From chemistry-request@server.ccl.net Mon Apr 3 03:03:35 2000 Received: from tigris.klte.hu (tigris.klte.hu [193.6.138.33]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id DAA11982 for ; Mon, 3 Apr 2000 03:03:31 -0400 Received: from anti07 (193.6.133.59) by tigris.klte.hu (MX V5.1-A Vn6f) with SMTP for ; Mon, 3 Apr 2000 09:04:15 +0100 Message-ID: <002b01bf9d3b$0b91d080$3b8506c1@chem.klte.hu> From: "Tamas E. Gunda" To: References: <200003310118.JAA19735@ms.dicp.ac.cn> Subject: Re: CCL:about coordinate of lone pair electron Date: Mon, 3 Apr 2000 09:05:50 +0200 MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-2" Content-Transfer-Encoding: 7bit X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 5.00.2615.200 X-MimeOLE: Produced By Microsoft MimeOLE V5.00.2615.200 >----- Original Message ----- >From: student > Dear netter: > i am sorry for ask this question again,because i has not got answer from anyone as now. > my question is that : > Are there web page or free software for automatically adding coordination of lone pair electron of O,N,P,S from file in which > there are only coordinations of atoms in CCL. > > thanks in advance!!!! Usually molecular mechanics programs are dealing with lone-pairs. I don't know about free softwares, but for example PCModel can add lone-pairs to atoms (older versions do as well). Your file format should be supported by PCM, if not - you have only coordinates - it is usually easy to edit it manually to mimick an xray file by adding a=b=c=1, alpha=beta=gamma=90. regards Dr Tamas E. Gunda Research Group for Antibiotics of the Hungarian Acad. Sci. University of Debrecen, POBox 36 H-4010 Debrecen, Hungary tel.: (+36-52) 316666/2472 fax: (+36-52) 512914 e-mail: tamasgunda@tigris.klte.hu home-page: www.klte.hu/~gundat/gunda.htm To: Sent: Friday, March 31, 2000 8:21 PM Subject: CCL:about coordinate of lone pair electron From chemistry-request@server.ccl.net Mon Apr 3 03:09:54 2000 Received: from ccl.net (atlantis.ccl.net [192.148.249.4]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id DAA12044 for ; Mon, 3 Apr 2000 03:09:54 -0400 Received: from gigi.excite.com ([199.172.152.110]) by ccl.net (8.9.3/8.9.3/OSC 2.0) with ESMTP id DAA11165 for ; Mon, 3 Apr 2000 03:09:46 -0400 (EDT) Received: from ringo.excite.com ([199.172.152.145]) by gigi.excite.com (InterMail vM.4.01.02.40 201-229-119-123) with ESMTP id <20000403070816.EJSI29588.gigi.excite.com@ringo.excite.com> for ; Mon, 3 Apr 2000 00:08:16 -0700 Message-ID: <20340830.954745696783.JavaMail.imail@ringo.excite.com> Date: Mon, 3 Apr 2000 00:08:16 -0700 (PDT) From: Zilvinas Rinkevicius To: CHEMISTRY@www.ccl.net Subject: C80 geometry Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Excite Inbox X-Sender-Ip: 193.219.32.154 Dear CCL users, Any one can point me at C80 geometry experimental determination data or just provide me with exact C80 Ih symmetry geometry. Thanking in advance, with best regards, Zilvinas Rinkevicius, Kaunas Technology University, Faculty of Fundamental Sciences, Studentu st. 50, Kaunas 3000, Lithuania. _______________________________________________________ Get 100% FREE Internet Access powered by Excite Visit http://freelane.excite.com/freeisp From chemistry-request@server.ccl.net Mon Apr 3 03:58:53 2000 Received: from uldns1.unil.ch (uldns1.unil.ch [130.223.8.20]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id DAA12401 for ; Mon, 3 Apr 2000 03:58:52 -0400 Received: from pcbch3207h.unil.ch ([130.223.143.63] helo=pcbch3207h ident=aborel) by uldns1.unil.ch with esmtp (Exim 2.12 #1) for chemistry@ccl.net id 12c1ky-00000e-00; Mon, 3 Apr 2000 09:58:44 +0200 Message-ID: X-Mailer: XFMail 1.4.0 on Linux X-Priority: 3 (Normal) Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 8bit MIME-Version: 1.0 Date: Mon, 03 Apr 2000 09:58:44 +0200 (MET DST) Organization: University of Lausanne Sender: aborel@pcbch3207h From: Alain Borel To: chemistry@ccl.net Subject: Electrostatic potential in Gaussian98 Hello, I'm trying to compute the electrostatic potential on the Connoly surface of several molecules. I have a gaussian CUBE file of the ESP and the coordinates of the grid points for the surface and have managed to interpolate the values of the ESP on this grid. Unfortunately I'm not quite sure of the meaning of the numbers I get :-( Could someone in this distinguished assembly explain to me what definition is used in Gaussian for the ESP, and in what units it is expressed? Thank you in advance Alain Borel Institute of Inorganic and Analytical Chemistry University of Lausanne (Switzerland) ---------------------------------- Alain Borel Year 2000: not the 21st century Date: 03-Apr-00 Time: 09:42:56 From chemistry-request@server.ccl.net Mon Apr 3 04:35:29 2000 Received: from ccl.net (atlantis.ccl.net [192.148.249.4]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id EAA12817 for ; Mon, 3 Apr 2000 04:35:29 -0400 Received: from qorws1.uab.es (qorws1.uab.es [158.109.12.1]) by ccl.net (8.9.3/8.9.3/OSC 2.0) with SMTP id EAA12058 for ; Mon, 3 Apr 2000 04:34:09 -0400 (EDT) Received: by qorws1.uab.es (940816.SGI.8.6.9/930416.SGI) id LAA12542; Mon, 3 Apr 2000 11:33:02 -0700 From: "Pascal Bonnet" Message-Id: <10004031133.ZM12540@qorws1.uab.es> Date: Mon, 3 Apr 2000 11:33:02 -0700 In-Reply-To: Zilvinas Rinkevicius "CCL:C80 geometry" (Jan 21, 5:25pm) References: <20340830.954745696783.JavaMail.imail@ringo.excite.com> X-Mailer: Z-Mail (3.2.2 10apr95 MediaMail) To: Zilvinas Rinkevicius Subject: Re: CCL:C80 geometry Cc: CHEMISTRY@www.ccl.net Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Hi, you can look at this web page: http://shachi.cochem2.tutkie.tut.ac.jp/Fuller/Fuller.html hope this helps, >On Jan 21, 5:25pm, Zilvinas Rinkevicius wrote: > Subject: CCL:C80 geometry > Dear CCL users, > > Any one can point me at C80 geometry experimental determination data or just > provide me with exact C80 Ih symmetry geometry. > > Thanking in advance, > with best regards, > Zilvinas Rinkevicius, > Kaunas Technology University, > Faculty of Fundamental Sciences, > Studentu st. 50, Kaunas 3000, > Lithuania. > > > > > > _______________________________________________________ > Get 100% FREE Internet Access powered by Excite > Visit http://freelane.excite.com/freeisp > > > -= 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 > > > > >-- End of excerpt from Zilvinas Rinkevicius -- ******************************************************************************** Pascal Bonnet pascal@qorws1.uab.es Unitat Quimica Organica and Institut de Chimie Organique et Analytique Facultat de Ciences UFR Sciences - UPRES-A 6005 Universitat Autonoma de Barcelona Rue de Chartres - BP 6759 08193 Bellaterra (SPAIN) 45067 ORLEANS CEDEX 2 - France Tel: 34935811266 Tel: 0238494577 Fax: 34935811265 ******************************************************************************** From chemistry-request@server.ccl.net Mon Apr 3 05:45:12 2000 Received: from mailserver.unimi.it (mailserver.unimi.it [159.149.10.1]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id FAA13202 for ; Mon, 3 Apr 2000 05:45:12 -0400 Received: from vega (vega.farma.unimi.it [159.149.79.32]) by mailserver.unimi.it (8.9.3/8.9.3) with SMTP id LAA10203 for ; Mon, 3 Apr 2000 11:44:59 +0200 (MET DST) Message-ID: <011c01bf9d51$3f565ec0$204f959f@farma.unimi.it.farma.unimi.it> From: "Giulio Vistoli" To: "CCL" Subject: Announcing VEGA 1.1 Final Release Date: Mon, 3 Apr 2000 11:44:46 +0200 Organization: Ist. Chimica Farmaceutica MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 5.00.2615.200 X-MimeOLE: Produced By Microsoft MimeOLE V5.00.2615.200 Dear CCLers, we are glad to announce that the final 1.1 release of VEGA package is now ready for free download on our web server (http://users.unimi.it/~ddl). VEGA was developed to create a bridge between most of the molecular software packages, like Quanta/CHARMm, Insight II, MoPac, BioDock, etc. In this tool have been also implemented some features that are useful to analyze, display and manage the 3D structures of molecules. VEGA is written in high portable code (standard C language) and can be executed on a lot of hardware systems simply recompiling the source code. The program is already tested on the following operating systems: IRIX (Silicon Graphics), Windows 9x/NT PCs, Linux, NetBSD, AmigaOS, etc. The most important features implemented in VEGA are: - Supported input file formats: MSI Quanta/CHARMm CRD and DCD, Cambridge Data File (CSSR), QMC, Gromos, Interchange File Format (IFF), Tripos Sybyl (Mol2), MSI Quanta MSF, Protein Data Bank (PDB), Protein Data Bank Fat (PDBF), MSI/Biosym Insight II (.car), MoPac internal coordinates, cartesian coordinates (XYZ). - Supported output file formats: MSI Quanta/CHARMm CRD, Cambridge Data File (CSSR), Fasta, Gromos, Interchange File Format (IFF), Tripos Sybyl (Mol2), MSI Quanta MSF, Protein Data Bank (PDB), Protein Data Bank with atomic charges (PDBQ), Protein Data Bank Fat (PDBF), Protein Data Bank simplified, MSI/Biosym .car (old and new), MoPac internal coordinates, MSI/Biosym surface, MSI Quanta surface, VRML, cartesian coordinates (XYZ). - Multiple files load for assemblies creation. - Atomic charge attribution with Gasteiger method or through a template of residues. - Force field attribution for AMBER, CHARMm, CVFF, MENG and any other user defined template. A simple language to define the atom types is built-in. - Calculation of molecular surface (Van der Waals, accessible to solvent and Molecular Electrostatic Potential). - Calculation of ligand-receptor interaction energy (only with CVFF force field) for each residue involved in the binding. - Evaluation of logP (Broto/Moreau, Ghoose/Crippen, Virtual logP*) and lipole (Broto/Moreau, Ghoose/Crippen). - Dynamic trajectory analysis (interatomic distance, angle, torsion, angle between two planes, molecular surface, surface diameter, molecular volume, volume diameter, dipole, Virtual logP*). - Coordinates normalization. - Molecule solvatation with any type of cluster. - Deletion of water molecules and hydrogen atoms. - Residue renumbering. * Implemented only in full version of VEGA package. Thank you for your attention. Giulio Vistoli & Alessandro Pedretti -- Ist. di Chimica Farmaceutica e Tossicologica Viale Abruzzi, 42 I-20131 Milano (Italy) Tel. +39-02-29502230 Fax +39-02-29514197 E-Mail: giulio.vistoli@unimi.it WWW: http://users.unimi.it/~ddl From chemistry-request@server.ccl.net Mon Apr 3 04:42:42 2000 Received: from smtp.csc.fi (pobox5.csc.fi [193.166.0.99]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id EAA12899 for ; Mon, 3 Apr 2000 04:42:41 -0400 Received: from isosirri (isosirri.csc.fi [193.166.1.218]) by smtp.csc.fi (8.9.3/8.9.3/CSC) with SMTP id LAA27834 for ; Mon, 3 Apr 2000 11:42:32 +0300 From: "Leif Laaksonen" To: "Chemistry@Ccl. Net" Subject: Cerius2 trajectory file format Date: Mon, 3 Apr 2000 11:45:38 +0300 Message-ID: Hi, I have been trying to understand the Cerius2 trajectory