From jamejias@obelix.cica.es Fri Nov 18 04:28:17 1994 Received: from obelix.cica.es for jamejias@obelix.cica.es by www.ccl.net (8.6.9/930601.1506) id EAA03741; Fri, 18 Nov 1994 04:05:52 -0500 From: Date: Fri, 18 Nov 1994 10:06:11 +0100 Received: from localhost by obelix.cica.es (8.6.4.2/X1.00) id KAA01789; Fri, 18 Nov 1994 10:06:11 +0100 Message-Id: <199411180906.KAA01789@obelix.cica.es> To: CHEMISTRY@ccl.net Subject: Software for crystal generation? Dear Netters We need to generate a crystal from unit cell data. Is there any code which, given those data, gives the position of a number of atoms in the crystal? We are trying to do embedded cluster calculations for corundum type crystal. We need the positions of the point charges representing the environment. This point charges array should have the C3 symmetry of the cluster. Thank you in advance Jose Antonio Mejias Departamento de Quimica Fisica Universidad de Sevilla Sevilla Spain e-mail: jamejias@obelix.cica.es From paulo@chep101.uni-bielefeld.de Fri Nov 18 07:27:35 1994 Received: from hermes.hrz.uni-bielefeld.de for paulo@chep101.uni-bielefeld.de by www.ccl.net (8.6.9/930601.1506) id HAA05455; Fri, 18 Nov 1994 07:23:18 -0500 Received: from chep101.uni-bielefeld.de by hermes.hrz.uni-bielefeld.de with SMTP (16.8/16.2) id AA24221; Fri, 18 Nov 94 13:26:43 +0100 Message-Id: <9411181226.AA24221@hermes.hrz.uni-bielefeld.de> Received: by chep101; Fri, 18 Nov 94 13:26:11 mez Date: Fri, 18 Nov 94 13:26:11 mez From: Paulo Netz To: CHEMISTRY@ccl.net Subject: CCL:GROMOS torsion angles Dear Netters I am working with Monte Carlo and Molecular Dynamics simulations on the structure and dynamics of polyacrylamide gels. I have written a program that uses the parameters of the GROMOS force field. But the definition and criteria of choice of the dihedral terms in this force field seem ambiguous to me. For example for the structure: a e \ / c - d / \ b f one specific quadruple of atoms has to be chosen (among the 4 possible quadruples) to build a torsion term, because, according to the GROMOS manual: " for each bond between atoms with sequence number j and k only one quadruple of atoms i-j-k-l is chosen to form dihedral PHI_n ". The question is which term should be chosen (and why) and what about the dismissing of the remaining terms (if I choose a-c-d-f there is no torsion force contribution to the atoms e and b and this seems to be wrong). Also the value of the torsion angle is ambiguous. Can someone help me? Thanks a lot in advance. paulo@chep101.uni-bielefeld.de Paulo A. Netz graduate student Fakultaet Chemie - Physikalische Chemie I Universitaet Bielefeld - Germany From noy@tci005.uibk.ac.at Fri Nov 18 11:27:34 1994 Received: from uibk.ac.at for noy@tci005.uibk.ac.at by www.ccl.net (8.6.9/930601.1506) id KAA07665; Fri, 18 Nov 1994 10:29:34 -0500 Received: from tci005.uibk.ac.at by uibk.ac.at with SMTP id AA10615 (5.65c/IDA-1.4.4 for ); Fri, 18 Nov 1994 16:06:39 +0100 Received: by tci005.uibk.ac.at (AIX 3.2/UCB 5.64/CFIBK-2e.AIX) id AA40788; Fri, 18 Nov 1994 16:06:39 +0100 From: noy@tci005.uibk.ac.at (Noy) Message-Id: <9411181506.AA40788@tci005.uibk.ac.at> Subject: Parallelized MD To: chemistry@ccl.net Date: Fri, 18 Nov 1994 16:06:39 +0100 (NFT) X-Mailer: ELM [version 2.4 PL23] Content-Type: text Content-Length: 815 Dear cyber-chemists, There are so so so many tools for parallel programing freely available on the net, PVM3, TCGMSG, P4, CHARM, HPF and so on ...... What is suitable specially for parallelizing existing MD code ? What is