.39.130]) by server.ccl.net (8.11.0/8.11.0) with SMTP id f4BEB0I03541 for ; Fri, 11 May 2001 10:11:00 -0400 Received: by popserver.healthtech.com from localhost (router,SLMail V4.3); Fri, 11 May 2001 10:09:13 -0400 for Received: from wendy-h [140.239.39.184] by popserver.healthtech.com [140.239.39.130] (SLmail 4.3.0.3454) with SMTP id 1625B61A5F48417989D6DDAFC2C5FACF for ; Fri, 11 May 2001 10:09:09 -0400 Message-Id: <4.1.20010511100111.0099a570@140.239.39.130> X-Sender: whori@140.239.39.130 X-Mailer: QUALCOMM Windows Eudora Pro Version 4.1 Date: Fri, 11 May 2001 10:04:35 -0400 To: chemistry@ccl.net From: "Wendy Hori" Subject: HPC for Genomics & Proteomics 1st Call Mime-Version: 1.0 Content-Type: multipart/alternative; boundary="=====================_2650609==_.ALT" X-SLUIDL: 908E221B-9771489F-90E9AB94-23AE782C --=====================_2650609==_.ALT Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable FIRST ANNOUNCEMENT AND CALL FOR PAPERS Cambridge Healthtech Institute=92s=20 High Performance Computing Strategic Applications for Genomics & Proteomics September 20-21, 2001 Wyndham San Diego at Emerald Plaza Hotel San Diego, California The success of the drug discovery process is now directly related to a company=92s computation capabilities. Results and research projects that= were unimaginable a few years ago are accessible with today=92s super computers. Industry sources expects the IT life science market to explode to more than= $9 billion by 2003. Major IT companies have made significant investments and formed partnerships, with IBM and Compaq each committing $100 million. Data overload from automation and robust database technology, means that= companies have an immense amount of data on both drug targets and lead compounds. The downside is that these companies are not equipped in infrastructure or organization to efficiently take full advantage of this gold mine. There is also the question of staff: Do we have the right people? How do we use our existing in-house bioinformatics team? Should we outsource or build our= own? What=92s a fair contract for services, profit-sharing and leasing? How many teraflops is enough? This meeting will seek to cover these issues for= biotech, pharma , software and hardware engineers, application specialists and= anyone who envisions the marriage of supercomputers and the life sciences.=20 Other Topics to be Covered:=20 Compute Farms Distributed Computing Clustering Beowulf Architecture Parallel Processing Integrating Applications specific to Life Sciences Data-compilation Automation Achieving Better Performance with Database Work through Shared Memory= Systems Affordable Supercomputing: Supercomputers vs desktop compute farms Novel Integrated Supercomputing Solutions to Help Scientists concentrate on domain tasks, not on Computer Science. Case Studies Interoperability of Databases If you would like to submit a proposal to give a presentation or display a poster at this meeting please send us, by fax or email, a title and brief= 3-5 sentence summary of a proposed topic on your recent work in the area of High Performance Computing . The deadline for submission is May 11, 2001. All proposals are subject to review by the Scientific Advisory Committee to= ensure the overall quality of the conference program. For more information, please contact Wendy Hori at: Cambridge Healthtech Institute, 1037 Chestnut Street, Newton Upper Falls, MA 02464 Tel: 617 630-1382 =95 Fax: 617 630-1325 =95 Email: whori@healthtech.com For sponsorship and exhibit information, please contact Jim MacNeil. Tel: 617-630-1341, Email: jmacneil@healthtech.com To register on-line, please visit our web site: www.healthtech.com Wendy Hori =20 Conference Director =20 Cambridge Healthtech Institute =20 1037 Chestnut St. =20 Newton Upper Falls, MA 02464 Phone: 617-630-1382 Fax: 617-630-1325 Email: whori@healthtech.com Check out our websites! www.healthtech.com www.beyondgenome.com www.httexpo.com =20 =20 =20 =20 =20 =20 --=====================_2650609==_.ALT Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable FIRST ANNOUNCEMENT AND CALL FOR PAPERS
Cambridge Healthtech Institute=92s
High Performance Computing
Strategic Applications for Genomics & Proteomics
September 20-21, 2001
Wyndham San Diego at Emerald Plaza Hotel  San Diego,=20 California

