From chemistry-request@server.ccl.net Tue Aug 31 02:02:19 1999 Received: from mailbox.syr.edu (root@mailbox.syr.edu [128.230.18.5]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id CAA01238 for ; Tue, 31 Aug 1999 02:02:18 -0400 Received: from syr.edu (curie.syr.edu [128.230.187.116]) by mailbox.syr.edu (8.9.2/8.9.2) with ESMTP id BAA10479 for ; Tue, 31 Aug 1999 01:54:57 -0400 (EDT) Sender: desingh@mailbox.syr.edu Message-ID: <37CB6F4E.28A2D5FB@syr.edu> Date: Tue, 31 Aug 1999 01:59:42 -0400 From: Deepak Singh Organization: Dept. of Chem & Biochem, Syracuse University X-Mailer: Mozilla 4.61C-SGI [en] (X11; I; IRIX64 6.5 IP30) X-Accept-Language: en MIME-Version: 1.0 To: Computational Chemistry List Subject: MD text Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi Folks, Can someone suggest an advanced text which covers MD simulations (particularly for proteins) and covers a broad range of aspects aspects incl. algorithms, trajectory evaluation, important results etc. I think McCammon and Harvey while good is a little dated, while the book "Computer Simulations of liquids" is out of print and impossible to get hold of through any means at my disposal. Rappaport is the other one I have looked at and it is not quite what I am looking for. HELP!!! Thanks and regards Deepak. -- ********************************************************************** Deepak Singh Tel : (315)443 1739 (w) Graduate Student (315)472 9659 (h) Dept. of Chemistry Fax : (315)443 4070 Syracuse University email : desingh@syr.edu 1-014 CST, Syracuse URL : http://web.syr.edu/~desingh NY 13244 "Violence is the last refuge of the incompetent." --- Salvor Hardin ********************************************************************** From chemistry-request@server.ccl.net Tue Aug 31 01:57:57 1999 Received: from bushbaby.alfred.edu (bushbaby.alfred.edu [149.84.197.201]) by server.ccl.net (8.8.7/8.8.7) with SMTP id BAA01204 for ; Tue, 31 Aug 1999 01:57:56 -0400 Received: from localhost (parkbw@localhost) by bushbaby.alfred.edu (950413.SGI.8.6.12/950213.SGI.AUTOCF) via SMTP id DAA16280 for ; Tue, 31 Aug 1999 03:22:06 -0400 Date: Tue, 31 Aug 1999 03:22:06 -0400 (EDT) From: Byeongwon Park To: CHEMISTRY@ccl.net Subject: ewald summation (P3M,FMM) Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear all, Can someone provide or point me a source code for Ewald summation using "particle-particel particle-mesh" and "Fast multipole method"? The parallel version would be much better. Thank you, Byeongwon _____________________________________________________________________ / | \ |Byeongwon Park | E-mail) parkbw@bushbaby.alfred.edu | |NYS College of Ceramics| | |Alfred University | | |Alfred NY 14802 | | \_______________________|_____________________________________________/ From chemistry-request@server.ccl.net Tue Aug 31 03:01:57 1999 Received: from ccl.net (atlantis.ccl.net [192.148.249.4]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id DAA01537 for ; Tue, 31 Aug 1999 03:01:57 -0400 Received: from mercury.chem.csiro.au (mercury.chem.CSIRO.AU [138.194.50.8]) by ccl.net (8.8.6/8.8.6/OSC 1.1) with ESMTP id CAA12961 for ; Tue, 31 Aug 1999 02:54:31 -0400 (EDT) Received: from [138.194.46.107] (cpr-46107.chem.csiro.au [138.194.46.107]) by mercury.chem.csiro.au (8.9.1/8.9.1) with ESMTP id QAA20288; Tue, 31 Aug 1999 16:52:57 +1000 (EST) X-Sender: win097@mail.chem.csiro.au Message-Id: Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Tue, 31 Aug 1999 16:54:06 +1000 To: CHMINF-L@LISTSERV.INDIANA.EDU, chemistry@ccl.net From: "Dr. Dave Winkler" Subject: Summary of large QSAR dataset question reponses Here is a summary of responses to my question on the availability of large (>1000 compound) QSAR data sets: o Yvonne Martin (yvonne.c.martin@abbott.com) has a ~1500 data set of MAO inhibitors available if a confidentiality agreement is signed o Several people (Marc Nicklaus (mn1@helix.nih.gov), Wolf-Dietrich Ihlenfeldt (Wolf-Dietrich.Ihlenfeldt@ccc.chemie.uni-erlangen.de)) mentioned the archive of structures and cancer and HIV data available at the NIH/NCI site or the Enhanced NCI Database Browser (http://www2.ccc.uni-erlangen.de/ncidb/ or the US mirror) o Michael K. Gilson" is in the early stages of creating a web-accessible database of noncovalent binding affinities. o Two commercial interests provided details of their databases: Kevin P. Cross" of Columbus Molecular Software had sets of NCI data for sale in conjunction with the LeadScope Software; Al Leo from Pomona College gave details of C-QSAR and associated QSAR databases. o Suzanne Sirois suggested the QSAR Society site at http://www.pharma.ethz.ch/qsar/ however this has only small QSAR data sets. Cheers, Dave Dr. David A. Winkler Email: dave.winkler@molsci.csiro.au Senior Principal Research Scientist Voice: 61-3-9545-2477 CSIRO Molecular Science Fax: 61-3-9545-2446 Private Bag 10,Clayton South MDC 3169 http://www.csiro.au Australia http://www.molsci.csiro.au From chemistry-request@server.ccl.net Tue Aug 31 12:48:11 1999 Received: from