your suggestion if one wants to work on a cluster of heterogenous computer environment. sincerely, ---------------------------------------------------------------------------- Teerakiat Kerdcharoen (NOY) Institute of General and Inorganic and Theoretical Chemistry Innrain 52a, A-6020 Innsbruck AUSTRIA e-mail: noy@tci2.uibk.ac.at, noy@tci.uibk.ac.at, c72454@cx.uibk.ac.at : noy@atc.atccu.chula.ac.th, noy@atc2.atccu.chula.ac.th ( Bangkok ) ---------------------------------------------------------------------------- *** I have no past and no future. I just have today. From tds26@cas.org Fri Nov 18 11:34:40 1994 Received: from srv01s4.cas.org for tds26@cas.org by www.ccl.net (8.6.9/930601.1506) id KAA07995; Fri, 18 Nov 1994 10:48:52 -0500 Date: Fri, 18 Nov 94 10:48:49 EST From: tds26@cas.org (Tom Steckert (Ext. 2639)) Message-Id: <9411181048.AA13548@cas.org> Subject: Introducing CXF - Chemical eXchange Format To: chemistry@ccl.net CAS INTRODUCES CXF To encourage consistency in the development of chemical substance software and use of substance data, CAS (Chemical Abstracts Service) has introduced a standard data exchange format called CXF (Chemical eXchange Format). CXF, available free of charge, provides representation of chemical substances and queries, including atoms, fragments, molecules, and reactions. Also available are various substance types, including organics, inorganics, polymers, salts, hydrates, multi-component mixtures and biosequences. A single data exchange format is intended to facilitate information exchange among various systems and organizations. Therefore CXF is expressed in Abstract Syntax Notation One (ASN.1), an International Organization for Standardization (ISO) open systems interconnection standard compatible with numerous software programs. Interest in chemical information interchange processing and standards has a long history at CAS, which is committed to maintaining open access to the CXF format. CAS eventually plans to make available free of charge on the Internet routines to aid conversion between CXF and other selected formats, and software to validate the content of files containing CXF data. For more information, interested users should contact Thomas Steckert or Joseph Mockus at (614) 447-3600. Internet addresses are: tsteckert@cas.org and jmockus@cas.org. Questions and comments also are welcome. The specification is available via anonymous ftp from info.cas.org, directory pub/cxf. ============================================================================= Tom Steckert tsteckert@cas.org Chemical Abstracts Service (614) 447-3600 P.O. Box 3012 Columbus, OH 43210 From soperpd@nylon.es.dupont.com Fri Nov 18 18:29:43 1994 Received: from gatekeeper.es.dupont.com for soperpd@nylon.es.dupont.com by www.ccl.net (8.6.9/930601.1506) id SAA01082; Fri, 18 Nov 1994 18:15:46 GMT Received: by gatekeeper.es.dupont.com; id AA05957; Fri, 18 Nov 94 13:15:45 -0500 Received: by esds01.es.dupont.com; id AA23255; Fri, 18 Nov 94 13:15:43 -0500 Received: by nylon.es.dupont.com (931110.SGI/920502.SGI)for @esds01.es.dupont.com:chemistry@ccl.net id AA07101; Fri, 18 Nov 94 13:16:03 -0500 Date: Fri, 18 Nov 94 13:16:03 -0500 From: soperpd@nylon.es.dupont.com (Paul D. Soper) Message-Id: <9411181816.AA07101@nylon.es.dupont.com> To: chemistry@ccl.net Subject: CCL: 3D structure to flat representation Do you know of any programs (public domain or commercial) which can take a 3D structure or a connectivity graph and produce a drawing similar to those from ChemDraw or