The success of the drug discovery process is now directly related to a company=92s computation capabilities. Results and research projects that were unimaginable a few years ago are accessible with today=92s super computers. Industry sources expects the IT life science market to explode to more than $9 billion by 2003. Major IT companies have made significant investments and formed partnerships, with IBM and Compaq each committing $100 million. Data overload from automation and robust database technology, means that companies have an immense amount of data on both drug targets and lead compounds.  The downside is that these companies are not equipped in infrastructure or organization to efficiently take full advantage of this gold mine.  There is also the question of staff: Do we have the right people?  How do we use our existing in-house bioinformatics team?  Should we outsource or build our own? What=92s a fair contract for services, profit-sharing and leasing? How many teraflops is enough? This meeting will seek to cover these issues for biotech, pharma , software  and hardware engineers, application specialists and anyone who envisions the marriage of supercomputers and the life sciences.

Other Topics to be Covered:=20
Compute Farms
Distributed Computing
Clustering
Beowulf Architecture
Parallel Processing
Integrating Applications specific to Life Sciences
Data-compilation Automation
Achieving Better Performance with Database Work through Shared Memory Systems
Affordable Supercomputing: Supercomputers vs desktop compute farms
Novel Integrated Supercomputing Solutions to Help Scientists concentrate on domain tasks, not on Computer Science.
Case Studies
Interoperability of Databases

If you would like to submit = a proposal to give a presentation or display a poster at this meeting please send us, by fax or email, a title and brief 3-5 sentence summary of a proposed topic on your recent work in the area of High Performance Computing . The deadline for submission is May 11, 2001. All proposals are subject to review by the Scientific Advisory Committee to ensure the overall quality of the conference program.

For more information, please contact Wendy Hori at:
Cambridge Healthtech Institute, 1037 Chestnut Street, Newton Upper Falls, MA 02464
Tel: 617 630-1382 =95 Fax: 617 630-1325 =95 Email: whori@healthtech.com
For sponsorship and exhibit information, please contact Jim MacNeil. Tel: 617-630-1341, Email: jmacneil@healthtech.com

To register on-line, please visit our web site: www.healthtech.com

Wendy Hori        &n= bsp;         &nb= sp;         &nbs= p;         
Conference Director       &nbs= p;          = ;   
Cambridge Healthtech Institute       &nb= sp;  
1037 Chestnut St.        &nb= sp;         &nbs= p;    
Newton Upper Falls, MA 02464
Phone: 617-630-1382
Fax: 617-630-1325
Email: whori@healthtech.com
Check out our websites!
www.healthtech.com
www.beyondgenome.com
www.httexpo.com


                


