From chemistry-request@ccl.net Fri Jan 2 18:37:19 2004 Received: from daimi.au.dk (daimi.au.dk [130.225.16.1]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i02NalTC018734 for ; Fri, 2 Jan 2004 18:36:47 -0500 Received: (from gopher@localhost) by daimi.au.dk (8.12.10/8.12.10) id i02NakiC019183; Sat, 3 Jan 2004 00:36:46 +0100 From: Rene Thomsen Received: from 0x50c63fb8.arcnxx15.adsl-dhcp.tele.dk (0x50c63fb8.arcnxx15.adsl-dhcp.tele.dk [80.198.63.184]) by webmail.daimi.au.dk (IMP) with HTTP for ; Sat, 3 Jan 2004 00:36:46 +0100 Message-ID: <1073086606.3ff6008e956e7.-at-.webmail.daimi.au.dk> Date: Sat, 3 Jan 2004 00:36:46 +0100 To: chemistry.-at-.ccl.net Subject: CEC2004 call for papers, Special session on Evolutionary Computation in Bioinformatics and Computational Biology MIME-Version: 1.0 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 8bit User-Agent: Internet Messaging Program (IMP) 3.2.2 X-Originating-IP: 80.198.63.184 X-Spam-Status: No, hits=-0.3 required=7.0 tests=USER_AGENT_IMP version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) CEC 2004 - Call for Papers Special session on Evolutionary Computation in Bioinformatics and Computational Biology The sixth Congress on Evolutionary Computation (CEC 2004), sponsored by the IEEE Neural Networks Society, IEE, and the Evolutionary Programming Society, will be held in Portland Marriott Downtown, Portland, Oregon, USA, June 19-23. 2004. See http://cec2004.org for more details. Bioinformatics and computational biology present a number of difficult optimization problems with large search spaces. Recent applications of evolutionary computation in this area suggest that they are well suited to this area of research. This special session will highlight applications of evolutionary computation to a broad range of topics including drug docking, protein folding, sequence alignment, genomics, proteomics, metabolics, and medicine. Particular interest will be directed towards novel applications of evolutionary computation to problems in these areas. Submission deadlines Submission of papers: 31. January 2004 Notification of acceptance: 15. February 2004 Camera-ready paper: 1. March 2004 Papers should follow the formatting guidelines for CEC2004 regular papers (see http://cec2004.org/Submission.htm for more details), and should be submitted through the CEC04 submission website (see http://cec2004.org/review/upload.php). Remember to select the "Evolutionary computation in Bioinformatics and Computational Biology" in the "Additional topics" field. Submissions should be in PDF format and should not exceed 8 pages in length. This includes all figures, tables, graphs, photos, and bibliography entries. Special session organizer: Reni Thomsen BiRC - Bioinformatics Research Center Department of Computer Science University of Aarhus Ny Munkegade, Bldg. 540 DK-8000 Aarhus C Denmark E-mail: thomsen.-at-.daimi.au.dk From chemistry-request@ccl.net Sat Jan 3 00:22:36 2004 Received: from mail.ccnu.edu.cn ([202.114.32.3]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i035LuTC023130 for ; Sat, 3 Jan 2004 00:22:02 -0500 Received: (eyou send program); Sat, 03 Jan 2004 13:21:47 +0800 Message-ID: <273107307.27502:at:mail.ccnu.edu.cn> Received: from 202.114.34.252 by 202.114.32.3 with HTTP; Sat, 03 Jan 2004 13:21:47 +0800 X-WebMAIL-MUA: [202.114.34.252] From: "" To: help:at:gaussian.com Date: Sat, 03 Jan 2004 13:21:47 +0800 CC: CHEMISTRY:at:ccl.net Reply-To: "" Subject: BU-NOSPAM: I have known the reason about ONIOM Content-Type: text/plain X-Spam-Status: No, hits=4.7 required=7.0 tests=DEAR_SOMETHING,MSG_ID_ADDED_BY_MTA_2,NO_REAL_NAME, QUOTED_EMAIL_TEXT,RCVD_IN_RFCI version=2.55 X-Spam-Level: **** X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Dear sir, I have known the reason why the G03 program