ChemWindows? (These drawings are like those one would find in an organic chemistry textbook.) I'm looking for something more sophisticated than simply removing the z coordinate from an xyz file. Please respond to me (soperpd@esvax.dnet.dupont.com) and I will summarize for the list. ----------------------------------------------------------------- Paul Soper All the usual disclaimers apply DuPont Central Research soperpd@esvax.dnet.dupont.com P.O. Box 80328 Tel (302)-695-1757 Wilmington, DE 19880-0328 FAX (302)-695-8412 ----------------------------------------------------------------- From hinsenk@ERE.UMontreal.CA Fri Nov 18 19:30:04 1994 Received: from effraie.CC.UMontreal.CA for hinsenk@ERE.UMontreal.CA by www.ccl.net (8.6.9/930601.1506) id SAA01544; Fri, 18 Nov 1994 18:47:37 GMT Received: from eole.ERE.UMontreal.CA by effraie.CC.UMontreal.CA with SMTP id AA11523 (5.65c/IDA-1.4.4 for chemistry@ccl.net); Fri, 18 Nov 1994 13:39:32 -0500 Received: from cyclone.ERE.UMontreal.CA by eole.ERE.UMontreal.CA (940406.SGI/5.17) id AA02839; Fri, 18 Nov 94 13:39:18 -0500 Received: by cyclone.ERE.UMontreal.CA (940406.SGI/5.17) id AA11631; Fri, 18 Nov 94 13:38:59 -0500 Date: Fri, 18 Nov 94 13:38:59 -0500 From: hinsenk@ERE.UMontreal.CA (Hinsen Konrad) Message-Id: <9411181838.AA11631@cyclone.ERE.UMontreal.CA> To: chemistry@ccl.net Subject: MuPAD Today I got several mails telling me that the ftp server I had given as a source for MuPAD doesn't work. I checked this and it seems to be true; however, this is probably just a temporary problem, since yesterday I had no problems at all getting in. Note however that the server always has a limit of 15 users, so it might be difficult to succeed. At night (in Europe) it is typically easy. If all you want is information, you can write to MuPAD-distribution@uni-paderborn.de You can also try the WWW page http://math-www.uni-paderborn.de/~cube/ but you won't find it very useful right now, since it contains mostly links to the ftp server. Some remarks about how to get MuPAD: the ftp server contains a free demo version (restricted memory space). If you send a license agreement to Paderborn, you will get a password with which you can convert the demo version to a full version. This is free for non-commercial users. MuPAD comes with an on-line manual; a more extensive printed version and a tutorial are available via any bookstore (but I don't remember the price). ------------------------------------------------------------------------------- Konrad Hinsen | E-Mail: hinsenk@ere.umontreal.ca Departement de Chimie | Tel.: +1-514-343-6111 ext. 3953 Universite de Montreal | Fax: +1-514-343-7586 C.P. 6128, succ. A | Deutsch/Esperanto/English/Nederlands/ Montreal (QC) H3C 3J7 | Francais (phase experimentale) ------------------------------------------------------------------------------- From hinsenk@ERE.UMontreal.CA Fri Nov 18 20:29:45 1994 Received: from effraie.CC.UMontreal.CA for hinsenk@ERE.UMontreal.CA by www.ccl.net (8.6.9/930601.1506) id TAA03521; Fri, 18 Nov 1994 19:39:43 GMT Received: from eole.ERE.UMontreal.CA by effraie.CC.UMontreal.CA with SMTP id AA12209 (5.65c/IDA-1.4.4 for chemistry@ccl.net); Fri, 18 Nov 1994 14:38:14 -0500 Received: from cyclone.ERE.UMontreal.CA by eole.ERE.UMontreal.CA (940406.SGI/5.17) id AA15637; Fri, 18 Nov 94 14:38:13 -0500 Received: by cyclone.ERE.UMontreal.CA (940406.SGI/5.17) id AA12804; Fri, 18 Nov 94 14:38:12 -0500 Date: Fri, 18 Nov 94 14:38:12 -0500 From: hinsenk@ERE.UMontreal.CA (Hinsen Konrad) Message-Id: <9411181938.AA12804@cyclone.ERE.UMontreal.CA> To: chemistry@ccl.net In-Reply-To: <9411181506.AA40788@tci005.uibk.ac.at> (noy@tci005.uibk.ac.at) Subject: Re: CCL:Parallelized MD There are so so so many tools for parallel programing freely available on the net, PVM3, TCGMSG, P4, CHARM, HPF and so on ...... What is suitable specially for parallelizing existing MD code ? My experience is limited to PVM, which implements general message-passing for a large variety of hardware setups. Within the limits of the message-passing paradigm, I see no important limitations imposed by PVM. However, doing parallel calculations on a workstation cluster with PVM will quickly demonstrate the limits of the hardware; communication via Ethernet is slow (which of course is not PVM's fault). For programs with medium to large communication requirements, parallelization on a cluster will give hardly any speedup. Anyway, most of the work necessary for parallelizing existing code will go into the modification of the algorithms involved, not into interfacing to a toolkit. Before you spend too much time modifying code, have a look at the DL_POLY program, which was recently developed at Daresbury (UK) specifically for parallel machines, including workstation clusters. You will find more information on it at CCP5's WWW server: http://www.dl.ac.uk/CCP/CCP5/main.html ------------------------------------------------------------------------------- Konrad Hinsen | E-Mail: hinsenk@ere.umontreal.ca Departement de Chimie | Tel.: +1-514-343-6111 ext. 3953 Universite de Montreal | Fax: +1-514-343-7586 C.P. 6128, succ. A | Deutsch/Esperanto/English/Nederlands/ Montreal (QC) H3C 3J7 | Francais (phase experimentale) ------------------------------------------------------------------------------- From garciae@ucsub.Colorado.EDU Fri Nov 18 19:12:52 1994 Received: from ucsub.Colorado.EDU for garciae@ucsub.Colorado.EDU by www.ccl.net (8.6.9/930601.1506) id SAA01326; Fri, 18 Nov 1994 18:15:13 -0500 Received: (from garciae@localhost) by ucsub.Colorado.EDU (8.6.9/8.6.9/CNS-3.5) id QAA82050; Fri, 18 Nov 1994 16:14:26 -0700 Date: Fri, 18 Nov 1994 16:13:57 -0700 (MST) From: Garcia Edgardo To: CHEMISTRY@ccl.net Subject: CCL: ab initio data base Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi netters, Does someone know any references and/or internet address of a data base with ab initio results for general molecules ? I knew about something like that at Gainsville, Florida, but I'm not sure. Do they have a data base ? Thanks. Dr. Edgardo Garcia Univ. of Colorado Boulder CO From chen@agouron.com Fri Nov 18 21:12:53 1994 Received: from agouron.com for chen@agouron.com by www.ccl.net (8.6.9/930601.1506) id UAA02145; Fri, 18 Nov 1994 20:31:19 -0500 Received: from agouron.agouron.com by agouron.com via SMTP (940715.SGI.52/930901.SGI) for chemistry@ccl.net id AA01607; Fri, 18 Nov 94 17:31:07 -0800 Received: from localhost by agouron (8.6.4.2/10.3) id RAA03374; Fri, 18 Nov 1994 17:31:06 -0800 Date: Fri, 18 Nov 1994 17:31:06 -0800 From: chen@agouron (Chris Chen) Message-Id: <199411190131.RAA03374@agouron> To: chemistry@ccl.net Subject: 3D database searching [ I post it for a friend ] Hi, netters! We are looking for good literatures of 3D database searching for drug design purpose. The databases are ones such as Cambridge crystal database, and other 3D structure databases. I will post a summary if desired. Thanks in advance. -- Chris Chen chen@agouron.com Agouron Pharmaceuticals, Inc., San Diego, CA 92121 Voice: (619) 622-7940, FAX: (619) 622-7999