From chemistry-request@server.ccl.net Mon Oct 21 06:01:36 2002 Received: from cuces.unisi.it ([193.205.4.2]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g9LA1ZK03649 for ; Mon, 21 Oct 2002 06:01:35 -0400 Received: from CONVERSION-DAEMON.unisi.it by unisi.it (PMDF V6.0-025 #30546) id <01KNXCIA66HS002HOE@unisi.it> for chemistry@ccl.net; Mon, 21 Oct 2002 12:01:32 +0100 (MET) Received: from unisi.it (ccmaol3.chim.unisi.it [192.167.123.208]) by unisi.it (PMDF V6.0-025 #30546) with ESMTPA id <01KNXCI7XDZK002JAH@unisi.it> for chemistry@ccl.net; Mon, 21 Oct 2002 12:01:30 +0100 (MET) Date: Mon, 21 Oct 2002 11:59:34 +0200 From: "Nicolas Ferre'" Subject: G98: save an intermediate CASSCF wavefunction Sender: ferre@unisi.it To: chemistry@ccl.net Message-id: <3DB3D006.485FED73@unisi.it> Organization: Universita` di Siena MIME-version: 1.0 X-Mailer: Mozilla 4.61i [en_US] (X11; I; AIX 4.3) Content-type: text/plain; charset=us-ascii Content-transfer-encoding: 7BIT X-Accept-Language: fr, en Dear CCL, I'd like to know if there's a way to save a CASSCF wavefunction in the G98's checkpoint file at every iteration of the wavefunction optimization, in order to restart the calculation if necessary ? The keyword SCF=SAVE (that corresponds to IOP(5/36=1)) does not seem to work in the case of a CASSCF calculation. I didn't find any corresponding thing in the CASSCF source file (l510.F). Otherwise, is there a way to restart such a calculation from a read-write file ? Many thanks. Nicolas -- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Nicolas FERRE' (PhD) phone/fax : +39-0577-234278 Dipartimento di Chimica Universita` di Siena mailto:ferre@unisi.it via Aldo Moro 53100 SIENA (Italia) http://ccmaol1.chim.unisi.it/ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ From chemistry-request@server.ccl.net Mon Oct 21 03:11:24 2002 Received: from umhsp02.umh.ac.be ([193.190.192.27]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g9L7BNK32480 for ; Mon, 21 Oct 2002 03:11:23 -0400 Received: from europe.umh.ac.be (europe.umh.ac.be [193.190.132.12]) by umhsp02.umh.ac.be (8.12.5/8.12.5) with ESMTP id g9L7Bb85049306; Mon, 21 Oct 2002 09:11:37 +0200 Received: by europe.umh.ac.be with Internet Mail Service (5.5.2653.19) id ; Mon, 21 Oct 2002 09:05:37 +0200 Message-ID: From: Jean-Philippe Calbert To: "'Ohyun Kwon'" , "'chemistry@ccl.net'" Subject: RE : ZINDO MO visualization in G98 Date: Mon, 21 Oct 2002 09:05:36 +0200 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2653.19) Content-Type: text/plain; charset="iso-8859-1" X-Scanned-By: MIMEDefang 2.1 (www dot roaringpenguin dot com slash mimedefang) Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id g9L7BOK32481 Hi Tommy, I wanted to let you know that Zoa v2.0 (http://zoa.freeservers.com) can do what you want, the molecular orbital for Zindo-G98 are stored in the fort.7 and when you open the log file, Zoa ask you the location of the fort.7 and also enable you to rename it for further use. Have a nice day Jean-Phi -----Message d'origine----- De : Ohyun Kwon [mailto:okwon@u.arizona.edu] Envoyé : dimanche 20 octobre 2002 22:36 À : chemistry@ccl.net Objet : CCL:ZINDO MO visualization in G98 Dear CCLers' I would like to know what is the iop option for printing population analysis of zindo in G98. I want to display molecular orbitals of zindo results by using molden program. I tried to used iop(6/7=3) as well as iop(5/33=1) or iop(5/3=2), but they do not work for molden. I would appreciate any advice on this matter. Thank you in advance! Best wishes, Tommy Kwon, Ph.D University of Arizona -= This is automatically added to each message by mailing script =- CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net From chemistry-request@server.ccl.net Mon Oct 21 08:44:42 2002 Received: from iris.chimfarm.unipg.it ([141.250.13.4]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g9LCifK06879 