         =        
         =           &= nbsp;         &n= bsp;         &nb= sp;                  =           &= nbsp;         &n= bsp;         &nb= sp;
         =           &= nbsp;         &n= bsp;         &nb= sp;
         =           &= nbsp;         &n= bsp;         &nb= sp;
--=====================_2650609==_.ALT-- From chemistry-request@server.ccl.net Fri May 11 11:43:59 2001 Received: from interlock.herc.com ([199.221.7.2]) by server.ccl.net (8.11.0/8.11.0) with SMTP id f4BFhxI04436 for ; Fri, 11 May 2001 11:43:59 -0400 Received: from csdnsg1.herc.com ([147.116.14.51]) by interlock.herc.com with SMTP id LAA24554 (InterLock SMTP Gateway for ); Fri, 11 May 2001 11:43:58 -0400 Subject: crystal viewing software To: chemistry@ccl.net Cc: X-Mailer: Lotus Notes Release 5.0.2b December 16, 1999 Message-Id: From: Goutam.Das@betzdearborn.com Date: Fri, 11 May 2001 10:42:06 -0500 X-Priority: 3 (Normal) X-Mimetrack: Serialize by Router on CSDNSG1/Servers/Herc(Release 5.0.1b|September 30, 1999) at 05/11/2001 11:28:38 AM Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Dear CCLer's: Is there any program (freeware) to visualize pdb files containing crystallographic information? I mean the program should create several unit cells from the pdb files. I am aware of the msi software, but are there any others out there. Thanking everyone in anticipation. Goutam Das BetzDearborn Division of Hercules 9669 Grogan's Mill Road The Woodlands, TX 77380 281.367.6201 ext 425 // Fax: 281.363.7780 From chemistry-request@server.ccl.net Fri May 11 13:04:42 2001 Received: from outbound.mail.uoguelph.ca ([131.104.96.18]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f4BH4fI05335 for ; Fri, 11 May 2001 13:04:41 -0400 Received: from msnet.mathstat.uoguelph.ca (msnet.mathstat.uoguelph.ca [131.104.32.59]) by outbound.mail.uoguelph.ca (8.9.3 (PHNE_21697)/8.9.3) with ESMTP id NAA00885; Fri, 11 May 2001 13:04:40 -0400 (EDT) Received: from MSNET/SpoolDir by msnet.mathstat.uoguelph.ca (Mercury 1.48); 11 May 01 13:03:55 -0500 Received: from SpoolDir by MSNET (Mercury 1.48); 11 May 01 13:03:49 -0500 From: "Bill Smith" Organization: Math & Stats, University of Guelph To: chemistry@ccl.net, Stefan Portmann Date: Fri, 11 May 2001 13:03:48 -0400 MIME-Version: 1.0 Content-type: text/plain; charset=US-ASCII Content-transfer-encoding: 7BIT Subject: Re: CCL:Abstract Management System Message-ID: <3AFBE32D.12449.5EBC7B0@localhost> Priority: normal In-reply-to: <3AFBF483.B6621CCA@igc.phys.chem.ethz.ch> X-mailer: Pegasus Mail for Win32 (v3.12c) Have a look at the following URL. http://www.ozonesoftware.com/ On 11 May 2001, at 16:17, Stefan Portmann wrote: > Dear Colleagues > > I'm a co-organizer of WATOC'02 (The World Association of Theoretically > Oriented Chemists; http://www.watoc02.ch) taking place in Lugano > Switzerland in August 2002. > > I'm currently evaluating an electronic abstract submitting and > management system for the congress. > Can you tell me, what you are using for your conference? I'm > interested in both, commercial and self made solutions. > > Thanks for your input > Stefan > Best Regards, W. R. Smith, Professor Dept. of Mathematics and Statistics and School of Engineering Room 546 MacNaughton Building University of Guelph Stone Road and Gordon Streets Guelph, Ontario, CANADA N1G 2W1 Tel: 519-824-4120, ext. 3038; FAX: 519-837-0221; http://www.mathstat.uoguelph.ca/faculty/smith/ From chemistry-request@server.ccl.net Fri May 11 13:11:18 2001 Received: from ergo.ibaf.cs.cnr.it ([194.119.197.4]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f4BHBHI05473 for ; Fri, 11 May 2001 13:11:17 -0400 Received: from unicz.it (ergo.ibaf.cs.cnr.it [194.119.197.4]) by ergo.ibaf.cs.cnr.it (8.11.0/8.11.0/SuSE Linux 8.11.0-0.4) with ESMTP id f4BHG2V09079 for ; Fri, 11 May 2001 19:16:02 +0200 X-Authentication-Warning: ergo.ibaf.cs.cnr.it: Host ergo.ibaf.cs.cnr.it [194.119.197.4] claimed to be unicz.it Sender: workshop@cs.cnr.it Message-ID: <3AFC1E52.5BD3FAC5@unicz.it> Date: Fri, 11 May 2001 19:16:02 +0200 From: 1st workshop in Magna Graecia Organization: =?iso-8859-1?Q?Universit=E0?