From 9702029k@lv.levels.unisa.edu.au Mon Jul 27 00:26:18 1998 Received: from bROLga.Levels.UniSA.Edu.Au (SYSTEM@Brolga.levels.unisa.edu.au [130.220.16.11]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id AAA08968 Mon, 27 Jul 1998 00:26:15 -0400 (EDT) Received: from xiy205359.unisa.edu.au ("port 1176"@XIY205359.Levels.UniSA.Edu.Au) by Levels.UniSA.Edu.Au (PMDF V5.1-10 #27872) with SMTP id <01IZWBO4LDNG8WWQLL@Levels.UniSA.Edu.Au> for chemistry@www.ccl.net; Mon, 27 Jul 1998 13:56:10 +0930 Received: by xiy205359.unisa.edu.au with Microsoft Mail id <01BDB967.CA4C25C0@xiy205359.unisa.edu.au>; Mon, 27 Jul 1998 14:06:46 +0930 Date: Mon, 27 Jul 1998 14:06:40 +0930 From: Josh Bowden <9702029k@lv.levels.unisa.edu.au> Subject: IDE RAID 0 for computational speed? To: "'chemistry@www.ccl.net'" Message-id: <01BDB967.CA4C25C0@xiy205359.unisa.edu.au> MIME-version: 1.0 Content-type: text/plain; charset="us-ascii" Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by www.ccl.net id AAA08968 Hello, I am wondering if anybody has experience with RAID 0 setup for workstations running ab-initio programs. I would think that this would be a v.good way to increase disk access speed and a good way to increase disk storage space. Does RAID 0 increase integral file R/W access and therefore increase computational speed? or are other areas the bottleneck in a computer+ab-initio program? Is anyone usinig IDE HD RAID cards, such as those from Promise Tech. and have you found that these increase computational performance? Thankyou for your time. I will summarise. Josh. Josh Bowden University of South Australia Ian Wark Research Institute 9702029k@lv.levels.unisa.edu.au From lavelle@mbi.ucla.edu Mon Jul 27 01:24:33 1998 Received: from theta1.ben2.ucla.edu (theta1.ben2.ucla.edu [164.67.131.35]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id BAA09353 Mon, 27 Jul 1998 01:24:32 -0400 (EDT) Received: from ewald.mbi.ucla.edu (ewald.mbi.ucla.edu [128.97.39.21]) by theta1.ben2.ucla.edu (8.8.8/8.8.8) with SMTP id WAA133518; Sun, 26 Jul 1998 22:24:32 -0700 Received: from pc-ll.chem.ucla.edu by ewald.mbi.ucla.edu (5.65v3.2/1.1.10.5/09Oct97-1217PM) id AA05380; Sun, 26 Jul 1998 22:24:32 -0700 Message-Id: <9807270524.AA05380@ewald.mbi.ucla.edu> X-Sender: lavelle@mbi.ucla.edu X-Mailer: QUALCOMM Windows Eudora Pro Version 4.0 Date: Sun, 26 Jul 1998 22:38:53 -0700 To: Josh Bowden <9702029k@lv.levels.unisa.edu.au>, "'chemistry@www.ccl.net'" From: Laurence Lavelle Subject: Re: CCL:IDE RAID 0 for computational speed? In-Reply-To: <01BDB967.CA4C25C0@xiy205359.unisa.edu.au> Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Hi Josh, With respect to SCSI RAID 0 the answer is a big yes, yes. However if you are using the HyperCube or Gaussian products with NT as the OS then the answer is maybe. Both companies have limited the file size to 2GB which they say is based on FAT 32. I have communicated with them many times about implementing NTFS. It is a simple procedure and both companies have indicated that they will support the NTFS file structure in their next release. For FAT the max file size is 2^32 bytes (4.3 GB). For NTFS, the max is 2^64 bytes (1.8 x 10^10 GB). I don't think this is much of limitation. Laurence >Date: Wed, 13 May 1998 10:45:25 -0700 >From: Laurence Lavelle >Subject: Ab initio file size > >Please pass this on to your developers. > >The Win32 API provides for a 64-bit file seek pointer and files >4GB. Assuming that the underlying file system can support large files, which NTFS can. It is simple to detect NT and then support 64-bit file pointer semantics. > >Basically all