for ; Mon, 21 Oct 2002 08:44:41 -0400 Received: from mc.chimfarm.unipg.it ([141.250.13.99] helo=mc) by iris.chimfarm.unipg.it with smtp (Exim 2.04 #2) id 183igi-00006R-00 for chemistry@ccl.net; Mon, 21 Oct 2002 12:58:09 -0700 Message-ID: <000f01c27900$8cbd43d0$630dfa8d@mc> Reply-To: "menix" From: "menix" To: Subject: Molecular surface determination Date: Mon, 21 Oct 2002 14:51:13 +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 Hy all, I need a software that, given a molecule as input, gives me the coordinates of molecular surface's points. better if it is a computational routine that I can include in my own routine. thanks From chemistry-request@server.ccl.net Mon Oct 21 08:21:12 2002 Received: from as1200.organik.uni-erlangen.de ([131.188.128.6]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g9LCLBK06401 for ; Mon, 21 Oct 2002 08:21:11 -0400 Received: from mol-net.de (aragorn.chemie.uni-erlangen.de [131.188.127.230]) by as1200.organik.uni-erlangen.de (8.8.7/8.1.11-FAU) with ESMTP id OAA18106 for ; Mon, 21 Oct 2002 14:21:11 +0200 (MET DST) Message-ID: <3DB3F19C.68626628@mol-net.de> Date: Mon, 21 Oct 2002 14:22:52 +0200 From: Info - Molecular Networks GmbH Reply-To: sacher@mol-net.de Organization: Molecular Networks GmbH X-Mailer: Mozilla 4.76 [en] (Windows NT 5.0; U) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net Subject: Announcement: CLIFF - a new file format converter Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit CLIFF 1.17 Announcement – a new program for file format conversion ------------------------------------- Molecular Networks GmbH is pleased to announce a new program called CLIFF for the interconversion of more than 40 different chemical structure exchange file formats. CLIFF supports most of the commonly used formats for chemical compounds (SMILES, SDF, MOL, MOL2, ...) and reactions (RXN, RDF). CLIFF (Chemical Libraries - Interconversion of File Formats) is a powerful program which provides a series of functionality, which goes beyond a simple conversion tool: * generation of 2D coordinates by a state-of-the-art 2D structure layout module of the CACTVS system licensed from Xemistry GmbH * template-based 2D structure arrangement * enrichment of datasets with additional information, such as molecular weight, number of H-donors, etc. * automatic hydrogen addition or removal * features for the removal of counterions in salts It can be applied to * interfacing a variety of chemical information and data processing systems * maintenance and standardization of compound and reaction databases * preprocessing of datasets by adding missing data or converting to file formats required by other programs As it was designed to handle large datasets of hundreds of thousands of chemical structures the program is available as a command line program. CLIFF is available for x86 Linux, SGI IRIX, Sun Solaris, or Windows NT/2000/XP. For further information please visit our website http://www.mol-net.de/ or contact us via fax +49 9131 815669 or by e-mail info@mol-net.de -- Molecular Networks GmbH Dr. Oliver Sacher Nägelsbachstr. 25 91052 Erlangen, Germany Email: sacher@mol-net.de Web: http://www.mol-net.de From chemistry-request@server.ccl.net Mon Oct 21 09:21:05 2002 Received: from soul.helsinki.fi ([128.214.3.1]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g9LDL5G07970 for ; Mon, 21 Oct 2002 09:21:05 -0400 Received: from localhost (mpjohans@localhost) by soul.helsinki.fi (8.9.3/8.9.3) with ESMTP id QAA06313; Mon, 21 Oct 2002 16:20:56 +0300 (EET DST) X-Authentication-Warning: soul.helsinki.fi: mpjohans owned process doing -bs Date: Mon, 21 Oct 2002 16:20:56 +0300 (EET DST) From: Mikael Johansson X-Sender: To: Subject: Winter School in Theoretical Chemistry, 2002 Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hello All! It