= degli Studi di Catanzaro "Magna Graecia" X-Mailer: Mozilla 4.76 [en] (X11; U; Linux 2.2.16 i686) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net Subject: Final Programme - 1st MGMC Workshop Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear Collegue, We are pleased to inform you that the Final Programme of the 1st MGMC Workshop is now available at our website http://www.unicz.it/ricerca/convegni/ You will find new information about : Oral Communications Accepted Posters Social Programme Optional Touristic Programme (deadline for reservations June 1st 2001) Standard and Daily Registration Our Sponsors For additional information, please, feel free to contact us via e-mail or call the Organizing Secretariat. Best regards and see you in Copanello. The Organizing Commitee "Insieme per la Ricerca" From chemistry-request@server.ccl.net Fri May 11 14:23:32 2001 Received: from admin.cnrs-orleans.fr ([163.9.1.2]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f4BINVI06099 for ; Fri, 11 May 2001 14:23:31 -0400 Received: from chinon.cnrs-orleans.fr (chinon.cnrs-orleans.fr [163.9.6.107]) by admin.cnrs-orleans.fr (8.9.1a/jtpda-5.3.2) with ESMTP id UAA00085 ; Fri, 11 May 2001 20:23:29 +0200 (MET DST) Received: (from hinsen@localhost) by chinon.cnrs-orleans.fr (8.9.3/8.9.3) id UAA28171; Fri, 11 May 2001 20:23:10 +0200 Date: Fri, 11 May 2001 20:23:10 +0200 Message-Id: <200105111823.UAA28171@chinon.cnrs-orleans.fr> X-Authentication-Warning: chinon.cnrs-orleans.fr: hinsen set sender to hinsen@cnrs-orleans.fr using -f From: Konrad Hinsen To: Guangping_Li/CAS/UNO/UNEBR@unomail.unomaha.edu CC: chemistry@ccl.net In-reply-to: <86256A49.00521C91.00@unomail.unomaha.edu> (Guangping_Li/CAS/UNO/UNEBR@unomail.unomaha.edu) Subject: Re: CCL:normal inquiry References: <86256A49.00521C91.00@unomail.unomaha.edu> > Does anyone know of any software which can be used to extract the amino > sequence of a peptide from a PDB (protein data bank) file? Get Python (www.python.org) plus Scientific Python (http://dirac.cnrs-orleans.fr/programs/scientific.html) and then use the following script: -------------------------------------------------- > from Scientific.IO.PDB import * import sys s = Structure(sys.argv[1]) for chain in s.peptide_chains: print s.sequence() -------------------------------------------------- Run as "python script.py pdb_file", where script.py is the name of the small script file shown above. -- ------------------------------------------------------------------------------- Konrad Hinsen | E-Mail: hinsen@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@server.ccl.net Fri May 11 15:07:15 2001 Received: from Salicet.ucd.ie ([137.43.1.23]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f4BJ7EI06617 for ; Fri, 11 May 2001 15:07:14 -0400 Received: from CONVERSION-DAEMON.Salicet.ucd.ie by Salicet.ucd.ie (PMDF V6.0-24 #36961) id <0GD600E01QFY8X@Salicet.ucd.ie> for CHEMISTRY@ccl.net; Fri, 11 May 2001 20:07:14 +0100 (BST) Received: from elvira.ucd.ie ([137.43.24.26]) by Salicet.ucd.ie (PMDF V6.0-24 #36961) with ESMTP id <0GD6009GJQFYIN@Salicet.ucd.ie> for CHEMISTRY@ccl.net; Fri, 11 May 2001 20:07:10 +0100 (BST) Date: Fri, 11 May 2001 20:07:18 +0100 From: Laurence Cuffe Subject: G98, Solvation using the Onsager model. To: CHEMISTRY@ccl.net Message-id: <3AFC4676.7398.5E43BCA@localhost> Organization: University College Dublin X-Mailer: Pegasus Mail for Win32 (v3.12c) Content-type: TEXT/PLAIN Priority: normal Dear All Using the onsager model for solvation in g98 you are required to input two parameters, the solvent dielectric constant and the molecular volume. The molecular volume is generally derived from a gas phase calculation, and is determined, as I understand the code, by using a monte carlo procedure to sample the wave function. It occurred to me that perhaps, it would be more appropriate to try and determine this by finding a self consistent value using the following procedure: 1)Calculate a volume for the gas phase molecule 2)Use this value in a new calculation to find a volume for the wave function of the solvated molecule. 