you do is declare file pointers using an __int64 data type and >then pass this type (as 2 32-bit values) to the SetFilePosition() API before >reading or writing. NT will then happily create a file of whatever size is >required. Probably require about an hours work by a decent programmer. > >Thanks >Laurence At 02:06 PM 7/27/98 +0930, Josh Bowden wrote: >Hello, > >I am wondering if anybody has experience with RAID 0 setup for workstations running ab-initio programs. I would think that this would be a v.good way to increase disk access speed and a good way to increase disk storage space. Does RAID 0 increase integral file R/W access and therefore increase computational speed? or are other areas the bottleneck in a computer+ab-initio program? Is anyone usinig IDE HD RAID cards, such as those from Promise Tech. and have you found that these increase computational performance? > >Thankyou for your time. >I will summarise. > >Josh. > >Josh Bowden >University of South Australia >Ian Wark Research Institute >9702029k@lv.levels.unisa.edu.au > >-------This is added Automatically by the Software-------- >-- Original Sender Envelope Address: 9702029k@lv.levels.unisa.edu.au >-- Original Sender From: Address: 9702029k@lv.levels.unisa.edu.au >CHEMISTRY@www.ccl.net: Everybody | CHEMISTRY-REQUEST@www.ccl.net: Coordinator >MAILSERV@www.ccl.net: HELP CHEMISTRY or HELP SEARCH | Gopher: www.ccl.net 73 >Anon. ftp: www.ccl.net | CHEMISTRY-SEARCH@www.ccl.net -- archive search > Web: http://www.ccl.net/chemistry.html > From dbrown@oxmol.co.uk Mon Jul 27 04:35:06 1998 Received: from dreamon.oxmol.co.uk (dreamon.oxmol.co.uk [193.132.141.15]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id EAA10210 Mon, 27 Jul 1998 04:35:04 -0400 (EDT) Received: from oxmol.co.uk (edison.oxmol.co.uk [193.132.141.10]) by dreamon.oxmol.co.uk (8.9.0/8.9.0/2) with ESMTP id JAA07069; Mon, 27 Jul 1998 09:34:33 +0100 (BST) Sender: dbrown@oxmol.co.uk Message-ID: <35BC3B98.E7C6F895@oxmol.co.uk> Date: Mon, 27 Jul 1998 09:34:32 +0100 From: David Brown Reply-To: dbrown@oxmol.co.uk Organization: Oxford Molecular Ltd X-Mailer: Mozilla 4.05 [en] (X11; I; HP-UX B.10.20 9000/778) MIME-Version: 1.0 To: chemistry@www.ccl.net Subject: Re: CCL:PDB 3D queries? Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit You should look at Iditis from Oxford Molecular, a comprehensive database of derived information from the PDB. To give just a flavor of the information available, the DISULPH table contains: Four letter Brookhaven PDB code One letter model code One letter polypeptide chain label for first Cys residue Amino acid identifier of residue for first Cys residue One letter polypeptide chain label for partner Cys residue Amino acid identifier of residue for partner Cys residue Bridge assignment responsibility Extended Kabsch and Sander secondary structure assigment for first Cys residue Number of amino acid residues between two Cys residues Extended Kabsch and Sander secondary structure assigment for partner Cys residue Inter C-alpha distance between two Cys residues Inter C-beta distance between two Cys residues Inter S-gamma distance between two Cys residues Standard chi-1 torsion angle for first Cys residue Standard chi-2 torsion angle for first Cys residue Standard chi-3 torsion angle for first Cys residue Standard chi-2 torsion angle for partner Cys residue Standard chi-1 torsion angle for partner Cys residue Incremental count of number of bridges in protein > Hi, > > What packages allow one to query the PDB in the same way one can query the > Cambridge small-molecule database (eg. extract a histogram of NH...OC distances > & angles, ring-ring distances & angles, atom-ring distances & angles, specified > types of bond torsions and angles, etc.)