is soon again time for the annual Winter School in Theoretical Chemistry. This years topic is "Large Molecules: Linear Scaling and Related Electronic Structure Calculation Methods". The School takes place on December 9-12 at the University of Helsinki, Finland. Visit the home page of the School for more info: http://www.chem.helsinki.fi/Info/WinterSchool/ws2002.html A brief summary is also found below. Have a nice day, Mikael Johansson University of Helsinki Department of Chemistry mikael.johansson@helsinki.fi http://www.helsinki.fi/~mpjohans/ Phone: +358-9-191 50185 FAX : +358-9-191 50169 =========================== Winter School in Theoretical Chemistry, 2002 Large Molecules: Linear Scaling and Related Electronic Structure Calculation Methods TIME: 9-12 December, 2002. (Start at 10:00 on Monday) VENUE: Department of Chemistry, University of Helsinki, A.I. Virtanens plats 1, 00014 Helsinki, Finland. LECTURERS: Fred Manby, Kari Rissanen, Ulf Ryde, Joachim Sauer, Gustavo Scuseria, and Thomas Bondo Pedersen FEES: University students and staff: none. ADMISSION: Participants are requested to register by 15 November, 2002 at the address below: Dr Juha Vaara, Dept. of Chemistry, P.O. Box 55 (A.I. Virtasen aukio 1), FIN-00014 University of Helsinki, Finland. Telephone: +358-9-191 50181. FAX: +358-9-191 50169. E-mail: jvaara@chem.helsinki.fi From chemistry-request@server.ccl.net Mon Oct 21 11:32:08 2002 Received: from cornell.edu ([132.236.56.6]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g9LFW8G11511 for ; Mon, 21 Oct 2002 11:32:08 -0400 Received: from cornell.edu (grumpy.lassp.cornell.edu [128.84.241.119]) by cornell.edu (8.9.3/8.9.3) with ESMTP id LAA04292 for ; Mon, 21 Oct 2002 11:32:04 -0400 (EDT) Sender: cc236@cornell.edu Message-ID: <3DB41DF3.A4C5E142@cornell.edu> Date: Mon, 21 Oct 2002 11:32:03 -0400 From: Connie Chang X-Mailer: Mozilla 4.77 [en] (X11; U; Linux 2.2.19-6.2.1smp i686) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net Subject: Gaussian script question Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi all -- I'm trying to construct a Hessian matrix using Gaussian. I'm working on a 140 atom molecule with mainly carbons. But when I ask it to do a frequency calculation with PM3, the calculation dies after running for four days or so on a Pentium IV processor... I have access to a cluster, but I can only submit Gaussian jobs (.gjf) as a batch file. I think I'll just ask Gaussian to do a series of single point calculations from an already minimized structure. Does anyone know the best way to do this? I'll have to ask Gaussian to give me 140*3*2 single point calculations. Could I do this all in one .gjf file by using the --Link1-- separator between calculations? Or is it better to break it up? And if it is, how should I break it up? Thanks, Connie From chemistry-request@server.ccl.net Mon Oct 21 12:27:18 2002 Received: (from root@localhost) by server.ccl.net (8.11.6/8.11.0) id g9LGRIt12864 for chemistry@ccl.net; Mon, 21 Oct 2002 12:27:18 -0400 Received: from mail.ic.sunysb.edu ([129.49.1.4]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g9LFIlG11253 for ; Mon, 21 Oct 2002 11:18:47 -0400 Received: from postal.ic.sunysb.edu (mail [129.49.1.4]) by mail.ic.sunysb.edu (8.11.6/8.11.6) with SMTP id g9LFIlW14435 for ; Mon, 21 Oct 2002 11:18:47 -0400 (EDT) Received: from smtp.ic.sunysb.edu ([129.49.1.24]) by postal.ic.sunysb.edu (NAVGW 2.5.2.9) with SMTP id M2002102111184714058 for ; Mon, 21 Oct 2002 11:18:47 -0400 Received: from sparky.ic.sunysb.edu (daemon@sparky.ic.sunysb.edu [129.49.1.3]) by smtp.ic.sunysb.edu (8.11.6/8.11.6) with ESMTP id g9LFIlT14428 for ; Mon, 21 Oct 2002 11:18:47 -0400 (EDT) Received: from localhost (yonyang@localhost) by sparky.ic.sunysb.edu (8.11.6/8.11.6) with ESMTP id g9LFIle28539 for ; Mon, 21 Oct 2002 11:18:47 -0400 (EDT) Date: Mon, 