From chemistry-request@server.ccl.net Tue Apr 15 15:19:47 2003 Received: from mail.fqspl.com.pl ([212.244.147.20]) by server.ccl.net (8.11.6/8.11.0) with SMTP id h3FJJl309987 for ; Tue, 15 Apr 2003 15:19:47 -0400 Received: (qmail 27413 invoked by uid 505); 15 Apr 2003 19:10:31 -0000 Received: from magda@fqspl.com.pl by mail by uid 502 with qmail-scanner-1.13 ( Clear:. Processed in 0.545425 secs); 15 Apr 2003 19:10:31 -0000 Received: from pn223.poznan.cvx.ppp.tpnet.pl (HELO magda) (217.99.115.223) by mail.fqspl.com.pl with SMTP; 15 Apr 2003 19:10:30 -0000 Message-ID: <06be01c30383$88271e50$ef7063d9@fqspl.com.pl> Reply-To: "Karabon Magdalena" From: "Karabon Magdalena" To: Subject: Seminar: "Property Prediction and Reaction Modelling with Computer Aided Chemistry" Date: Tue, 15 Apr 2003 21:14:11 +0200 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 5.50.4920.2300 X-MimeOLE: Produced By Microsoft MimeOLE V5.50.4920.2300 Seminar: "Property Prediction and Reaction Modelling with Computer Aided Chemistry" date: 24th of April, 2003 (13:30 - 15:00) place: Crowne Plaza Hotel, Heathrow, London, UK The prediction of biological, chemical and physical properties such as reaction rates, UV-Visible & IR spectra, water solubility, vapour pressure, polymer properties, environmental fate, etc., will be illustrated with CAChe, a computer aided chemistry package for the experimental chemist that runs on a desktop PC. Prediction of reaction pathways, thermodynamics and kinetics will also be discussed. Computer aided chemistry can be used to improve success rate in the laboratory and speed up research by pre-screening candidates and testing ideas, before investing valuable laboratory time. This presentation reviews the expanding scope of computer-aided chemistry. (presentation - 55 mins; demonstration - 25 mins) Sponsored by Fujitsu. For details and free registration please contact Ms. Magda Karabon at magda@fqspl.com.pl or call: + 48 12 429 43 45 From chemistry-request@server.ccl.net Tue Apr 15 15:19:49 2003 Received: from mail.fqspl.com.pl ([212.244.147.20]) by server.ccl.net (8.11.6/8.11.0) with SMTP id h3FJJm309993 for ; Tue, 15 Apr 2003 15:19:49 -0400 Received: (qmail 27421 invoked by uid 505); 15 Apr 2003 19:10:32 -0000 Received: from magda@fqspl.com.pl by mail by uid 502 with qmail-scanner-1.13 ( Clear:. Processed in 0.44895 secs); 15 Apr 2003 19:10:32 -0000 Received: from pn223.poznan.cvx.ppp.tpnet.pl (HELO magda) (217.99.115.223) by mail.fqspl.com.pl with SMTP; 15 Apr 2003 19:10:31 -0000 Message-ID: <06bf01c30383$88f9feb0$ef7063d9@fqspl.com.pl> Reply-To: "Karabon Magdalena" From: "Karabon Magdalena" To: Subject: Seminar: Active-Site Identification, Ligand Design and QSAR; New Windows-based SW Tools Date: Tue, 15 Apr 2003 21:15:40 +0200 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 5.50.4920.2300 X-MimeOLE: Produced By Microsoft MimeOLE V5.50.4920.2300 Seminar: "Active-Site Identification, Ligand Design and QSAR; New Windows-based SW Tools" date: 24th of April, 2003 (10.30 am - noon) place: Crowne Plaza Hotel, Heathrow, London, UK A presentation and demonstration of the latest Windows-based tools for analysing proteins, locating active sites and designing ligands will be offered, including examples of homology modelling, rational drug design, pharmocaphore modelling, 3D sequence alignment and superposition, and novel quantum methods for calculating electronic properties of whole proteins. Quantitative Structure-activity Relationships (QSAR) and fast screening methods for predicting properties such as pKa, water solubility, HIA, Rule-of-5, carcinogenicity, antibacterial activity, etc. will also be reviewed. (presentation - 55 mins; demonstration - 25 mins) Sponsored by Fujitsu. For details and free registration please contact Ms. Magda Karabon at magda@fqspl.com.pl or call: + 48 12 429 43 45 