alchemy.chem.utoronto.ca (alchemy.chem.utoronto.ca [142.150.224.224]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id MAA04687 for ; Tue, 31 Aug 1999 12:48:11 -0400 Received: (from elewars@localhost) by alchemy.chem.utoronto.ca (8.9.3/8.9.3) id MAA04563 for chemistry@ccl.net; Tue, 31 Aug 1999 12:40:40 -0400 (EDT) Date: Tue, 31 Aug 1999 12:40:40 -0400 (EDT) From: "E. Lewars" Message-Id: <199908311640.MAA04563@alchemy.chem.utoronto.ca> To: chemistry@ccl.net Subject: SCHROEDINGER, PSI, POEM 1999 August 31 If you'll excuse me for asking a question peripheral to computational chemistry: Those of us who use Gaussian have likely come across, from its store of quotations, this ditty: Erwin with his psi can do Calculations quite a few. But one thing has not been seen: Just what does psi really mean. This was written by the famous organic chemist Walter Hueckel (brother of Erich of MO fame), about Erwin Schroedinger's wavefunction (psi). The translation is by Felix Bloch. Could someone please send me the original German and the reference to where it first appeared, or at least some book or journal in which it can be found? Thanks E. Lewars ========================= From chemistry-request@server.ccl.net Tue Aug 31 14:39:02 1999 Received: from helix.nih.gov (helix.nih.gov [128.231.2.3]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id OAA05085 for ; Tue, 31 Aug 1999 14:39:02 -0400 Received: (from mn1@localhost) by helix.nih.gov (8.9.1a/8.9.1) id OAA6433628; Tue, 31 Aug 1999 14:31:32 -0400 (EDT) Date: Tue, 31 Aug 1999 14:31:32 -0400 From: "M. Nicklaus" To: CHEMISTRY@ccl.net cc: "M. Nicklaus" Subject: Re: CCL:Summary of large QSAR dataset question reponses In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII On Tue, 31 Aug 1999, Dr. Dave Winkler wrote: > o Several people (Marc Nicklaus (mn1@helix.nih.gov), Wolf-Dietrich > Ihlenfeldt (Wolf-Dietrich.Ihlenfeldt@ccc.chemie.uni-erlangen.de)) mentioned > the archive of structures and cancer and HIV data available at the NIH/NCI > site or the Enhanced NCI Database Browser > (http://www2.ccc.uni-erlangen.de/ncidb/ or the US mirror) Structure files and biological data files can be downloaded from the Web site of NCI's Developmental Therapeutics Program (DTP), at http://dtp.nci.nih.gov/docs/3d_database/structural_information/structural_data.html Structure files with approx. 246k open NCI compounds in SD file format can also be downloaded from http://cactus.cit.nih.gov/ncidb/download.html (the "US mirror" mentioned by Dave). Marc ------------------------------------------------------------------------ Marc C. Nicklaus National Institutes of Health E-mail: mn1@helix.nih.gov Bldg 37, Rm 5B29 Phone: (301) 402-3111 37 Convent Dr, MSC 4255 Fax: (301) 496-5839 BETHESDA, MD 20892-4255 USA http://rex.nci.nih.gov/RESEARCH/basic/medchem/mcnbio.htm Laboratory of Medicinal Chemistry, National Cancer Institute ------------------------------------------------------------------------ From chemistry-request@server.ccl.net Tue Aug 31 14:44:14 1999 Received: from Ba.Chem.UH.EDU (Ba-el0.Chem.UH.EDU [129.7.190.40]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id OAA05134 for ; Tue, 31 Aug 1999 14:44:13 -0400 Received: (from beck@localhost) by Ba.Chem.UH.EDU (8.9.2/8.9.2) id NAA06067; Tue, 31 Aug 1999 13:33:45 -0500 (CDT) From: "Brian W. Beck" Message-Id: <199908311833.NAA06067@Ba.Chem.UH.EDU> Subject: Re: CCL:MD text To: desingh@syr.edu (Deepak Singh), CHEMISTRY@server.ccl.net (Computational Chemistry List) Date: Tue, 31 Aug 1999 13:33:45 -0500 (CDT) In-Reply-To: <37CB6F4E.28A2D5FB@syr.edu> from "Deepak Singh" at Aug 31, 1999 01:59:42 AM Reply-to: "Brian W. Beck" Operating-System: OSF1 V4.0 1229 Organization: Institute for Molecular Design, University of Houston Phone: 713-743-3264 FAX: 713-743-2709 X-Mailer: ELM [version 2.5 PL0] MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Deepak Singh wrote: > > Hi Folks, > > Can someone suggest an advanced text which covers MD simulations > (particularly for proteins) and covers a broad range of aspects aspects > incl. algorithms, trajectory evaluation, important results etc. > I think McCammon and Harvey while good is a little dated, while the > book "Computer Simulations of liquids" is out of print and impossible to > get hold of through any means at my disposal. Rappaport is the other > one I have looked at and it is not quite what I am looking for. > > Molecular Dynamics Simulations: Elementary Methods by Haile Molecular Modelling:Principles and Applications by Leach Understanding Molecular Simulation: From Algorithms to Applications by Frenkel & Smit Computer-Aided Molecular Design: Theory and Applications by Doucet & Weber -Brian -- ============================================================== | Brian W. Beck |E-mail Address: beck@uh.edu | | Inst. Molec. Design| | | Univ. of Houston |URL: | | 220 Fleming |http://www.chem.uh.edu/pettitt/beck | | Houston, TX, USA |VOICE (713) 743-3264 | | 77204-5641 |FAX (713) 743-2709 | ==============================================================