21 Oct 2002 11:18:47 -0400 (EDT) From: Yong Liang Yang To: chemistry@ccl.net Subject: HF/PCM Optimization of big boron/nitrogen containing molecule Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hello,dear mates: I am now trying to do geometry optimization in Gaussian 98(HF/6-31G*/PCM) for a big molecule. The system I am playing with is a molecule containing Boron and nitrogen. Considering the Boron maybe the negative charge center,I want to times the van der waal radius of Boron by 1.2, but I just do not know how to do or express this in my input section of G98,could anybody give me some advice? Additionally, is there anybody who could give me some advice in doing PM3-SM3 semi-empirical method of geometry optimization for this molecule? Thanks! Yongliang Yang Department of Chemistry SUNY-Stony Brook Stony Brook,11794 From chemistry-request@server.ccl.net Mon Oct 21 11:36:10 2002 Received: from mail-01.med.umich.edu ([141.214.93.149]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g9LFa9G11615 for ; Mon, 21 Oct 2002 11:36:09 -0400 Received: from gwia-01-MTA by mail-01.med.umich.edu with Novell_GroupWise; Mon, 21 Oct 2002 11:36:08 -0400 Message-Id: X-Mailer: Novell GroupWise Internet Agent 6.0.2 Date: Mon, 21 Oct 2002 11:35:57 -0400 From: "Renxiao Wang" To: Subject: Release of X-CScore v1.0: New scoring function available Mime-Version: 1.0 Content-Type: text/plain; charset=Windows-874 Content-Disposition: inline Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id g9LFaAG11616 Please disregard this message if you have received it before. —----------------------------------------------------------------------- Dear All, We would like to announce the release of X-CScore v1.0, a program for estimating protein-ligand binding affinites. Basically, X-CScore is a consensus scoring scheme that consists of three individual empirical scoring functions. It makes fast prediction based purely on protein-ligand complex structures and thus will see its major application to molecular docking approaches. The X-CScore algorithm is described in details on J. Comp.-Aided Mol. Des. 2002, 16:11-26. We have set up a web site for releasing this program, which is at http://sw16.im.med.umich.edu/software/xtool/. All you need to do is to fill out a user license agreement and fax it to us, then you will receive an email describing how to download the whole X-CScore packet. The packet includes the source codes, user manual, and other supplementary material. The X-CScore program is written in ANSI C++ and has been tested on UNIX and LINUX platforms. There is NO CHARGE for obtaining this program, applied to all the users from industry and academia. If you experience any problem in downloading or using this program, you may contact us directly. Happy scoring, Renxiao Wang, Ph.D. Research Investigator Department of Internal Medicine University of Michigan Medical School renxiao@med.umich.edu From chemistry-request@server.ccl.net Mon Oct 21 09:30:17 2002 Received: from yangtze.hku.hk ([147.8.148.244]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g9LDUGG08298 for ; Mon, 21 Oct 2002 09:30:16 -0400 Received: from localhost (lhhu@localhost) by yangtze.hku.hk (8.11.6/8.9.3) with ESMTP id g9LDfHL23978 for ; Mon, 21 Oct 2002 21:41:17 +0800 Date: Mon, 21 Oct 2002 21:41:17 +0800 (HKT) From: Hu LiHong To: chemistry@ccl.net Subject: Standalone CHARMm help! Message-ID: MIME-Version: 1.0 Content-Type: MULTIPART/Mixed; BOUNDARY="143914132-1298156793-1035171366=:22430" Content-ID: This message is in MIME format. The first part should be readable text, while the remaining parts are likely unreadable without MIME-aware tools. Send mail to mime@docserver.cac.washington.edu for more info. --143914132-1298156793-1035171366=:22430 Content-Type: TEXT/PLAIN; CHARSET=US-ASCII Content-ID: Dear all, I have tried CHARMM calculation many times, there are always some problem happened. Who has used the CHARMM to calculate protein can share some experience with me. In my calculation, I feel CHARMM is a terrible program. The total energy calculated by sd and abnr have so much difference I can't imagine. I don't know what wrong with it. I want to consult a CHARMM expert about protein calculation. 