3) repeat the above procedure until a consistent value was reached. As a test molecule I took water with the O-H distance 1.05 angstroms and the H-O-H angle 105.0 degrees. Using HF and the default STO3G basis set I got the following set of values: Gas phase: recommended A0 2.46 1st solvated calc recomended A0 2.61 2nd solvated calc recommended A0 2.33 3rd solvated calc recomended A0 2.37 4th solvated calc recomended A0 2.46 Which leads to the question is step 2 valid? if so what went wrong with step 3? All the best Laurence Cuffe From chemistry-request@server.ccl.net Fri May 11 11:35:25 2001 Received: from server.nybc.org ([192.94.249.2]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f4BFZNI04319 for ; Fri, 11 May 2001 11:35:23 -0400 Received: from iris.nybc.org (iris.nybc.org [192.94.249.42]) by server.nybc.org (Sun Internet Mail Server sims.4.0.2000.10.12.16.25.p8) with ESMTP id <0GD60038KGLFII@server.nybc.org> for chemistry@ccl.net; Fri, 11 May 2001 11:34:27 -0400 (EDT) Received: from nybc.org (localhost [127.0.0.1]) by iris.nybc.org (SGI-8.9.3/8.9.3) with ESMTP id LAA04598; Fri, 11 May 2001 11:38:44 -0400 (EDT) Date: Fri, 11 May 2001 11:38:44 -0400 From: Asim Kumar Debnath Subject: Re: CCL:normal inquiry Sender: debnath@iris.nybc.org To: Guangping_Li/CAS/UNO/UNEBR@unomail.unomaha.edu Cc: chemistry@ccl.net Message-id: <3AFC0783.4F44C2F1@nybc.org> Organization: New York Blood Center MIME-version: 1.0 X-Mailer: Mozilla 4.75C-SGI [en] (X11; I; IRIX 6.5 IP22) Content-type: MULTIPART/ALTERNATIVE; BOUNDARY="Boundary_(ID_sl4WFujXB121OJCmseFiGg)" X-Accept-Language: en References: <86256A49.00521C91.00@unomail.unomaha.edu> --Boundary_(ID_sl4WFujXB121OJCmseFiGg) Content-type: text/plain; charset=us-ascii Content-transfer-encoding: 7BIT Hi Jim: You can extract sequence of any pdb structure directly from the RCSB Protein Data Bank site (http://www. rcsb.org/pdb/). When you search for a pdb file, it will give you a Summary information page. The left side of the page will give you a number of choices and the last one is "sequence details". If you click on that item, it will show the sequence and download options. You can download that sequence in FASTA format. Hope this helps. Asim Guangping_Li/CAS/UNO/UNEBR@unomail.unomaha.edu wrote: > Dear friends: > > Does anyone know of any software which can be used to extract the amino > sequence of a peptide from a PDB (protein data bank) file? > > I'm looking for several experimental peptide PDB files for demonstration too, > and these peptides better have 10-20 amino residues. > > Thanks for your help. > > Jim > > -= 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 -- ======================================================================= *** *** **** Asim K. Debnath, Ph.D. **** Lindsley F. Kimball Research Institute **** *** The New York Blood Center **** **** 310 E 67 Th Street **** ** **** New York, NY 10021 **** **** **** Tel. (212) 570-3373 **** ** **** Fax. (212) 570-3299 **************** E-mail: asim_debnath@nybc.org ************** ======================================================================== --Boundary_(ID_sl4WFujXB121OJCmseFiGg) Content-type: text/html; charset=us-ascii Content-transfer-encoding: 7BIT Hi Jim:
    You can extract sequence of any pdb structure directly > from the RCSB Protein Data Bank site (http://www. rcsb.org/pdb/). When you search for a pdb file, it will give you a Summary information page. The left side of the page will give you a number of choices and the last one is "sequence details". If you click on that item, it will show the sequence and download options. You can download that sequence in FASTA format.
    Hope this helps.