? > > I will summarize responses. Thanks, > > Bryan Marten, PhD > Schering-Plough Pharmaceuticals > bryan.marten@spcorp.com David ________________ Dr David R Brown | ## ## ## | dbrown@oxmol.co.uk Oxford Molecular Ltd | ## ## ## |WWW http://www.oxmol.co.uk/ The Magdalen Centre | ## ## ## |FTP ftp.oxmol.co.uk Oxford Science Park | ###### | Oxford OX4 4GA | ## | Tel: (01865)784600 | ## | Fax: (01865)784601 | #### | --------------- From chchae@plaza1.snu.ac.kr Mon Jul 27 05:28:08 1998 Received: from plaza1.snu.ac.kr (plaza1.snu.ac.kr [147.46.10.9]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id FAA10446 Mon, 27 Jul 1998 05:28:06 -0400 (EDT) From: chchae@plaza1.snu.ac.kr Received: (from chchae@localhost) by plaza1.snu.ac.kr (8.8.8H1/8.8.8) id SAA91966 for CHEMISTRY@www.ccl.net; Mon, 27 Jul 1998 18:27:33 +0900 Date: Mon, 27 Jul 1998 18:27:33 +0900 Message-Id: <199807270927.SAA91966@plaza1.snu.ac.kr> To: CHEMISTRY@www.ccl.net Subject: [Q]semiempirical parameters for Pt Dear computational chemists. Does any one know about the semiempirical (MNDO, AM1, ... ) calculations of compounds containing the Pt (platinum). Thank you. Chong Hak Chae (chchae@plaza1.snu.ac.kr) From bruno@antas.agraria.uniss.it Mon Jul 27 07:51:11 1998 Received: from ssmain.uniss.it (ssmain.uniss.it [193.205.8.2]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id HAA10799 Mon, 27 Jul 1998 07:51:05 -0400 (EDT) Received: from antas.agraria.uniss.it (antas.agraria.uniss.it [193.205.10.3]) by ssmain.uniss.it with SMTP (8.8.8/8.8.8) id NAA16719; Mon, 27 Jul 1998 13:49:48 +0200 (METDST) Date: Mon, 27 Jul 1998 13:49:45 +0100 (NFT) From: "Dr. Bruno Manunza" To: Vladimir Gusev cc: chemistry@www.ccl.net Subject: Re: CCL:Web examples of modeling lipid bilayers In-Reply-To: <3.0.5.32.19980722213011.0090de10@mail.javanet.com> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII On Wed, 22 Jul 1998, Vladimir Gusev wrote: > Hello CCL, > > I would appreciate any pointers to the modeling (MD or MC) of systems with > lipid bilayers presented on the web. > > Thank you in advance. > > Vladimir Dear Vladimir, have a look to: http://www.lrz-muenchen.de/~heller/membrane/membrane.html and http://www.umass.edu/microbio/rasmol/bilayers.htm hope it helps bye Bruno Dr Bruno Manunza Molecular Modeling Lab DISAABA (Dept. of Agricultural Environm. Sci) University of Sassari V.le Italia 39 07100 Sassari, ITALY phone: 39 79 229215 fax: 39 79 229276 e-mail: bruno@antas.agraria.uniss.it web: http://antas.agraria.uniss.it From bersuker@ne059.cm.utexas.edu Fri Jul 24 10:01:22 1998 Received: from ne059.cm.utexas.edu (ne059.cm.utexas.edu [146.6.145.59]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with SMTP id KAA26282 Fri, 24 Jul 1998 10:01:22 -0400 (EDT) Received: from ne056.cm.utexas.edu by ne059.cm.utexas.edu (AIX 3.2/UCB 5.64/4.03) id AA06041; Fri, 24 Jul 1998 09:00:03 -0500 Message-Id: <35B89274.AB3BF551@eeyore.cm.utexas.edu> Date: Fri, 24 Jul 1998 08:56:04 -0500 From: "Isaac B. Bersuker" Organization: The University of Texas at Austin X-Mailer: Mozilla 4.04 [en] (WinNT; I) Mime-Version: 1.0 To: Rino Ragno Cc: chemistry@www.ccl.net Subject: Re: CCL:molecule fragmentation code References: Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit If you look for methods (algorithms) of such fragmentation, see our paper in Internat. J. Quant.Chem. 63 (1997) 1051-63. Regards Isaac Bersuker Rino Ragno wrote: > Hi to everyone, > > I am looking for a code to fragment