From chemistry-request@ccl.net Tue Jun 10 00:21:44 2003 Received: from mx1.ustc.edu.cn ([218.22.21.1]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h5A4LUkr024124 for ; Tue, 10 Jun 2003 00:21:39 -0400 Received: from dxl ([202.38.82.79]) by mx1.ustc.edu.cn (8.8.7/8.8.6) with ESMTP id MAA16564 for ; Tue, 10 Jun 2003 12:10:40 +0800 Message-Id: <200306100410.MAA16564_at_mx1.ustc.edu.cn> Date: Tue, 10 Jun 2003 12:12:27 +0800 From: 6!Q8@W Reply-To: dxl_at_mail.ustc.edu.cn To: CCls Subject: CCL: help-TD calculation in g98 Organization: VP9z?F4sQ!<|;/Q'J5QiJR X-mailer: FoxMail 4.0 beta 2 [cn] Mime-Version: 1.0 Content-Type: multipart/mixed; boundary="=====000_Dragon751088317432_=====" This is a multi-part message in MIME format. --=====000_Dragon751088317432_===== Content-Type: text/plain; charset="GB2312" Content-Transfer-Encoding: base64 RGVhciBDQ2xzo7oNCg0KoaGhoaGhSW4gYSBURCBjYWxjdWxhdGlvbiwgSSBnb3QgdGhlIHJlc3Vs dCBsaWtlIHRoaXM6DQoJDQoJoaEgRXhjaXRlZCBTdGF0ZSAgIDE6ICAgU2luZ2xldC1BJyAgICAg MS4xNzYxIGVWIDEwNTQuMTkgbm0gIGY9MC4yNzAyDQogICAgICAxOSAtPiAyMCAgICAgICAgIDEu NDY4NTENCiAgICAgIDE5IC0+IDI0ICAgICAgICAtMC4xMDA3Ng0KCQ0KCUlmIHRoZSBjb2VmZmlj aWVudCBvZiB0aGUgd2F2ZWZ1bmN0aW9uIGlzIGJpZ2dlciB0aGFuIDEuMDAsIHdoYXQgZG9lcyBp dCBtZWFuPw0KDQogICAgVGhhbmsgeW91IGZvciB5b3VyIGhlbHAhoaGhoaGhoaGhoaGhoaGhoQ0K IAkJCQkNCqGhoaGhoaGhoaGhoaGhoaGhoaGhoaGhoaGhoaFEaW5nIFh1bmxlaQ0KoaGhoaGhoaGh oaGhoaGhoaGhoaGhoaGhoaGhoTIwMDMtMDYtMDkNCl9fX19fX19fX19fX19fX19fX19fX19fX19f X19fX19fX19fX19fX19fX19fX18NCkRpbmcgWHVubGVpLCBQaC5ELiBDYW5kaWRhdGUNCk9wZW4g TGFib3JhdG9yeSBvZiBCb25kIFNlbGVjdGl2ZSBDaGVtaXN0cnkNCm5pdmVyc2l0eSBvZiBTY2ll bmNlICYgVGVjaG5vbG9neSBvZiBDaGluYQ0KPkhlZmVpLCBBbmh1aSAyMzAwMjYsIFAuUi5DaGlu YQ0KVGVsLjogMDA4Ni01NTEtMzYwMzQxOA0KRmF4LjogMDA4Ni01NTEtMzYwMjk2OQ0KRS1tYWls OiBkeGxAbWFpbC51c3RjLmVkdS5jbg0KaHR0cDovL3d3dy5ic2MudXN0Yy5lZHUuY24vfmR4bA0K DQo9ID0gPSA9ID0gPSA9ID0gPSA9ID0gPSA9ID0gPSA9ID0gPSA9ID0gDQo= --=====000_Dragon751088317432_===== Content-Type: image/gif; name="LittleBoy.GIF" Content-Transfer-Encoding: base64 Content-Disposition: FoxmailIcon; filename="LittleBoy.GIF" R0lGODlhIAAgANQAAGCXzwCAgGBnYP/IkPzJmpFjPBsNA2Q8HxQDACIGAk4HADYDAA0AAP///wAA ANPT05KSkm5ubmVlZUZGRiUlJRgYGBEREQ8PDwcHBwMDAwAAAAAAAAAAAAAAAAAAAAAAACH/C05F VFNDQVBFMi4wAwEAAAAh/sJodHRwOi8vd3d3LnJ0bHNvZnQuY29tL2FuaW1hZ2ljLwoKQ3JlYXRl ZCB3aXRoIEFuaW1hZ2ljIEdJRiBWIDEuMjJhCmJ5IFJpZ2h0IHRvIExlZnQgU29mdHdhcmUgSW5j LgoKVG8gc3VwcHJlc3MgdGhpcyBtZXNzYWdlIGluIHRoZSByZWdpc3RlcmVkIHZlcnNpb24KdW5j aGVjayAiT3B0aW9ucyB8IEFuaW1hZ2ljIGNvbW1lbnQgZnJhbWUiCgAh+QQJGQABACwAAAAAIAAg AAAF1mAgjmRpnmiqrqrjvjCLugNsO3LpDPz91rgcggf07XqyYa/nI9ZWytqy6HQGT1HrtEq8mhjc 45b7NImB5DTSrP6py6UoLfweLEwGpuBcJ95LYEANYm5vfyQOeQ4Ng12LfFyHIw5gi41AApdqkiIO CUxdjJppnAGBYYyQBQUERAoleW2QRAWuJFmOfbW1rySnfVy7A70jsV3ARAc8xCO/RXNkC8rDWGGz ZAgpzsgD2Srbfd4rCZ/ALjki5OXWXjKWoz2D6AEvooM2ojEtAADvqfz+BgE0EQIAIfkECRkAAQAs AAAAACAAIAAABc5gII5kaZ5oqq6q474wi7oDbDty6Qz8/da4HIIH9O16smGv5yPWVsrasuh0Bk9R 67RKvJoY3OOW+zSJgeQ00qz+qculKC38HixMhum5TryXwFKBVHV+JA55R2KJhGZgMFt7XIUjDglM XZhvkyKAYW5OBQUERAoleW2RRAWkJFldqVWrq6UknXxcsgO0I6eZtwMHPLsjtkVzZAvBulievwgp xb8DzyrRfNQrCZa3Ljki2tueXjIODeaR5eMrL+bnNu0xLQAA5e0NDvP18PkmIQAh+QQJGQABACwA AAAAIAAgAAAF02AgjmRpnmiqrqrjvjCLug9sO3LpPPz91rgchgf07XqyYa/nI9ZWytqy6HQGT1Hr tEq8mjLc45b7NImB5DTSrP6py6UoLfx+VEwWpuRcJ95LYEANYm5vfyQOeQ4Ng12LfFyHIw5gi41A