format to be able to read them with gOpenMol. I contacted MSI and got a link to a web page with the format. However, a hex dump of the trajectory file showed me that the internal format did not resemble the description I got from MSI. Is there anybody on the net who help me to get the right format? Regards, -leif laaksonen From chemistry-request@server.ccl.net Mon Apr 3 08:31:44 2000 Received: from tdsede-exg.tdsede.dom ([194.235.134.66]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id IAA15083 for ; Mon, 3 Apr 2000 08:31:43 -0400 Received: by TDSEDE.EXG with Internet Mail Service (5.5.2232.9) id ; Mon, 3 Apr 2000 13:32:29 +0100 Message-ID: <314CB0E40556D2118D930000C07CAAF60EC0E5@TDSEDE.EXG> From: Paulo Couto To: "Computational Chemistry List (E-mail)" Subject: SCF convergence and SCI-PCM using G98 Date: Mon, 3 Apr 2000 13:32:28 +0100 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2232.9) Content-Type: text/plain Greetings All I am trying to run geometry optimization calculations on water clusters ( n=1-6 ), using G98 at the HF/6-311++G** theory level with the SCRF=SCIPCM option and water as solvent. The problem is that SCF's don't converge at all. Can anyone suggest a better parametrization to this method or an alternative method to simulate solvation effects at this theory level? References are also welcome. ########## Sample input for single center method, for the water molecule, using a special grid: #P RHF/6-311++G** SCF=(tight,MaxCycle=512) GUESS=always TEST #OPT=(MaxCycle=100) SCRF=(SCIPCM) NOSYMM TEST ... 78.39 0.0004 434 1 2 ############ I also tried the multicenter method with default parametrization and different sets of integration points. The result is the same: no SCF convergence. Thanks in Advance Paulo Couto (pauloc@tduarte.pt) From chemistry-request@server.ccl.net Mon Apr 3 09:38:07 2000 Received: from lithium.theochem.uni-duesseldorf.de (root@lithium.theochem.uni-duesseldorf.de [134.99.82.3]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id JAA15493 for ; Mon, 3 Apr 2000 09:38:06 -0400 Received: from borussia.theochem.uni-duesseldorf.de (borussia.theochem.uni-duesseldorf.de [134.99.82.13]) by lithium.theochem.uni-duesseldorf.de (8.8.7/8.8.8) with ESMTP id PAA13048; Mon, 3 Apr 2000 15:37:52 +0200 Received: from [[UNIX: localhost]] ([[UNIX: localhost]]) by borussia.theochem.uni-duesseldorf.de (8.8.7/8.8.8) id PAA01057; Mon, 3 Apr 2000 15:37:54 +0200 From: Wibke Sudholt Reply-To: wibke@theochem.uni-duesseldorf.de To: CHEMISTRY@ccl.net Subject: Looking for a Code to Solvate Molecules Date: Mon, 3 Apr 2000 14:59:00 +0200 X-Mailer: KMail [version 0.7.9] Content-Type: text/plain Cc: wibke@theochem.uni-duesseldorf.de MIME-Version: 1.0 Message-Id: <00040315375302.00975@borussia> Content-Transfer-Encoding: 8bit Dear CCLers, I am looking for a program (preferably freeware Fortran code) which is capable of the following (or parts of it): * reads in the xyz coordinates of a solute molecule and reads in the xyz coordinates of an (arbitrary, not only water) solvent molecule * generates xyz coordinates of a cubic box filled with the solute molecule surrounded by some kind of random mixture of solvent molecules (needs not to be equilibrated or may have some order left) * controles the size of the system by density, box size, number of solvent molecules etc. I have checked the internet with no success, as most of such programs can only handle water or need predefined boxes filled with solvent molecules (programs which generate those would also be a help). Is anybody out there aware of such a program and willing to share his/her code/knowledge with me? Thank you very much in