From chemistry-request@server.ccl.net Wed Apr 16 01:50:53 2003 Received: from dux.ru ([193.125.210.65]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h3G5or323567 for ; Wed, 16 Apr 2003 01:50:53 -0400 Received: from dux.ru (localhost [127.0.0.1]) by dux.ru (8.12.6/8.12.6) with ESMTP id h3G5vgG3002872 for ; Wed, 16 Apr 2003 09:57:50 +0400 (MSD) (envelope-from dima@xenon.spb.ru) Received: (from uucp@localhost) by dux.ru (8.12.6/8.12.1/Submit) with UUCP id h3G5vfFn002870 for chemistry@ccl.net; Wed, 16 Apr 2003 09:57:41 +0400 (MSD) (envelope-from dima@xenon.spb.ru) Received: from goblin ([192.168.3.2]) by shadow with smtp (Exim 3.35 #1 (Debian)) id 195fmG-00042u-00 for ; Wed, 16 Apr 2003 09:48:12 +0400 Message-ID: <00d301c303db$da947770$0203a8c0@goblin> From: "Dmitry Rozmanov" To: "CCL" References: Subject: Re: Gamess: problems with DFT Hessian Date: Wed, 16 Apr 2003 09:48:49 +0400 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 5.50.4807.1700 X-MimeOLE: Produced By Microsoft MimeOLE V5.50.4910.0300 Thank you alot. I will follow this way. I think PES is quite flat in my case, it is in the region of water rotation and barriers are low. So, what are resonable values for "good" convergence then? Ten times less then defaults? ---Dmitry. ----- Original Message ----- From: "Gerard Harbison" To: "Dmitry Rozmanov" Sent: Wednesday, April 16, 2003 6:04 AM Subject: Re: Gamess: problems with DFT Hessian > > On Tuesday, April 15, 2003, at 05:26 PM, Dmitry Rozmanov wrote: > > > Dmitry: > > Several things could be wrong; for example, if you don't have your > statpt convergence adequately tight and the potential surface is pretty > flat, an optimization can terminate quite distant from the stationary > point. Similarly, if the scf convergence isn't tight, or if you've used > defaults for itol, icut and possibly qmttol, there may be significant > inaccuracy in calculating your gradients (remember that taking a first > derivative generally makes a problem more ill-conditioned). Generally, > after running an optimization with standard defaults, I run a second > optimization with very tight convergence criteria, before calculating > the Hessian. if you don't do this, even if the Hessian runs, you'll > probably get rather poor values for the energies and eigenstates. > > Gerard S Harbison > Professor of Chemistry > University of Nebraska at Lincoln > gerry@setanta.unl.edu > From chemistry-request@server.ccl.net Wed Apr 16 01:08:38 2003 Received: from ccl.net ([192.148.249.4]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h3G58c321869 for ; Wed, 16 Apr 2003 01:08:38 -0400 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 h3G58ct21041 for ; Wed, 16 Apr 2003 01:08:38 -0400 (EDT) Date: Wed, 16 Apr 2003 01:08:35 -0400 (EDT) From: Jan Labanowski To: chemistry@ccl.net Subject: EMRS FALL MEETING AND High Presure School (fwd) Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=X-UNKNOWN Content-Transfer-Encoding: 8BIT European Materials Research Society 2003 FALL MEETING Warsaw (Poland) September 15th - 19th, 2003 http://www.unipress.waw.pl/emrs European Materials Research Society 2003 FALL MEETING Warsaw University of Technology Warsaw University of Technology Warsaw (Poland) September 15th - 19th, 2003 e-mail: emrs@unipress.waw.pl Meeting Chairs K. J. Kurzydlowski e-mail: kjk@inmat.pw.edu.pl W. £ojkowski e-mail: wl@unipress.waw.pl A. Mycielski e-mail: mycie@ifpan.edu.pl P. Siffert e-mail: emrs@phase.c-strasbourg.fr The EMRS Fall meeting will be the counterpart of the well established Spring Meetings in Strasbourg. It will support further integration of Central Europe in the European Research Area and better exploiting of its huge research potential.. Particular attention will be given to interdisciplinary training aspect, and participation of young researchers. The 2003 Fall Meeting will include 7 