Asim

Guangping_Li/CAS/UNO/UNEBR@unomail.unomaha.edu wrote:

 Dear friends:

   Does anyone know of any software which can be used to extract the amino
sequence of a peptide from a PDB (protein data bank) file?

   I'm looking for several experimental peptide PDB files for demonstration too,
and these peptides better have 10-20 amino residues.

   Thanks for your help.

   Jim

-= 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

-- 



=======================================================================

             ***
             ***                
            ****                Asim K. Debnath, Ph.D.
           ****                 Lindsley F. Kimball Research Institute 
          ****  ***             The New York Blood Center
         ****    ****           310 E 67 Th Street
        ****  **  ****          New York, NY 10021
       ****  ****  ****         Tel. (212) 570-3373
      ****    **    ****        Fax. (212) 570-3299
       ****************         E-mail: asim_debnath@nybc.org
        **************                                  
                                        
========================================================================
  --Boundary_(ID_sl4WFujXB121OJCmseFiGg)-- From chemistry-request@server.ccl.net Fri May 11 13:02:56 2001 Received: from postoffice.mail.cornell.edu ([132.236.56.7]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f4BH2uI05287 for ; Fri, 11 May 2001 13:02:56 -0400 Received: from cornell.edu (sweet1.foodsci.cornell.edu [132.236.147.65]) by postoffice.mail.cornell.edu (8.9.3/8.9.3) with ESMTP id NAA11549; Fri, 11 May 2001 13:02:55 -0400 (EDT) Sender: dwood@cornell.edu Message-ID: <3AFC17A7.8EA03D59@cornell.edu> Date: Fri, 11 May 2001 12:47:35 -0400 From: "Dr. Richard L. Wood" X-Mailer: Mozilla 4.75C-SGI [en] (X11; I; IRIX 6.5 IP32) X-Accept-Language: en MIME-Version: 1.0 To: "chemistry@ccl.net" Subject: Re: CCL:HPC for Genomics & Proteomics 1st Call References: <4.1.20010511100111.0099a570@140.239.39.130> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi all Is anyone out there at ALL concerned about the consequences of our "knowing" the human genome? That is to say, that throwing all the money in the world at a, while seemingly well-intentioned, research project won't necessarily keep it from being used to discriminate. Richard -- Richard L. Wood, Ph. D. Physical/Computational Chemist Post-doctoral Associate Cornell University, Ithaca, NY 14853 From chemistry-request@server.ccl.net Fri May 11 14:39:39 2001 Received: from ccl.net ([192.148.249.4]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f4BIddI06267 for ; Fri, 11 May 2001 14:39:39 -0400 Received: from oscdesk53.ccl.net (oscdesk53.ccl.net [192.148.249.53]) by ccl.net (8.9.3/8.9.3/OSC 2.0) with ESMTP id OAA12503; Fri, 11 May 2001 14:39:38 -0400 (EDT) Date: Fri, 11 May 2001 14:39:39 -0400 From: Gerald Lushington To: chemistry@ccl.net cc: gerald@ccl.net Subject: FINAL REMINDER: Emerging Methods for CCM Workshop Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear Colleagues, This is a final reminder regarding the upcoming workshop on Emerging Methods in Computational Chemistry and Materials Science -- please see the announcement below for more information. Please also note: - By request from assorted interested individuals, we have added an addition session on "DoD Perspectives on Computational Chemistry and Materials Science Research" to be held the afternoon of June 1. - The deadline for special rates at the conference hotel (Sheraton Four Points in Aberdeen MD) is nearly upon us: May 15, 2001 - The workshop registration deadline is not far behind: May 24, 2001 Thank you all for your time and interest. We hope to see you in Aberdeen in a few weeks! - Gerry Lushington WORKSHOP ON EMERGING METHODS FOR COMPUTATIONAL CHEMISTRY AND MATERIALS SCIENCE Sheratons Four Points, Aberdeen MD, May 31 - June 1, 2001 We would like to welcome all interested government, industrial and academic researchers to PET-CCM's second Emerging Methods workshop. Building on the success of our 1999 incarnation off this event, we have assembled an excellent slate of