a given molecule into chunks. The > fragments should have the breaking point in common. > > Is any of you aware of such a piece of code (better if in C)? > > Thanks to all. > > -- Rino Ragno > > ++----------------------------------------------------------------------++ > ++----------------------------------------------------------------------++ > || || > || Dr. Rino Ragno E-mail: ragno@uniroma1.it || > || Institute for Biomedical Computing or: rino@gpc.wustl.edu || > || Center for Molecular Design or: ragno@axcasp.caspur.it || > || Box8036, Washington University Phone : 314-362-2272 || > || 700 South Euclid Avenue FAX : 314-362-0234 || > || St. Louis, Missouri 63110 || > || U. S. A. || > || || > || WEB PAGE : www.ibc.wustl.edu/cmd/people/rino/rino.html || > || || > ++----------------------------------------------------------------------++ > ++----------------------------------------------------------------------++ > > --- > Administrivia: This message is automatically appended by the mail exploder: > CHEMISTRY@www.ccl.net: Everybody | CHEMISTRY-REQUEST@www.ccl.net: Coordinator > MAILSERV@www.ccl.net: HELP CHEMISTRY or HELP SEARCH | Gopher: www.ccl.net 73 > Anon. ftp: www.ccl.net | CHEMISTRY-SEARCH@www.ccl.net -- archive search > Web: http://www.ccl.net/chemistry.html > --- From BRYAN.MARTEN@spcorp.com Mon Jul 27 12:24:36 1998 Received: from ans2.spri.sp.com (sp2.spcorp.com [198.16.9.3]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with SMTP id MAA17685 Mon, 27 Jul 1998 12:24:35 -0400 (EDT) Received: by sp2.spcorp.com id AA13748 (InterLock SMTP Gateway 3.0 for chemistry@www.ccl.net); Mon, 27 Jul 1998 12:24:35 -0400 Received: by sp2.spcorp.com (Internal Mail Agent-1); Mon, 27 Jul 1998 12:24:35 -0400 Mime-Version: 1.0 Date: Mon, 27 Jul 1998 11:40:16 -0400 Message-Id: <001829FF.1322@inet.spri.sp.com> From: BRYAN.MARTEN@spcorp.com (BRYAN MARTEN) Subject: Re[2]: PDB 3D queries? To: chemistry@www.ccl.net Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Content-Description: cc:Mail note part Thanks to several people for pointing me to IsoStar for doing 3D searches of the PDB. I am interested in alternatives to IsoStar, though. I have yet to use IsoStar, but from its web page's FAQ (http://www.ccdc.cam.ac.uk/isostar/ faq.html) I see that there are some potentially significant limitations, particularly if you are interested in general amino acid-amino acid interactions or oddball queries. With IsoStar, all interactions internal to proteins are excluded from the database (see FAQ excerpt below). Also, the types of queries which can be made are limited (see other FAQ excerpt below). Bryan Marten bryan.marten@spcorp.com Excerpted from IsoStar FAQ: Exactly which contacts does IsoStar include from the PDB? First, we don't include contacts between protein atoms - only between protein atoms and ligand atoms, protein atoms and water, and ligand atoms and water. Secondly, we only use PDB structures with a resolution better than 2.5A. Thirdly, when there is a "family" of PDB structures which are identical except for one or more mutated residues in the protein, we only use one of them. Fourthly, we have excluded covalently-bound protein-ligand complexes. Finally, some structures were excluded because we couldn't process them correctly or were unsure of the ligand structure. Why are there no results for some central-group/contact-group combinations in IsoStar, when I'm sure there are structures in the databases that contain them? Two possible reasons. First, we just may not have done the search yet. It takes quite a long time to do them all. Secondly, we don't