symposia, plenary session, and some training activities for young researchers or scientists wishing to extend their expertise to new fields. It is intended that the conference will be augmented by an exhibition of products and services of interest to those participating in the event. Symposium A : NOVEL WIDE BANDGAP MATERIALS FOR OPTOELECTRONIC AND ELECTRONIC APPLICATIONS Symposium B : DEVELOPMENT OF METHODS FOR CHARACTERIZING THE MICROSTRUCTURE OF NOVEL MATERIALS Symposium C : 5th INTERNATIONAL WORKSHOP ON MOLECULAR BEAM EPITAXY AND VAPOUR PHASE EPITAXY GROWTH PHYSICS AND TECHNOLOGY Symposium D : COLOSSAL MAGNETORESISTANCE - NEW MATERIALS AND NEW IDEAS Symposium E : MATERIALS FOR MEDICAL APPLICATIONS Symposium F : FUNCTIONAL NANOMATERIALS FOR OPTOLECTRONIC AND OTHER APPLICATIONS Symposium G : BULK AND GRADED NANOMETALS Sattelite Event : Vth HIGH PRESSURE SCHOOL on High Pressure Methods in Biotechnology -- ========================================================== Witold Lojkowski, Doc. Dr hab. Head of Nanomaterials Lab, Coordinator of Center of Excellence High Pressure Research Center, Polish Academy of Sciences Sokolowska 29, 01-142 Warsaw, Poland. POBox65 Phone +48 22 6324302, fax +48 22 6324218 e-mail wl@unipress.waw.pl, http://www.unipress.waw.pl ========================================================= From chemistry-request@server.ccl.net Wed Apr 16 03:11:25 2003 Received: from mail.fqspl.com.pl ([212.244.147.20]) by server.ccl.net (8.11.6/8.11.0) with SMTP id h3G7BO326249 for ; Wed, 16 Apr 2003 03:11:25 -0400 Received: (qmail 2787 invoked by uid 505); 16 Apr 2003 07:02:11 -0000 Received: from victor@fqspl.com.pl by mail by uid 502 with qmail-scanner-1.13 ( Clear:. Processed in 0.044542 secs); 16 Apr 2003 07:02:11 -0000 Received: from unknown (HELO PION) (212.244.147.4) by mail.fqspl.com.pl with SMTP; 16 Apr 2003 07:02:11 -0000 Message-ID: <014501c303e7$656a7470$2d0a0a0a@fqspl.com.pl> From: "Victor Anisimov" To: Cc: References: <00d201c3031f$2b274810$2d0a0a0a@fqspl.com.pl> <3E9C155F.348B9BD2@attglobal.net> Subject: Re: CCL:New linear scaling method Date: Wed, 16 Apr 2003 09:11:26 +0200 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 6.00.2800.1106 X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2800.1106 Dear CCLers, John McKelvey has asked me a question regarding the local minimum problem. I believe the problem is very important to be discussed on the list. Therefore I post my answer to the list. ----- Original Message ----- From: > Victor, > > How would the problem of local minima be handled if the program were to do a > geometry optimizatopn on 10**5 atoms? > > Regards! > > John McKelvey Dear John, Perhaps you agree, that the local minimum problem is a separate one to the linear scaling solution of the diagonalization of Fock matrix. LocalSCF method itself resolves just the diagonalization problem. The same do other respected linear scaling methods, e.g. MOZYME, D&C, CG-DMS. However I agree that the local minimum problem has to be addressed if one is serious about protein modeling. This requires molecular dynamics averaging applied after some preliminary structure refinement done by geometry optimization. Taking the present program code one can do full geometry optimization for 100,000+ real protein on a single-CPU PC. I bet QM MD for about 1,000 atoms protein is a feasible job for a 10 CPUs Linux cluster nowadays. Although this has to be implemented first. Full QM MD modeling of proteins is not a long future. The present LocalSCF code works just on 1 CPU. Being parallelized it could utilize about 1000 CPUs quite effectively. This unusual level of parallelization is not just my imagination. This capability comes from extremely high localization level of the LocalSCF method. As the LocalSCF preprint shows, LMOs expanded just on 30 atomic centers are enough to get 0.001 RMS error on atomic charges. This level of localization is extremely favorable for parallelization. We already made some tests on 1 CPU machine applying D&C technique on the top of LALM, which is a similar to the LocalSCF engine. 