advance for your help Wibke Sudholt Institute of Theoretical Chemistry Heinrich-Heine-University Duesseldorf, Germany wibke@theochem.uni-duesseldorf.de From chemistry-request@server.ccl.net Mon Apr 3 11:41:05 2000 Received: from unomail.unomaha.edu (unomail.unomaha.edu [137.48.1.6]) by server.ccl.net (8.8.7/8.8.7) with SMTP id LAA16397 for ; Mon, 3 Apr 2000 11:41:04 -0400 From: Douglas_Stack/CAS/UNO/UNEBR@unomail.unomaha.edu Received: by unomail.unomaha.edu(Lotus SMTP MTA v4.6.4 (830.2 3-23-1999)) id 862568B6.0055962F ; Mon, 3 Apr 2000 10:34:50 -0500 X-Lotus-FromDomain: UNIVERSITY OF NEBRASKA To: chemistry@ccl.net Message-ID: <862568B6.00559368.00@unomail.unomaha.edu> Date: Mon, 3 Apr 2000 10:34:40 -0500 Subject: Scaling of G98 on Clusters Mime-Version: 1.0 Content-type: text/plain; charset=us-ascii Content-Disposition: inline With the recent discussion of how G98 scales on Beowulf clusters, I have an additional question (we are thinking of putting together a cluster for G98 calculations and are deciding about specifics of configuration). If there seems to be little gain above 8 CPUs using 100MB ether net communication, is it possible to put together a 32 CPU cluster, use Linda for the G98 code, then have cluster management software give 8 CPUs per Gaussian job? In other words, using the Link 0 command, %NProc=8, would a 32 CPU cluster be able to run 4 jobs at 8 CPU each and still provide maximum usage to Gaussian users. Or does a Beowulf cluster require all CPUs by used in tandem. This leads to other question about cluster management software. I've seen several mentioned on different web sites. Any experience as to which offers the best mix of ease and functionality? Douglas E. Stack Assistant Professor Department of Chemistry University of Nebraska at Omaha Omaha, NE 68182-0109 (402) 554-3647 (402) 554-3888 (fax) destack@unomaha.edu From chemistry-request@server.ccl.net Mon Apr 3 10:36:56 2000 Received: from ccl.net (atlantis.ccl.net [192.148.249.4]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id KAA16134 for ; Mon, 3 Apr 2000 10:36:56 -0400 Received: from iacs.res.in (root@mahendra.iacs.res.in [202.54.54.226]) by ccl.net (8.9.3/8.9.3/OSC 2.0) with ESMTP id KAA17076 for ; Mon, 3 Apr 2000 10:36:37 -0400 (EDT) Received: from spsc.iacs.res.in ([192.168.1.112]) by iacs.res.in (8.8.5/8.8.5) with SMTP id UAA16434 for ; Mon, 3 Apr 2000 20:06:58 +0530 Message-ID: <001701bf9d7a$444e0d00$7001a8c0@iacs.res.in> From: "Mr. Subhasis Panja" To: Subject: help Date: Mon, 3 Apr 2000 20:08:21 +0530 MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 5.00.2314.1300 X-MimeOLE: Produced By Microsoft MimeOLE V5.00.2314.1300 Dear Sir, I am a student and I like to use the software MOPAC7 in purpose of some quantum chemical calcillation, in this regards to calcullate the energy states of a molecule in solution phase, I should have to include the SOLVENT parameters but I dont know the actual kewwords for including the solvent parameter and how to use that. So if you kindly suggest me how I can include the solvent parameters in calculation of energy states in solution phase, I will be grateful to you. Thanking you Sincerely your's Subhasis Panja My e-mail address is spsp@mahendra.iacs.res.in From chemistry-request@server.ccl.net Mon Apr 3 12:38:57 2000 Received: from mailer.psc.edu (mailer.psc.edu [128.182.58.100]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id MAA16752 for ; Mon, 3 Apr 2000 12:38:56 -0400 Received: from pscuxc.psc.edu (pscuxc.psc.edu [128.182.66.177]) by mailer.psc.edu (8.9.3/8.9.3/psc) with ESMTP id MAA08671 for ; Mon, 3 Apr 2000 12:38:43 -0400 (EDT) Received: from localhost (wymore@localhost) by pscuxc.psc.edu (8.9.3/8.9.3/psc) with ESMTP id LAA00967 for ; Mon, 3 Apr 2000 11:38:42 -0500 (EST) Date: Mon, 3 Apr 2000 11:38:42 -0500 (EST) From: Troy Wymore To: chemistry@server.ccl.net Subject: PSC BIOMEDICAL INITIATIVE WORKSHOPS 2000 Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII ************************************************************* PSC BIOMEDICAL INITIATIVE WORKSHOPS 2000 Pittsburgh Supercomputing Center's (PSC)Biomedical Initiative is hosting four NIH-sponsored training workshops this summer. We are asking your help once again in passing this information on to other researchers who might be interested in applying. Brief descriptions of the sessions are below but full details, including on-line application forms, may be found at our Web site: http://www.psc.edu/biomed/workshops/workshops.htm In addition, the web site for each individual workshop is cited following the respective description. METHODS AND APPLICATIONS OF MOLECULAR DYNAMICS TO BIOPOLYMERS JUNE 4-7 Application Deadline: April 21 This workshop will familiarize biomedical researchers with computational methods and provide practice in applying supercomputing resources to problems of concern in molecular dynamics. There will be lectures, extensive hands-on sessions, and discussion of general aspects of molecular dynamic software. CHARMM will be discussed in detail. Participants are encouraged to work on the examples provided or on their own experimental data. No prior supercomputing experience is necessary. For specific details, including an electronic application form, see: http://www.psc.edu/biomed/workshops/workshops.htm#MAMD BUILDING COMPUTING CLUSTERS FOR BIOMEDICAL RESEARCH JULY 13-15 Application Deadline: June 1 This workshop will provide a thorough discussion of the design, assembly, and maintenance of small (< 100 nodes) computing clusters, including relevant software and technical details. It will begin with a discussion of parallel programming to provide a context for the basic issues; proceed to an overview of components and definitions of common terms; and conclude with performance discussions for several known biomedical applications. A hands-on session in which participants will interact with a small "demo" cluster, submitting jobs through a scheduler and monitoring job and cluster status will be included. Among the discussion topics will be: "How do I get the best performance for my money?" "What hardware is appropriate for my application?" "How do I administer my cluster?" and "What should I do about security?" For specific details, including an electronic application form, see: http://www.psc.edu/biomed/workshops/workshops.htm#biomedcluster2000 STRUCTURE DETERMINATION USING NMR JULY 26-29 Application Deadline: June 14 The objective of this workshop is to introduce participants to the different techniques for the elucidation of solution structures of biological macromolecules from nuclear magnetic resonance data. The programs AMBER and MORASS will be discussed. In addition to lectures, there will be extensive hands-on sessions. Participants are encouraged to work on the examples provided or on their own experimental data. No prior supercomputing experience is necessary. For specific details, including an electronic application form, see: http://www.psc.edu/biomed/workshops/workshops.htm#NMR NUCLEIC ACID AND PROTEIN SEQUENCE ANALYSIS AUGUST 13-18 Application Deadline: June 30 This intense five-day workshop will teach the basics of sequence analysis, including: remote supercomputing; inferring structures and functions using internet alignments; pattern identification; inverse structure