speakers covering topics in the fields of: - Multiscale Materials Modeling - Mixed Quantum/Classical Simulations - Advanced Algorithm Development for a two day affair in Aberdeen MD. Attendance at the event is free for all, but we would ask all interested parties to please register online at: http://www.arl.hpc.mil/PET/cta/ccm/workshops/emerg01/reg.html AGENDA: THURSDAY A.M. (MAY 31) MULTISCALE MATERIALS MODELING 8:00 a.m. - 8:20 a.m. Registration, Coffee, etc. 8:20 a.m. - 8:30 a.m. Introductory Remarks 8:30 a.m. - 9:20 a.m. "Scalable algorithms for large multiscale simulations of nanomaterials on a Grid" Aiichiro Nakano (LSU) 9:20 a.m. - 10:10 a.m. "Real-Space Multiscale Methods in Density Functional Theory" Thomas Beck (Cincinnati) 10:10 a.m. - 10:30 a.m. break 10:30 a.m. - 11:20 a.m. "Bridging Length Scales in Materials: Coupling Atomistic and Continuum Models of Dislocation Dynamics" William Curtin (Brown) 11:20 a.m. - 12:00 p.m. round table discussion 12:00 p.m. - 1:30 p.m. lunch THURSDAY P.M. (MAY 31) MIXED QUANTUM / CLASSICAL TECHNIQUES: 1:30 p.m. - 2:20 p.m. "Mixed QM/MM Methods for Modeling Protein Active Site Chemistry" Richard Friesner (Columbia) 2:20 p.m. - 3:10 p.m. "Multi-scale Methods to Model Quantum Effects in Biological Systems" Darrin York (Minnesota) 3:10 p.m. - 3:30 p.m. break 3:30 p.m. - 4:20 p.m. "Quantum Bioinformatics: Methods and Applications" Kenneth Merz, Jr. (Penn State) 4:20 p.m. - 5:00 p.m. round table discussion FRIDAY A.M. (JUNE 1) ADVANCED ALGORITHM DEVELOPMENT I: 8:30 a.m. - 9:20 a.m. "Accelerated Molecular Dynamics Methods" Arthur Voter (LANL) 9:20 a.m. - 10:10 a.m. "Atomistic Measures of Materials Strength, Deformation and Toughness" Sidney Yip (MIT) 10:10 a.m. - 10:30 a.m. round table discussion 10:30 a.m. - 11:30 a.m. poster session 11:30 a.m. - 1:00 p.m. lunch FRIDAY P.M. (JUNE 1) ADVANCED ALGORITHM DEVELOPMENT II: 1:00 p.m. - 1:50 p.m. "An Introduction to Solid-Harmonic-Gaussian Density Functional Chemical Dynamics" Brett Dunlap (NRL) 1:50 p.m. - 2:40 p.m. "Fast methods for electronic structure calculations: Density Functional and Coupled Cluster Methods" Martin Head-Gordon (UC Berkeley) 2:40 p.m. - 3:00 p.m. round table discussion FRIDAY P.M. (JUNE 1) DOD PERSPECTIVES ON CCM RESEARCH: 3:15 p.m. - 3:45 p.m. "Title to be announced" Cary Chabalowski (ARL) 3:45 p.m. - 4:15 p.m. "Title to be announced" Chris Woodward (AFRL) 4:15 p.m. - 4:45 p.m. "Tight-Binding and Large Scale Materials Science Computations" Michael Mehl (NRL) 4:45 p.m. - 5:00 p.m. wrap up We are also planning to have a social event (informal supper and refreshments) on the evening of the 31st at Swan Harbor. People interested in participating in this event should please indicate this fact on their registration form, and bring along a $10.00 fee (per person) which will cover part of the cost of the meal and refreshments to be served. For more details on all of the above, as well as directions to the Sheraton and information on accomodations and deadlines, please consult the Workshop Web page at: http://www.arl.hpc.mil/PET/cta/ccm/workshops/emerg01/index.html or contact the organizers at: Margaret M. Hurley, Ph.D. US Army Research Laboratory Computational and Information Sciences Directorate Phone: 410-297-8568 Fax: 410-278-4983 Email: hurley@arl.army.mil Gerald H. Lushington Ph: 614-292-6036 Research Specialist Fax: 614-292-7168 OSC / PET-CCM e-mail: gerald@ccl.net 1224 Kinnear Road http://www.arl.hpc.mil/PET/cta/ccm Columbus OH 43212-1163 http://www.asc.hpc.mil/PET/CCM From chemistry-request@server.ccl.net Fri May 11 14:44:09 2001 Received: from mallard.duc.auburn.edu ([131.204.2.23]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f4BIi9I06335 for ; Fri, 11 May 2001 14:44:09 -0400 Received: from localhost (newhoir@localhost) by mallard.duc.auburn.edu (8.8.8+Sun/8.7.2) with SMTP id NAA08353 for ; Fri, 11 May 2001 13:44:09 -0500 (CDT) X-Authentication-Warning: mallard.duc.auburn.edu: newhoir owned process doing -bs Date: Fri, 11 May 2001 13:44:09 -0500 (CDT) From: Irene Newhouse X-Sender: newhoir@mallard To: chemistry@ccl.net Subject: Does anyone recall this article? Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII In the 1980s, there appeared in Reviews of Modern Physics an article by a prominent physicist [Kenneth Wilson??] on comp. chemistry[?]. I saved that article for many years, but it got lost in one of our moves & I'd like to get it again, on account of a passage in which the author says numerous physicists, convinced they could do it better than the chemists, have wasted man-years trying to write better codes, only to discover that they can't do it better. He had done his share thereof & concluded that chemists have done pioneering work in optimization techniques, use of which could benefit other fields. Does anyone recognize this? Thanks in advance! Irene Newhouse From chemistry-request@server.ccl.net Fri May 11 16:20:46 2001 Received: from popserver.healthtech.com ([140.239.39.130]) by server.ccl.net (8.11.0/8.11.0) with SMTP id f4BKKjI07829 for ; Fri, 11 May 2001 16:20:45 -0400 Received: by popserver.healthtech.com from localhost (router,SLMail V4.3); Fri, 11 May 2001 16:18:59 -0400 for Received: from wendyh [140.239.39.144] by popserver.healthtech.com [140.239.39.130] (SLmail 4.3.0.3454) with SMTP id 507539E9F83D47FB809C68554B8A465E for ; Fri, 11 May 2001 16:18:57 -0400 Message-Id: <4.1.20010511161102.00a59330@140.239.39.130> X-Sender: whori@140.239.39.130 X-Mailer: QUALCOMM Windows Eudora Pro Version 4.1 Date: Fri, 11 May 2001 16:14:28 -0400 To: chemistry@ccl.net From: "Wendy Hori" Subject: HPC for Genomics & Proteomics 1st Call deadline Mime-Version: 1.0 Content-Type: multipart/alternative; boundary="=====================_6935793==_.ALT" X-SLUIDL: 24C69C09-9396449E-A6FB3437-2D2A882B --=====================_6935793==_.ALT Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable The deadline for submissions has beeen changed to May 18, 2001 FIRST ANNOUNCEMENT AND CALL FOR PAPERS Cambridge Healthtech Institute=92s=20 High Performance Computing Strategic Applications for Genomics & Proteomics September 20-21, 2001, Wyndham San Diego at Emerald Plaza Hotel San Diego, California If you would like to submit a proposal to give a presentation or display a poster at this meeting please send us, by fax or email, a title and brief= 3-5 sentence summary of a proposed topic on your recent work in the area of High Performance Computing . The deadline for submission is May 18, 2001. All proposals are subject to review by the Scientific Advisory Committee to= ensure the overall quality of the conference program. For more information, please contact Wendy Hori at: Cambridge Healthtech Institute, 1037 Chestnut Street, Newton Upper Falls, MA 02464 Tel: 617 630-1382 =95 Fax: 617 630-1325 =95 Email: whori@healthtech.com For sponsorship and exhibit information, please contact Jim MacNeil. Tel: 617-630-1341, Email: jmacneil@healthtech.com To register on-line, please visit our web site: www.healthtech.com --=====================_6935793==_.ALT Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable The deadline for submissions has beeen changed to May 18, 2001
FIRST ANNOUNCEMENT AND CALL FOR PAPERS
Cambridge Healthtech Institute=92s
High Performance Computing
Strategic Applications for Genomics & Proteomics
September 20-21, 2001, Wyndham San Diego at Emerald Plaza Hotel  San Diego, California

If you would like to submit a proposal to give a presentation or display a poster at this meeting please send us, by fax or email, a title and brief 3-5 sentence summary of a proposed topic on your recent work in the area of High Performance Computing . The deadline for submission is May 18, 2001. All proposals are subject to review by the Scientific Advisory Committee to ensure the overall quality of the conference program.

For more information, please contact Wendy Hori at:
Cambridge Healthtech Institute, 1037 Chestnut Street, Newton Upper Falls, MA 02464
Tel: 617 630-1382 =95 Fax: 617 630-1325 =95 Email: whori@healthtech.com
For sponsorship and exhibit information, please contact Jim MacNeil. Tel: 617-630-1341, Email: jmacneil@healthtech.com

To register on-line, please visit our web site: www.healthtech.com
 --=====================_6935793==_.ALT--