1,000,000 atoms irregular linear peptide built from random combination of 14 different amino acids was divided on 300 fragments. Calculating each fragment sequentially on the one CPU gave the energy converged in 7 hours. Of course, the convergence criterion was quite loose but this was enough to show a feasibility of the D&C / LocalSCF concept. I believe the publishing of the LocalSCF paper makes a valuable contribution for the wide dissemination of the idea. As I mentioned in my previous posting the preprint is available from the Chemistry Preprint Server by URL http://preprint.chemweb.com/physchem/0304005 The server requires registration, but the registration is free. Hope, I answered your question. With kind regards, Victor -- Victor Anisimov FQS Poland From chemistry-request@server.ccl.net Wed Apr 16 07:58:16 2003 Received: from prserv.net ([32.97.166.51]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h3GBwG317265 for ; Wed, 16 Apr 2003 07:58:16 -0400 Received: from attglobal.net (dhcp065-029-075-111.indy.rr.com[65.29.75.111]) by prserv.net (asmtp1) with SMTP id <20030416115807251045iamve> (Authid: jmmckel); Wed, 16 Apr 2003 11:58:07 +0000 Message-ID: <3E9D0122.A23FB4E8@attglobal.net> Date: Wed, 16 Apr 2003 07:07:14 +0000 From: jmmckel@attglobal.net Reply-To: jmmckel@attglobal.net X-Mailer: Mozilla 4.51 [en]C-CCK-MCD (WinNT; I) X-Accept-Language: en MIME-Version: 1.0 To: Victor Anisimov CC: chemistry@ccl.net Subject: Re: CCL:New linear scaling method References: <00d201c3031f$2b274810$2d0a0a0a@fqspl.com.pl> <3E9C155F.348B9BD2@attglobal.net> <014501c303e7$656a7470$2d0a0a0a@fqspl.com.pl> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hello, My comments were in fact related to optimization of geometries for systems having 10**5 atoms, i.e. very large systems. This being made feasable because of MOPAC's extremely fast LocalSCF procedure. John McKelvey Victor Anisimov wrote: > Dear CCLers, > > John McKelvey has asked me a question regarding the local minimum > problem. I believe the problem is very important to be discussed on the > list. Therefore I post my answer to the list. > > ----- Original Message ----- > From: > > > Victor, > > > > How would the problem of local minima be handled if the program were to do > a > > geometry optimizatopn on 10**5 atoms? > > > > Regards! > > > > John McKelvey > > Dear John, > > Perhaps you agree, that the local minimum problem is a separate one to > the linear scaling solution of the diagonalization of Fock matrix. LocalSCF > method itself resolves just the diagonalization problem. The same do other > respected linear scaling methods, e.g. MOZYME, D&C, CG-DMS. > > However I agree that the local minimum problem has to be addressed if one > is serious about protein modeling. This requires molecular dynamics > averaging > applied after some preliminary structure refinement done by geometry > optimization. > > Taking the present program code one can do full geometry optimization > for 100,000+ real protein on a single-CPU PC. I bet QM MD for about > 1,000 atoms protein is a feasible job for a 10 CPUs Linux cluster nowadays. > Although this has to be implemented first. > > Full QM MD modeling of proteins is not a long future. The present LocalSCF > code > works just on 1 CPU. Being parallelized it could utilize about 1000 CPUs > quite > effectively. This unusual level of parallelization is not just my > imagination. > This capability comes from extremely high localization level of the > LocalSCF > method. As the LocalSCF preprint shows, LMOs expanded just on 30 atomic > centers are enough to get 0.001 RMS error on atomic charges. This level of > localization is extremely favorable for parallelization. > > We already made some tests on 1 CPU machine applying D&C technique on > the top of LALM, which is a similar to the LocalSCF engine. 