prediction; and visualization of macromolecular structures. Special emphasis will be placed on parameter selection and the mathematical and statistical properties of the algorithms and methods presented. Information will also be provided on the latest pattern identification techniques, including hidden Markov models, advanced position-specific weight matrix techniques, and bayesan estimation. For specific details, including an electronic application form, see: http://www.psc.edu/biomed/workshops/workshops.htm#NAPSA If you have any questions, please contact Nancy Blankenstein at blankens@psc.edu or 412/268-4960 (FAX). Many thanks for your interest and help. ******************************************************************************* From chemistry-request@server.ccl.net Mon Apr 3 13:40:51 2000 Received: from ice.lanl.gov (ice.lanl.gov [128.165.22.6]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id NAA17614 for ; Mon, 3 Apr 2000 13:40:50 -0400 Received: from localhost (localhost [[UNIX: localhost]]) by ice.lanl.gov (8.9.3/8.9.3) id LAA01128; Mon, 3 Apr 2000 11:40:08 -0600 From: Matt Challacombe Reply-To: MChalla@T12.LANL.Gov Organization: Group T-12, Theoretical Chemistry and Molecular Physics To: Douglas_Stack/CAS/UNO/UNEBR@unomail.unomaha.edu, chemistry@ccl.net Subject: Re: CCL:Scaling of G98 on Clusters Date: Mon, 3 Apr 2000 11:38:48 -0600 X-Mailer: KMail [version 1.0.28] Content-Type: text/plain References: <862568B6.00559368.00@unomail.unomaha.edu> In-Reply-To: <862568B6.00559368.00@unomail.unomaha.edu> MIME-Version: 1.0 Message-Id: <00040311400800.00953@ice> Content-Transfer-Encoding: 8bit Hi Douglas, I think you want a queing system. PBS is the queing system of choice for linux clusters. -Matt On Mon, 03 Apr 2000, Douglas_Stack/CAS/UNO/UNEBR@unomail.unomaha.edu wrote: > With the recent discussion of how G98 scales on Beowulf clusters, I have an > additional question (we are thinking of putting together a cluster for G98 > calculations and are deciding about specifics of configuration). > > If there seems to be little gain above 8 CPUs using 100MB ether net > communication, is it possible to put together a 32 CPU cluster, use Linda for > the G98 code, then have cluster management software give 8 CPUs per Gaussian > job? In other words, using the Link 0 command, %NProc=8, would a 32 CPU cluster > be able to run 4 jobs at 8 CPU each and still provide maximum usage to Gaussian > users. Or does a Beowulf cluster require all CPUs by used in tandem. > > This leads to other question about cluster management software. I've seen > several mentioned on different web sites. Any experience as to which offers the > best mix of ease and functionality? > > > > Douglas E. Stack > Assistant Professor > Department of Chemistry > University of Nebraska at Omaha > Omaha, NE 68182-0109 > (402) 554-3647 > (402) 554-3888 (fax) > destack@unomaha.edu > > > > -= 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 -- +-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ + Matt Challacombe, Ph.D. http://www.t12.lanl.gov/~mchalla/ + + Los Alamos National Laboratory email: mchalla@t12.lanl.gov + + Theoretical Division vmail: (505) 698-4112 + + Group T-12, Mail Stop B268 phone: (505) 665-5905 + + Los Alamos, New Mexico 87545 fax: (505) 665-3909 + + + + "The secret to mountain biking is pretty simple. The slower you go + + the more likely it is you'll crash." -- Julie Furtado + +-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ From chemistry-request@server.ccl.net Mon Apr 3 13:52:07 2000 Received: from deimos.cber.nih.gov (deimos.cber.nih.gov [128.231.52.2]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id