EpdqkiIOF0xdjJppnAGBYYyQERFOFCV5bZBErDyuI1mOfaystiOnfVy7D70isF3ARBO1X1U2m8rD WGGyZBgpv8g81irYwNsrF5/ALjki4eLTXjKWoz2D5QEvooM2ojEtEBDsqfn7g/0mQgAAOw== --=====000_Dragon751088317432_=====-- From chemistry-request@ccl.net Mon Jun 9 19:12:17 2003 Received: from aguila.dti.udec.cl (aguila.dti.udec.cl [152.74.16.12]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h59NCGkr014054 for ; Mon, 9 Jun 2003 19:12:16 -0400 Received: (qmail 2588 invoked from network); 9 Jun 2003 23:12:11 -0000 Received: from andes.dpi.udec.cl (HELO udec.cl) ([127.0.0.1]) (envelope-sender ) by 0 (qmail-ldap-1.03) with SMTP for ; 9 Jun 2003 23:12:11 -0000 Message-ID: <3EE51450.5060200:at:udec.cl> Date: Mon, 09 Jun 2003 20:12:16 -0300 From: "Dr. Antonio Buljan" User-Agent: Mozilla/5.0 (Macintosh; U; PPC; en-US; rv:1.0.2) Gecko/20030208 Netscape/7.02 X-Accept-Language: en,pdf MIME-Version: 1.0 To: chemistry:at:ccl.net Subject: Theoretical, Quantum & Computational Chemistry Content-Type: text/plain; charset=us-ascii; format=flowed Content-Transfer-Encoding: 7bit Hello Netters... Someone knows a dictionary definition for the following terms: Quantum Chemistry Theoretical Chemistry Computational Chemistry Also I will thank if someone send me a reference where are defined these terms Thanks in advance.... Antonio Buljan From chemistry-request@ccl.net Tue Jun 10 08:25:24 2003 Received: from mailer.gwdg.de (mailer.gwdg.de [134.76.10.26]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h5ACPNkr003487 for ; Tue, 10 Jun 2003 08:25:24 -0400 Received: from vrlab03.mpibpc.gwdg.de ([134.76.211.99] helo=mpi-bpc.mpg.de) by mailer.gwdg.de with esmtp (Exim 4.14) id 19PiBh-0002gV-MW; Tue, 10 Jun 2003 14:25:17 +0200 Message-ID: <3EE5CE25.9070700[at]mpi-bpc.mpg.de> Date: Tue, 10 Jun 2003 14:25:09 +0200 From: Vlad Cojocaru User-Agent: Mozilla/5.0 (X11; U; Linux i686; en-US; rv:1.0.1) Gecko/20020823 Netscape/7.0 X-Accept-Language: en-us, en, ro MIME-Version: 1.0 To: CCL , amber , VMD Subject: helix axis for A-RNA Content-Type: text/plain; charset=us-ascii; format=flowed Content-Transfer-Encoding: 7bit Dear coleagues, I have an RNA molecule that comprises two helical regions and one loop and I would like to follow the agle between the 2 helices during an MD trajectory. I was thinking to represent the helical axis of the two helices and then calculate the angle between the 2 axis. I was trying with VMD to represent the helical axis but yet I didnt have a lot of success. If somebody knows how coould one define and represent the helical axis of an A type RNA helix within VMD or other software I would kindly appreciate any suggestions. Best wishes, vlad -- Vlad Cojocaru Max Planck Institute for Biophysical Chemistry Department: 060 Am Fassberg 11, 37077 Goettingen, Germany tel: ++49-551-201.1327 e-mail: Vlad.Cojocaru[at]mpi-bpc.mpg.de home tel: ++49-551-9963204 From chemistry-request@ccl.net Tue Jun 10 07:52:12 2003 Received: from alcides.host4u.net (alcides.host4u.net [216.71.64.98]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h5ABqCkr002838 for ; Tue, 10 Jun 2003 07:52:12 -0400 Received: from there (CPE0007954b9f8e-CM.cpe.net.cable.rogers.com [24.43.141.144]) by alcides.host4u.net (8.11.6/8.11.6) with SMTP id h5ABqBh27367 for ; Tue, 10 Jun 2003 06:52:12 -0500 Message-Id: <200306101152.h5ABqBh27367[at]alcides.host4u.net> Content-Type: text/plain; charset="iso-8859-1" From: Aniko Simon Organization: SimBioSys Inc. To: chemistry[at]ccl.net Subject: CCL: Announcing eHiTS flexible ligand docking Date: Tue, 10 Jun 2003 07:50:04 -0400 X-Mailer: KMail [version 1.3.2] MIME-Version: 1.0 Content-Transfer-Encoding: 8bit SimBioSys, Inc. is pleased to announce the release of a new docking program: eHiTS (electronic High Throughput Screening), which is a software suite for fast, accurate flexible ligand docking and is also suitable for virtual screening of large databases. Features * Accurate (see results: http://www.simbiosys.ca/ehits/ehits_validation.html) * Fast (see results: http://www.simbiosys.ca/ehits/ehits_speed.html): - Typical docking speed per ligand per CPU is a few seconds in VHTS mode, - Accurate ligand docking is usually performed in under a minute. * Fully Automated (i.e. no need for any manual preprocessing or pre-modelling): - Automatic pocket detection on the protein surface - Automatic assignment of partial charges to atoms - Determines protonation states using all alternatives in a single docking run - Automatic correction for common PDB file format errors * Customizable scoring function: - Parameters and weights of all scoring components can be adjusted - automatic training utility to optimise the scoring parameters for a specific set of ligand-receptor complexes * Parallel execution is supported (SMP, Linux clusters, distributed grid computing) * Systematic search method on continuous search space making it truly exhaustive (i.e. not limited to discrete dihedral angle samples or grid positions) * Reliable, reproducible results (no random stochastic or evolutionary elements) Availability eHiTS is currently available on Unix platforms (e.g. Linux and SGI/Irix) For more information about eHiTS please visit our website at: http://www.simbiosys.ca/ or contact us at info[at]simbiosys.ca -- Aniko Simon Ph.D., aniko[at]simbiosys.ca, http://www.simbiosys.ca/ From chemistry-request@ccl.net Tue Jun 10 05:19:29 2003 Received: from pump2.york.ac.uk (pump2.york.ac.uk [144.32.128.12]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h5A9JSkr032314 for ; Tue, 10 Jun 2003 05:19:28 -0400 Received: from thallium.york.ac.uk (thallium.york.ac.uk [144.32.52.130]) by pump2.york.ac.uk (8.12.9/8.12.9) with ESMTP id h5A9JQeF029776 for ; Tue, 10 Jun 2003 10:19:26 +0100 (BST) Content-Type: text/plain; charset="utf-8" From: Grant Hill To: chemistry[at]ccl.net Subject: CCL:Extremely large basis sets -- summary Date: Tue, 10 Jun 2003 10:19:39 +0100 User-Agent: KMail/1.4.3 MIME-Version: 1.0 Message-Id: <200306101019.39245.jgh105[at]york.ac.uk> Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id h5A9JTkr032315 Hi, Thanks to everyone that replied, the original posting was: One of my current research interests requires a very large basis set, which would ideally support the elements of the first two periods (or at the very least hydrogen and oxygen). The basis set would need to be larger than (for example) aug-cc-pV6Z, and in principle be as close to the basis set limit as possible. Does anyone on the list know of any basis sets which may fulfil these requirements? Either a reference to a journal article, or a url for a website would be hugely appreciated. The replies ----------------- > From Matthias Mohr: If I was using DFT methods it was suggested that I could use plane-waves, as