1,000,000 atoms > irregular linear peptide built from random combination of 14 different amino > acids > was divided on 300 fragments. Calculating each fragment sequentially on the > one CPU gave the energy converged in 7 hours. Of course, the convergence > criterion was quite loose but this was enough to show a feasibility of the > D&C / LocalSCF concept. > > I believe the publishing of the LocalSCF paper makes a valuable contribution > for > the wide dissemination of the idea. As I mentioned in my previous posting > the > preprint is available from the Chemistry Preprint Server by URL > http://preprint.chemweb.com/physchem/0304005 > The server requires registration, but the registration is free. > > Hope, I answered your question. > > With kind regards, > Victor > > -- > Victor Anisimov > FQS Poland From jkl@ccl.net Tue Apr 15 00:12:31 2003 -0400 Return-Path: Message-ID: <20030415041230.18117.qmail@web12702.mail.yahoo.com> Received: from [203.197.255.52] by web12702.mail.yahoo.com via HTTP; Mon, 14 Apr 2003 21:12:30 PDT Date: Mon, 14 Apr 2003 21:12:30 -0700 (PDT) From: pankaj in your mailbox Reply-To: pankajdaga80@yahoo.com Subject: problem To: jkl@ccl.net MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Dear ccl.net Can anybody suggest me the way to carry out the geometry optimisation of the organic salts using MOPAC. for example i have a molecule which is tertiary amine. I want to carry out the geometry optimisation of the same and its hydrochloride salt. Is there a specific way to do it, as one cannot fix the distance between the N and Cl ions. this will lead to increase in the energy. Please suggest me a way out. Thanking you you can send your replies to at prdaga2001*[at]*yahoo.com thanking you cheeres Pankaj __________________________________________________ Do you Yahoo!? The New Yahoo! Search - Faster. Easier. Bingo http://search.yahoo.com From chemistry-request@server.ccl.net Wed Apr 16 08:50:26 2003 Received: from etsuex1.etsu.edu ([151.141.8.103]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h3GCoQ319195 for ; Wed, 16 Apr 2003 08:50:26 -0400 X-MimeOLE: Produced By Microsoft Exchange V6.0.6249.0 content-class: urn:content-classes:message MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Subject: AMBER? Date: Wed, 16 Apr 2003 08:48:47 -0400 Message-ID: X-MS-Has-Attach: X-MS-TNEF-Correlator: Thread-Topic: AMBER? Thread-Index: AcMEFokdeo/Shm83EdePkABAlXb8og== From: "Close, David M." To: Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id h3GCoT319196 I tried to do an AMBER calculation on guanine. The Gaussian manual said GaussView would generate the coordinates for this calculation. I tried this, but the calculation fails with 3 comments: stretching parameters undefined and 8 comments bending parameters undefined and a final comment not enough parameters to run AMBER. I do not have any information on AMBER other than the original 1995 JACS article. Any hints on how to proceed? Regards, Dave Close. From chemistry-request@server.ccl.net Wed Apr 16 09:15:56 2003 Received: from webmail.ufpe.br ([150.161.179.200]) by server.ccl.net (8.11.6/8.11.0) with SMTP id h3GDFk320223 for ; Wed, 16 Apr 2003 09:15:47 -0400 Received: (qmail 20078 invoked from network); 16 Apr 2003 12:34:50 -0000 Received: from localhost (HELO ufpe.br) (127.0.0.1) by 0 with SMTP; 16 Apr 2003 12:34:50 -0000 Received: from 150.161.5.227 (SquirrelMail authenticated user vivianni) by www.webmail.ufpe.br with HTTP; Wed, 16 Apr 2003 09:34:50 -0300 (BRT) Message-ID: <1282.150.161.5.227.1050496490.squirrel@www.webmail.ufpe.br> Date: Wed, 16 Apr 2003 09:34:50 -0300 (BRT) Subject: nwchem From: To: X-Priority: 3 Importance: Normal X-Mailer: SquirrelMail (version 1.2.11) MIME-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit Dear CCLers, I need results about charges for unit atoms. In the "nwchem" there is the "define" function. How I can use it? I didn´t undertand the manual. for example:???? c x y z h x y z h x y z h x y z define 1 1 2 3 4 (i.e, group 1 with the atoms 1, 2, 3 and 4)??????? Thanks, Vivianni. From chemistry-request@server.ccl.net Wed Apr 16 12:15:34 2003 Received: from ns0.scripps.edu ([192.42.82.58]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h3GGFX327365 for ; Wed, 16 Apr 2003 12:15:34 -0400 Received: from antigen.scripps.edu (antigen.scripps.edu [137.131.200.100]) by ns0.scripps.edu (8.11.7/TSRI-4.1rx) with SMTP id h3GGFWE11866 for ; Wed, 16 Apr 2003 09:15:33 -0700 (PDT) Received: from relay1.scripps.edu(137.131.200.29) by antigen.scripps.edu via csmap id 10215; Wed, 16 Apr 2003 09:05:22 -0700 (PDT) Received: from renoir.scripps.edu (renoir [137.131.252.25]) by relay1.scripps.edu (8.11.7/TSRI-4.2rAV) with ESMTP id h3GGFT414740; Wed, 16 Apr 2003 09:15:29 -0700 (PDT) Received: by renoir.scripps.edu (Postfix, from userid 1376) id A8222D59; Wed, 16 Apr 2003 09:15:29 -0700 (PDT) To: amber@heimdal.compchem.ucsf.edu, CHEMISTRY@ccl.net, william.wei@utoronto.ca Subject: Re: MPI run problem Reply-To: crowley@scripps.edu Message-Id: <20030416161529.A8222D59@renoir.scripps.edu> Date: Wed, 16 Apr 2003 09:15:29 -0700 (PDT) From: crowley@scripps.edu (Michael Crowley) Dear William, Can you check to make sure that you have both machines in your .rhosts files and that the permissions on that file are 600? Mike From chemistry-request@server.ccl.net Wed Apr 16 14:31:26 2003 Received: from ccl.net ([192.148.249.4]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h3GIVQ331083 for ; Wed, 16 Apr 2003 14:31:26 -0400 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 h3GIVRt19395; Wed, 16 Apr 2003 14:31:27 -0400 (EDT) Date: Wed, 16 Apr 2003 14:31:25 -0400 (EDT) From: Jan Labanowski To: chemistry@ccl.net cc: Jan Labanowski Subject: 2003.06.12-14 Midwest Theoretical Chemistry Conference Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; CHARSET=US-ASCII; X-MAC-TYPE=54455854; X-MAC-CREATOR=4D4F5353 Content-ID: 35th Midwest Theoretical Chemistry Conference (MWTCC) June 12-14, 2003 Iowa State University Ames, Iowa Plenary Speakers: Anne McCoy, Ohio State University Klaus Ruedenberg, Iowa State University Xiao Cheng Zeng, University of Nebraska-Lincoln For more information, please visit the conference website: http://www.pmodels.org/~mwtcc Sponsors: IBM Iowa State University Department of Chemistry, Iowa State University Iowa State University Institute for Physical Research and Technology and Center for Physical and Computational Mathematics From chemistry-request@server.ccl.net Wed Apr 16 11:35:10 2003 Received: from bureau6.utcc.utoronto.ca ([128.100.132.16]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h3GFZA325592 for ; Wed, 16 Apr 2003 11:35:10 -0400 Received: from mditdell.mdit.utoronto.ca ([128.100.251.12] HELO MditDell ident: IDENT-NOT-QUERIED [port 1149]) by bureau6.utcc.utoronto.ca with SMTP id <238360-18573>; Wed, 16 Apr 2003 11:34:59 -0400 From: "William Wei" To: "Amber List" , "CCLers" Subject: MPI run problem Date: Wed, 16 Apr 2003 11:36:31 -0500 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 (9.0.2910.0) X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2600.0000 Importance: Normal Hi all, I had and now again run into a connection problem. I am using SGI 44 processors supercomputer. While I run multiple processor MD simulation with sander, it told me connection refused: permission denied rsh: connection failed PI file like: server.UT.ca 0 /aspirin/software/amber7/amber7/exe/sander server.UT.ca 1 /aspirin/software/amber7/amber7/exe/sander My