NAA17699 for ; Mon, 3 Apr 2000 13:52:07 -0400 Received: from localhost by deimos.cber.nih.gov with SMTP (1.37.109.14/16.2) id AA112593537; Mon, 3 Apr 2000 13:38:58 -0400 Date: Mon, 3 Apr 2000 13:38:57 -0400 (EDT) From: Rick Venable To: Wibke Sudholt Cc: CHEMISTRY@ccl.net Subject: Re: CCL:Looking for a Code to Solvate Molecules In-Reply-To: <00040315375302.00975@borussia> Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII I have some CHARMM scripts I've developed for solvating within any orthorhombic shape (square corners), which I can provide if you are interested in them. I've also recently developed generalized scripts for adding ions to the resulting box, by replacing selected water molecules. On Mon, 3 Apr 2000, Wibke Sudholt wrote: > I am looking for a program (preferably freeware Fortran code) which is capable > of the following (or parts of it): > * reads in the xyz coordinates of a solute molecule and reads in the xyz > coordinates of an (arbitrary, not only water) solvent molecule > * generates xyz coordinates of a cubic box filled with the solute molecule > surrounded by some kind of random mixture of solvent molecules (needs not to > be equilibrated or may have some order left) > * controles the size of the system by density, box size, number of solvent > molecules etc. > I have checked the internet with no success, as most of such programs can only > handle water or need predefined boxes filled with solvent molecules (programs > which generate those would also be a help). > > Is anybody out there aware of such a program and willing to share his/her > code/knowledge with me? > > Thank you very much in advance for your help > > Wibke Sudholt > Institute of Theoretical Chemistry > Heinrich-Heine-University > Duesseldorf, Germany > wibke@theochem.uni-duesseldorf.de > > -= 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 > > > > > > Rick Venable =====\ |=| "Eschew Obfuscation" FDA/CBER Biophysics Lab |____/ |=| Bethesda, MD U.S.A. | \ / |=| ( Not an official statement or Rick_Venable@nih.gov | \ / |=| position of the FDA; for that, rvenable@speakeasy.org \/ |=| see http://www.fda.gov ) From chemistry-request@server.ccl.net Mon Apr 3 14:51:31 2000 Received: from hermes.bmc.uu.se (hermes.bmc.uu.se [130.238.39.159]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id OAA18055 for ; Mon, 3 Apr 2000 14:51:30 -0400 Received: from alpha2.bmc.uu.se ([130.238.37.65]) by hermes.bmc.uu.se (Post.Office MTA v3.5.3 release 223 ID# 0-62649U1500L1000S0V35) with SMTP id se; Mon, 3 Apr 2000 20:52:54 +0200 Received: from zorn.bmc.uu.se by alpha2.bmc.uu.se (5.65v3.2/1.1.10.5/07Jan00-1145AM) id AA23212; Mon, 3 Apr 2000 20:51:31 +0200 Date: Tue, 4 Apr 2000 00:11:56 +0200 (CEST) From: David van der Spoel X-Sender: spoel@zorn.bmc.uu.se To: wibke@theochem.uni-duesseldorf.de Cc: CHEMISTRY@ccl.net Subject: solvate Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Such a program "genbox" comes with the GROMACS set: http://md.chem.rug.nl/~gmx (and probably with many other MD packages). genbox supports rectangular and triclinic boxes (which basically means all periodic boxes) as well as nonperiodic systems (solvent layer). The type of solvent is determined by your input file, and can be any organic molecule, or mixture thereof. Groeten, David. ________________________________________________________________________ Dr. David van der Spoel Biomedical center, Dept. of Biochemistry s-mail: Husargatan 3, Box 576, 75123 Uppsala, Sweden e-mail: spoel@xray.bmc.uu.se www: http://zorn.bmc.uu.se/~spoel phone: 46 18 471 4205 fax: 46 18 511 755 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++