asked me to readd those parameters. Because these atoms are at the layer boundary, so they are replaced with other simple atoms, thus I must input parameter for these "other simple atoms". >From: "" >Reply-To: "" >To: CHEMISTRY:at:ccl.net >Subject: CCL: question about ONIOM > >Dear sir, > I am doing ONIOM calculation for an enzyme-ligand system including about 5100 > atoms. Is it possible to do this calculation with ONIOM method in G03 program? > When I try to do it, I got the following error information in the end of output > file: > -------------------------------------------------------------- > I= 2535 IAn= 7 Valence= 4. > JB= 1 J= 2536 IAn= 6 IBT= 1 Dist= 1.43D+00 > JB= 2 J= 2540 IAn= 6 IBT= 1 Dist= 1.40D+00 > JB= 3 J= 2544 IAn= 6 IBT= 1 Dist= 1.44D+00 > JB= 4 J= 2532 IAn= 6 IBT= 1 Dist= 1.51D+00 > Include all MM classes > Bondstretch undefined between atoms 151 159 > Bondstretch undefined between atoms 170 178 > Bondstretch undefined between atoms 1031 1032 > Bondstretch undefined between atoms 1032 1033 > Bondstretch undefined between atoms 1267 1275 > Bondstretch undefined between atoms 1479 1487 > Bondstretch undefined between atoms 2020 2026 > Angle bend undefined between atoms 150 151 159 > Angle bend undefined between atoms 152 151 159 > Angle bend undefined between atoms 169 170 178 > Angle bend undefined between atoms 171 170 178 > Angle bend undefined between atoms 1031 1032 1033 > MM function not complete > Error termination via Lnk1e in /usr/local/g03/l120.exe at Thu Jan 1 05:54:13 > 2004. > Job cpu time: 0 days 6 hours 59 minutes 11.2 seconds. > File lengths (MBytes): RWF= 731 Int= 0 D2E= 0 Chk= 93 Scr= > > 1 > ---------------------------------------------------------- > In fact, I have define those parameter in input files for G03. I found the > following content in the beginning part of output file to confirm it: > ----------------------------------------------------------------------- > Read MM parameter file: > Define 1.500 1 > Include all MM classes > MMInit generated parameter data with length LenPar=966946. > > GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad > Berny optimization. > Initialization pass. > ----------------------------------------------------------------------------- > Could you please tell me what's wrong with it? Thank you! > > > From chemistry-request@ccl.net Sat Jan 3 05:26:09 2004 Received: from yangtze.hku.hk (yangtze.hku.hk [147.8.148.244]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i03APbTC029538 for ; Sat, 3 Jan 2004 05:25:38 -0500 Received: from yangtze.hku.hk (yangtze.hku.hk [127.0.0.1]) by yangtze.hku.hk (8.12.8/8.12.8) with ESMTP id i03AOxXC017965 for ; Sat, 3 Jan 2004 18:24:59 +0800 Received: from localhost (alarry@localhost) by yangtze.hku.hk (8.12.8/8.12.8/Submit) with ESMTP id i03AOwjj017961 for ; Sat, 3 Jan 2004 18:24:59 +0800 Date: Sat, 3 Jan 2004 18:24:58 +0800 (HKT) From: alarry-.at.-yangtze.hku.hk To: CHEMISTRY-.at.-ccl.net Subject: Hessian matrix in G98 Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-Spam-Status: No, hits=0.8 required=7.0 tests=NO_REAL_NAME,USER_AGENT_PINE version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Dear cclers, Do anyone know how to print out the hessian matrix for large system in GAUSSIAN98 calculations? It looks like only output files of small molecules would contain the hessian matrix. Do any other users have similar experience? Any comment will be appreciated. Thanks for your help in advance. Larry From chemistry-request@ccl.net Sat Jan 3 13:25:03 2004 Received: from glaurung.gpcc.itd.umich.edu (glaurung.gpcc.itd.umich.edu [141.211.2.181]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i03IOVTC004703 for ; Sat, 3 Jan 2004 13:24:31 -0500 Received: from asteroids.gpcc.itd.umich.edu (asteroids.gpcc.itd.umich.edu [141.211.2.218]) by glaurung.gpcc.itd.umich.edu (8.9.3p2/4.3-mailhub) with ESMTP id NAA07554 for ; Sat, 3 Jan 2004 13:24:27 -0500 (EST) Received: from localhost (weishi@localhost) by asteroids.gpcc.itd.umich.edu (8.9.3p2/5.1-client) with ESMTP id NAA27230 for ; Sat, 3 Jan 2004 13:24:27 -0500 (EST) Precedence: first-class Date: Sat, 3 Jan 2004 13:24:27 -0500 (EST) From: Wei Shi X-X-Sender: weishi[at]asteroids.gpcc.itd.umich.edu To: chemistry[at]ccl.net Subject: CCL Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-Spam-Status: No, hits=0.0 required=7.0 tests=USER_AGENT_PINE version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Dear CCLers, Happy new year! I have one question for CHARMm about equilibration. Generally, the calculation is started from the X ray structure, then heating, equilibrating by velocity scale, and lastly production run without velocity scale in the NVE MD simulation. However, I found that many of the authors do not check the system to make sure it has been equilibrated before they take the production run. Fro example, Some authors observe the temperature is increasing with the potential energy drifting down in the production run. However, they still do the analysis. Is that a problem? Thanks for all your help, Wei Shi From chemistry-request@ccl.net Sat Jan 3 19:29:02 2004 Received: from kafka.net.nih.gov (kafka.net.nih.gov [165.112.130.10]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i040SUTC009846 for ; Sat, 3 Jan 2004 19:28:30 -0500 Received: from pollux.cber.nih.gov (pollux.cber.nih.gov [128.231.52.5]) by kafka.net.nih.gov (8.12.10/8.12.9) with ESMTP id i040SRcD020740; Sat, 3 Jan 2004 19:28:27 -0500 (EST) Date: Sat, 3 Jan 2004 19:17:50 -0500 From: Rick Venable To: Wei Shi cc: chemistry^at^ccl.net Subject: Re: CCL:CCL In-Reply-To: Message-ID: References: ReplyTo: Rick_Venable^at^nih.gov MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-Spam-Status: No, hits=-1.1 required=7.0 tests=EMAIL_ATTRIBUTION,IN_REP_TO,QUOTED_EMAIL_TEXT, RCVD_IN_NJABL,REFERENCES,REPLY_WITH_QUOTES,USER_AGENT_PINE, X_NJABL_OPEN_PROXY version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Certainly, a system with increasing T and decreasing potential energy is not at equilibrium, but obviously still relaxing. Depending on the magnitude of the drift and the analysis, the results may be misleading. Some additional notes about CHARMM usage-- NPT ensemble may be better, at least for equilibration after heating; a symmetric lattice such as cubic, truncated octahedron, or rhombic dodecahedron is usually appropriate for a solvated protein. I've observed quicker equilibration with velocity assignment (as opposed to velocity scaling). I guess it depends on your projects-- most of my CHARMM simulations start with coordinates from an extensive model building procedure On Sat, 3 Jan 2004, Wei Shi wrote: > I have one question for CHARMm about equilibration. Generally, the > calculation is started from the X ray structure, then heating, > equilibrating by velocity scale, and lastly production run without > velocity scale in the NVE MD simulation. However, I found that many of > the authors do not check the system to make sure it has been > equilibrated before they take the production run. Fro example, Some > authors observe the temperature is increasing with the potential > energy drifting down in the production run. However, they still do the > analysis. Is that a problem? =+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+= Rick Venable 29/500 FDA/CBER/OVRR Biophysics Lab 1401 Rockville Pike HFM-419 Rockville, MD 20852-1448 U.S.A. (301) 496-1905 Rick_Venable^at^nih.gov ALT email: rvenable^at^speakeasy.org ------------------------------------- "Don't blame me, I voted for Kang." Homer =+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=