1. I want to use QM/MM calculate protein to get binding energy between a ligand (about 30 atoms) and a protein (about 5300 atoms). Can I realize my calculation by standalone CHARMM 27.3 version? What keywords I should choose? (I knew I should use 'quan sele segi qm-atoms end method' for qmmm calculation) Can I find the binding energy in the qmmm calculation output file directly? (I mean just plus some energy terms to get the binding energy of two part.) 2. In QMMM calculation, should I minimize the structure of protein? If yes, I should minimize it before qmmm calculation or after qmmm calculation? Which minimization method should I choose? Until now, I have use SD and ABNR, both don't work well, SD is noconvergent method, I get energy (-19000 or so by 10000 nstep), but ABNR energy is (+1.4*E+61), is it horrible? And in the output files there are "Maximum group spatial extent (12A) exceeded" complainted, how can I extend the group boundary? 3. Could you provide me a sample input file for protein qmmm calculation not for small molecule? I attach my input file and Could you correct the mistake for me? I am very appropriated your great help, Best Wishes, Carol --143914132-1298156793-1035171366=:22430 Content-Type: TEXT/PLAIN; CHARSET=US-ASCII; NAME="qmmm.inp" Content-Transfer-Encoding: BASE64 Content-ID: Content-Description: Content-Disposition: ATTACHMENT; FILENAME="qmmm.inp" KiBTY3JpcHQgZmlsZSBwcm9kdWNlZCBieSBJTlNJR0hUDQoqDQohIFN0YXJ0 dXAgc2NyaXB0IGZvciBDSEFSTW0NCiENClVQUEVSICAhIGNhc2UgZm9yIGZp bGUgdG8gd3JpdGUNCkJPTUJMRVZFTCAtMg0KV1JOTEVWIDANClBSTkxFViA1 DQohIFNjcmlwdCB0byByZWFkIHBhcmFtZXRlciwgcHNmIGFuZCBjcmQgZmls ZQ0KIQ0KT1BFTiBSRUFEIFVOSVQgMjEgQ0FSRCBOQU1FICIvaG9tZS90bXAv bXNpL0kyMDAwL2lyaXg2bTQvYmlvc3ltX2xpYi8vQU1JTk9ILlJURiINClJF QUQgUlRGIFVOSVQgMjEgQ0FSRCANCkNMT1NFIFVOSVQgMjENCk9QRU4gUkVB RCBVTklUIDIxIENBUkQgTkFNRSAiL2hvbWUvdG1wL21zaS9JMjAwMC9pcml4 Nm00L2Jpb3N5bV9saWIvL0NIQVJNTV9zdXBwb3J0LnJ0ZiINClJFQUQgUlRG IFVOSVQgMjEgQ0FSRCBBUFBFTkQNCkNMT1NFIFVOSVQgMjENCg0KT1BFTiBS RUFEIFVOSVQgMjAgQ0FSRCBOQU1FICIvaG9tZS90bXAvbXNpL0kyMDAwL2ly aXg2bTQvYmlvc3ltX2xpYi8vUEFSTS5QUk0iDQpSRUFEIFBBUkEgVU5JVCAy MCBDQVJEIA0KQ0xPU0UgVU5JVCAyMA0KDQpPUEVOIFJFQUQgVU5JVCAyMCBD QVJEIE5BTUUgInBfMWFkc19mMW5fNV80LnBzZiINClJFQUQgUFNGIFVOSVQg MjAgQ0FSRA0KQ0xPU0UgVU5JVCAyMA0KDQpPUEVOIFJFQUQgVU5JVCAyMCBD QVJEIE5BTUUgInBfMWFkc19mMW5fNV80LmNyZCINClJFQUQgQ09PUiBVTklU IDIwIENBUkQNCkNMT1NFIFVOSVQgMjANCg0KDQoNCiEtLS0tLS0tLS0tLXFt bW0gY2FsY3VsYXRpb24gY29udHJvbC0tLS0tLS0tLS0tLQ0KDQpxdWFOIHNl bGUgc2VnaSBQXzFjIGVuZCBhbTEgZW5lcmd5DQoNCnVwZGF0IGluYmZycSAx MDAwIGN1dG5iIDk5OTkuMCBjdG9ubmIgOTk3LjAgY3RvZm5iIDk5OC4wIC0N CiAgICAgIGNkaWUNCg0KbmJvbmRzIGdyb3VwIGV4dGVuZGVkIHJtaW4gMA0K DQptaW5pIGFibnIgc3RlcCAwLjAxIG5zdGVwIDEwMDAwIG5wcmludCAyMCBp aGJmcnEgMCBpbmJmcnEgMCBzdHJpY3QgMC4wNQ0KDQplbmVyZ3kgcHJpbnQg K2VuZXJnaWVzICtmaXJzdF9kZXZpdmF0aXZlIA0KDQpXUklURSBUSVRMRSBV TklUIDYNCiogRklOQUwgRU5FUkdZID0gP1RPVEsgP0VORVINCg0KT1BFTiBX UklUIFVOSVQgNDEgQ0FSRCBOQU1FICJwXzFhZHNfZjFuXzVfNF9maW5hbC5j cmQiIA0KV1JJVCBDT09SIFVOSVQgNDEgQ0FSRA0KKiBDb29yZGluYXRlcyBh ZnRlciBzdGFnZQ0KKg0KDQoNClNUT1ANCg== --143914132-1298156793-1035171366=:22430-- From chemistry-request@server.ccl.net Mon Oct 21 13:23:07 2002 Received: from mail.csusb.edu ([139.182.2.16]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g9LHN7G14072 for ; Mon, 21 Oct 2002 13:23:07 -0400 Received: from mail.csusb.edu (localhost [127.0.0.1]) by mail.csusb.edu (8.12.5/8.12.5) with ESMTP id g9LHJE8s018636; Mon, 21 Oct 2002 10:19:14 -0700 (PDT) Received: from localhost (kcousins@localhost) by mail.csusb.edu (8.12.5/8.12.5/Submit) with SMTP id g9LHJECE018630; Mon, 21 Oct 2002 10:19:14 -0700 (PDT) Date: Mon, 21 Oct 2002 10:19:14 -0700 (PDT) From: Kimberley Cousins To: chemistry@ccl.net cc: concep@csci.csusb.edu Subject: is there a need? In-Reply-To: <3DB3F19C.68626628@mol-net.de> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII To all, A colleague of mine in computer science is working on collaborative java software for various disciplines. He asked me if (a) there were presently such an application (applications) for drawing chemical structures, and (b) if there were a need to develop such a tool. I believe what he is proposing is something like one of the java-based structure input formats (think Marvin) that could be modified in "real time" by collaborators across the world (think interactive white board) I would appreciate replies from those who know of any such existing tools, as well as opinions of its potential usefulness. Thanks Kimberley Cousins Associate Professor of Chemistry California State University, San Bernardino 5500 University Parkway San Bernardino, CA 92407 (909)880-5391 kcousins@csusb.edu http://chem.csusb.edu/~kcousins From chemistry-request@server.ccl.net Mon Oct 21 15:50:46 2002 Received: from GWIA.HSC.WVU.EDU ([157.182.105.18]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g9LJokG16885 for ; Mon, 21 Oct 2002 15:50:46 -0400 Received: from HSC-DOM5-MTA by GWIA.HSC.WVU.EDU with Novell_GroupWise; Mon, 21 Oct 2002 15:50:43 -0400 Message-Id: X-Mailer: Novell GroupWise Internet Agent 6.0.2 Date: Mon, 21 Oct 2002 15:50:10 -0400 From: "Peter Gannett" To: "<" Subject: amber and namd Mime-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Content-Disposition: inline All: I am exploring using NAMD to run dynamics and want to run some comparisons. I currently use amber/sander so I have topology/coordinate files in amber format. I know NAMD can use these and that a config script/file has to be set up. Being lazy, I was wondering if someone had such a file that would run a dynamics run with amber topology/coordinate files under NAMD. Thanks. Pete Gannett From chemistry-request@server.ccl.net Mon Oct 21 18:06:47 2002 Received: from ks.uiuc.edu ([130.126.120.73]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g9LM6lG18895 for ; Mon, 21 Oct 2002 18:06:47 -0400 Received: from verdun.ks.uiuc.edu (verdun.ks.uiuc.edu [130.126.120.129]) by ks.uiuc.edu (8.11.2/8.11.2) with ESMTP id g9LM6iB17890; Mon, 21 Oct 2002 17:06:44 -0500 (CDT) Received: from localhost (jim@localhost) by verdun.ks.uiuc.edu (8.10.2+Sun/8.9.1) with ESMTP id g9LM6Pu17909; Mon, 21 Oct 2002 17:06:25 -0500 (CDT) X-Authentication-Warning: verdun.ks.uiuc.edu: jim owned process doing -bs Date: Mon, 21 Oct 2002 17:06:25 -0500 (CDT) From: Jim Phillips To: Peter Gannett cc: "<" Subject: Re: CCL:amber and namd In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi, The AMBER-specific parameters and some example translations are at: http://www.ks.uiuc.edu/Research/namd/current/ug/node15.html I hope that's enough to get you started. -Jim On Mon, 21 Oct 2002, Peter Gannett wrote: > All: > > I am exploring using NAMD to run dynamics and want to run some > comparisons. I currently use amber/sander so I have topology/coordinate > files in amber format. I know NAMD can use these and that a config > script/file has to be set up. Being lazy, I was wondering if someone > had such a file that would run a dynamics run with amber > topology/coordinate files under NAMD. Thanks. > > Pete Gannett > > -= This is automatically added to each message by mailing script =- > CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins > Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net > > > > > From chemistry-request@server.ccl.net Mon Oct 21 19:09:19 2002 