computer have two name, one is "server.ut.ca", the other is "server.md.ut.ca". sander always try to find server.UT.ca . It is because I compiled sander before I used the name "server.MD.UT.ca". One account can run MD simulation but the other can not. These two accounts have same ~/.login ~/.cshrc. Could anyone give me some idea? Thanks a lot. Have a good day, William ------------------------- William Wei Faculty of Pharmacy 19 Russell Street Toronto, ON. M5S 2S2 Tel: 1-416-946-8469 Fax: 1-416-978-8511 Email: william@phm.utoronto.ca william.wei@utoronto.ca Http://phm.utoronto.ca/~william From chemistry-request@server.ccl.net Wed Apr 16 11:48:01 2003 Received: from cbdcom-emh1.apgea.army.mil ([131.92.10.15]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h3GFm0326065 for ; Wed, 16 Apr 2003 11:48:01 -0400 Received: by cbdcom-emh1.apgea.army.mil with Internet Mail Service (5.5.2656.59) id <2JTS9RB0>; Wed, 16 Apr 2003 11:48:00 -0400 Message-ID: <876D38F61109514A85ACA5772B7B07BB02D54965@mail1.apgea.army.mil> From: "Balboa, Alex Dr. SBCCOM" To: "'chemistry@ccl.net'" Subject: application to strip Mass Spectroscopy data out of Enhanced Chems tation software data files into ASCII text files Date: Wed, 16 Apr 2003 11:48:00 -0400 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2656.59) Content-Type: multipart/alternative; boundary="----_=_NextPart_001_01C3042F.8EC65D1A" This message is in MIME format. Since your mail reader does not understand this format, some or all of this message may not be legible. ------_=_NextPart_001_01C3042F.8EC65D1A Content-Type: text/plain; charset="iso-8859-1" Hi, I was wondering if there is an application that would be able to strip the binary data files created by Enhanced Chemstation software (G1701AA Version A.0.300) running under Windows95 Release B, into an ASCII test file (or any other universal usable file format) containing the m/z info, scan time info, absolute intensity info. If not, is there an application for parsing the .msp file (created by the NIST output format) to grab the m/z info, scan time info, absolute intensity info into an ASCII text file (or any other universal usable file format). Any feedback/comments would be gratefully appreciated. Thanks in advance. Sincerely, Alex Balboa Chemist US Army Soldier Biological, Chemical Command Chem-Bio Radiological Filtration Team Tech Dir, ECBC ATTN: AMSSB-RRT-PF Bldg E3549, Section C500, Cubicle 115 5183 Blackhawk Road Aberdeen Proving Ground-Edgewood Area, MD 21010-5424 Telephone: (410)436-5913 FAX: (410)436-7695 email: axbalboa@sbccom.apgea.army.mil ------_=_NextPart_001_01C3042F.8EC65D1A Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable application to strip Mass Spectroscopy data out of Enhanced = Chemstation software data files into ASCII text files

Hi,
I was wondering if there is an = application that would be able to strip the binary data files created = by Enhanced Chemstation software (G1701AA Version A.0.300) running = under Windows95 Release B, into an ASCII test file (or any other = universal usable file format) containing the m/z info, scan time info, = absolute intensity info.  If not, is there an application for = parsing the .msp file (created by the NIST output format) to grab the = m/z info, scan time info, absolute intensity info into an ASCII text = file (or any other universal usable file format).  Any = feedback/comments would be gratefully appreciated.

Thanks in advance.
Sincerely,
Alex Balboa
Chemist
US Army Soldier Biological, Chemical = Command
Chem-Bio Radiological Filtration = Team
Tech Dir, ECBC
ATTN:  AMSSB-RRT-PF
Bldg E3549, Section C500, Cubicle = 115
5183 Blackhawk Road
Aberdeen Proving Ground-Edgewood = Area, MD  21010-5424
Telephone: (410)436-5913
FAX: (410)436-7695
email: = axbalboa@sbccom.apgea.army.mil

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