use all PDB structures - for example, low resolution structures (poorer than 2.5A) are excluded. From tajkhors@mbp-sgi7.inet.dkfz-heidelberg.de Mon Jul 27 13:50:16 1998 Received: from mbp-sgi7.inet.dkfz-heidelberg.de (mbp-sgi7.inet.dkfz-heidelberg.de [193.174.59.125]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with SMTP id NAA19160 Mon, 27 Jul 1998 13:50:14 -0400 (EDT) Received: by mbp-sgi7.inet.dkfz-heidelberg.de (951211.SGI.8.6.12.PATCH1502/940406.SGI.AUTO) for chemistry@www.ccl.net id CAA08572; Tue, 28 Jul 1998 02:51:53 GMT From: "Emadeddin Tajkhorshid" Message-Id: <9807271951.ZM8570@mbp-sgi7.inet.dkfz-heidelberg.de> Date: Mon, 27 Jul 1998 19:51:44 -0700 Reply-To: E.Tajkhorshid@DKFZ-Heidelberg.de X-Mailer: Z-Mail (3.2.0 26oct94 MediaMail) To: chemistry@www.ccl.net (Computational Chemistry List) Subject: small peptide models Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Dear colleagues I am looking for some examples of small polypeptide structures which can be used for testing the efficiency of a program doing some semiempirical calculations. With this regard, the experimentally resolved structures which are not very large are the main intrest. Any other model which may be interesting or any reference with this regard is highly appreciated. Thanx for your assistance. -- Emad ********************************************************************* E. Tajkhorshid German Cancer Research Center; DKFZ Tel: +49 6221 42 2340 Dept. Molecular Biophysics (H0200) FAX: +49 6221 42 2333 P.O.Box 101949 69009 Heidelberg, Germany Email: E.Tajkhorshid@DKFZ-Heidelberg.de ********************************************************************* * "Never express yourself more clearly than you think." -Niels Bohr * ********************************************************************* From lazarid@smtp.fas.harvard.edu Mon Jul 27 19:45:56 1998 Received: from smtp4.fas.harvard.edu (root@smtp4.fas.harvard.edu [140.247.30.84]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id TAA22816 Mon, 27 Jul 1998 19:45:56 -0400 (EDT) Received: from login4.fas.harvard.edu (lazarid@login4.fas.harvard.edu [140.247.30.74]) by smtp4.fas.harvard.edu with ESMTP id TAA17368; Mon, 27 Jul 1998 19:45:56 -0400 (EDT) From: Themis Lazaridis Received: by login4.fas.harvard.edu with id TAA21638; Mon, 27 Jul 1998 19:45:55 -0400 (EDT) Date: Mon, 27 Jul 1998 19:45:55 -0400 (EDT) Message-Id: <199807272345.TAA21638@login4.fas.harvard.edu> To: CHEMISTRY@www.ccl.net Subject: color printers Can anybody recommend a color printer that works well for Acrobat PDF documents with color? We have an HP color printer here but it doesn't seem to be able to handle the large size of these jobs. Thanks. Themis Lazaridis Harvard, Chemistry From zain@kimia.um.edu.my Mon Jul 27 21:41:39 1998 Received: from kimia.um.edu.my ([202.185.71.1]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with SMTP id VAA23587 Mon, 27 Jul 1998 21:41:36 -0400 (EDT) Received: by kimia.kimia.um.edu.my (5.x/SMI-SVR4) id AA00056; Tue, 28 Jul 1998 09:38:06 +0800 Date: Tue, 28 Jul 1998 09:38:06 +0800 (MYT) From: S M Zain To: chemistry@www.ccl.net Subject: GAMESS executable for linux Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear cclers, I am in need of a compiled version of GAMESS US (latest version) under linux. I am running linux 2.0.32 (redhat linux5.0). I am running out of time and compiling one now would take more time than what i have. Please advice as well on licensing issues. Help is very much appreciated... Thanks.. Sharifuddin M. Zain Jabatan Kimia Universiti Malaya 50603 Kuala Lumpur Tel: 03-7594442 Fax: 03-9041715