Received: from donjuan.stud.chemie.tu-muenchen.de ([129.187.245.122]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g9LN9HG21841 for ; Mon, 21 Oct 2002 19:09:18 -0400 Received: from donjuan.stud.chemie.tu-muenchen.de (smmsp@localhost [127.0.0.1]) by donjuan.stud.chemie.tu-muenchen.de (8.12.3/8.12.3/Debian -4) with ESMTP id g9LN9IqE003093 for ; Tue, 22 Oct 2002 01:09:18 +0200 Received: (from banck@localhost) by donjuan.stud.chemie.tu-muenchen.de (8.12.3/8.12.3/Debian -4) id g9LN9HTV003091 for chemistry@ccl.net; Tue, 22 Oct 2002 01:09:17 +0200 From: Michael Banck Date: Tue, 22 Oct 2002 01:09:17 +0200 To: chemistry@ccl.net Subject: Re: CCL:is there a need? Message-ID: <20021021230917.GA3073@stud.ch.tum.de> Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Disposition: inline User-Agent: Mutt/1.3.28i + In-Reply-To: On Mon, Oct 21, 2002 at 10:19:14AM -0700, Kimberley Cousins wrote: > A colleague of mine in computer science is worki:ng on collaborative java > software for various disciplines. He asked me if > (a) there were presently such an application (applications) for > drawing chemical structures, and > (b) if there were a need to develop such a tool. There is the Chemistry Development Kit (CDK) http://cdk.sourceforge.net/ No idea if that is really what your colleague is looking for. Michael -- PS: Is there any good reason why @gmx.net is blocked from the list? From chemistry-request@server.ccl.net Mon Oct 21 16:38:12 2002 Received: from helium.acdlabs.com ([207.176.233.82]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g9LKcBG17747; Mon, 21 Oct 2002 16:38:11 -0400 Received: from notebdaria (noteb-daria.acdlabs.com [207.176.233.59]) by helium.acdlabs.com (8.10.2+Sun/8.10.2) with SMTP id g9LKcBD02846; Mon, 21 Oct 2002 15:38:11 -0500 (EST) Reply-To: From: "Daria Jouravleva" To: Cc: Subject: Re: Computer programs for estimating pKa values of small values Date: Mon, 21 Oct 2002 16:38:34 -0400 Message-ID: MIME-Version: 1.0 Content-Type: text/plain; charset="us-ascii" 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) Importance: Normal X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2600.0000 Reply-By: Fri, 18 Oct 2002 17:00:00 -0400 X-Message-Flag: Follow up In response to your request regarding the pKa prediction software made via CCL, I would like to draw your attention to ACD/pKa DB version 6.0: http://www.acdlabs.com/products/phys_chem_lab/pka/. This software is used by CAS to populate SciFinder organic data with calculated pKa values, and by the majority of pharmaceutical companies worldwide. ACD/Labs has tools to predict pKa for a wide variety of chemical organic classes. One can choose to calculate several pKa types (macroscopic, microscopic, single) for any number of compounds, from one per lifetime to thousands per day in automated mode (Batch version). If you are concerned about a handful of non-proprietary structures, you can use the online Interactive Laboratory (I-Lab) http://www.acdlabs.com/ilab/ that allows users to access the same prediction algorithms and databases of experimental pKa values on a pay-per-use basis. With best regards, Daria Jouravleva, Ph.D. Phone: (416) 368-3435 ext 248 US & Canada: (800) 304-3988 E-mail: daria@acdlabs.com -----Original Message----- From: Computational Chemistry List [mailto:chemistry-request@ccl.net] On Behalf Of Rami Reddy Sent: Thursday, October 17, 2002 12:42 PM To: chemistry@ccl.net Subject: CCL:Computer programs for estimating pKa values of small values We are looking for a computer program for estimating pKa values of small molecules (MW<500). If you know any good computer program(s), please let me know ASAP with all the details. Thanks, M. Rami Reddy Tel: (858)-622-3967 Emal: reddy@mbasis.com -= This is automatically added to each message by mailing script =- CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net