implimented in various CPMD codes - the size can be increased by adjusting the energy cutiff. It was pointed out the CPMD is not limited to dynamics, and can be used for standard optimizations. > From Rene Fournier: I could construct my own sequence of well-tempered basis sets to systematically approach the basis set limit (some details of how to do this were provided). Well-tempered basis sets were also suggested by Christoph van WC From Tanja van Mourik: I could look at the aug-pV7Z basis sets of Feller, Peterson and Sordo. > From Frank Jensen: I was directed to a series of papers (the most recent being JCP 118, 2459) on polarization consistent basis sets which systematically approach the limit. > From my own searching I'm also considering the universal Gaussian basis set (JCP 108,5225) which has been implimented in G03. Grant Hill From chemistry-request@ccl.net Tue Jun 10 07:36:59 2003 Received: from cuces.unisi.it (cuces.unisi.it [193.205.4.2]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h5ABaukr002581 for ; Tue, 10 Jun 2003 07:36:59 -0400 Received: from CONVERSION-DAEMON.cuces.unisi.it by cuces.unisi.it (PMDF V6.1-1 #30546) id <01KWXJFLV2I80031QF~at~cuces.unisi.it> for chemistry~at~ccl.net; Tue, 10 Jun 2003 13:36:51 +0100 (MET) Received: from student.unisi.it (morgana.smin.unisi.it [172.16.29.95]) by cuces.unisi.it (PMDF V6.1-1 #30546) with ESMTPA id <01KWXJFJJM7W0031N6~at~cuces.unisi.it> for chemistry~at~ccl.net; Tue, 10 Jun 2003 13:36:50 +0100 (MET) Date: Tue, 10 Jun 2003 13:41:44 +0200 From: Lucilla angeli Subject: Stereoglasses Sender: lucilla~at~cuces.unisi.it To: chemistry~at~ccl.net Message-id: <3EE5C3F8.FA82B0A1~at~student.unisi.it> MIME-version: 1.0 X-Mailer: Mozilla 4.79C-SGI [en] (X11; I; IRIX64 6.5 IP30) Content-type: text/plain; charset=us-ascii Content-transfer-encoding: 7bit X-Accept-Language: en --Dear CCLers Since Sigma-Aldrich doesn't supply mirror stereoglasses VCH designed by Vogtle and Schuss any more, does anyone know how can I get them? Thanks in advance Lucilla ********************************* Lucilla Angeli c/o Prof. Botta Dip. Farmaco Chimico Tecnologico Universita' degli Studi Di Siena Via Aldo Moro I-53100 Siena, Italy Phone: ++39 0577 234307 Fax: ++39 0577 234333 ********************************** From chemistry-request@ccl.net Tue Jun 10 01:11:41 2003 Received: from exmails1.chem.ucla.edu (exmails1.chem.ucla.edu [169.232.134.2]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h5A5Bfkr025810 for ; Tue, 10 Jun 2003 01:11:41 -0400 Received: from [128.97.147.221] (ch-21.psnet.ucla.edu [128.97.147.221]) (authenticated bits=0) by exmails1.chem.ucla.edu (8.12.8/8.12.8) with ESMTP id h5A5BZ7s005098; Mon, 9 Jun 2003 22:11:36 -0700 Mime-Version: 1.0 X-Sender: scerri~at~chlorine.chem.ucla.edu (Unverified) Message-Id: In-Reply-To: <3EE51450.5060200~at~udec.cl> References: <3EE51450.5060200~at~udec.cl> Date: Mon, 9 Jun 2003 22:11:34 -0700 To: "Dr. Antonio Buljan" From: Eric Scerri Subject: Re: CCL:Theoretical, Quantum & Computational Chemistry Cc: ccl Content-Type: text/plain; charset="us-ascii" ; format="flowed" Alexandre Hocquet has recently submitted an article to "Foundations of Chemistry" in which he reports the results of a survey in which he asked practitioners to explain how they regard these terms. Although the paper is currently under review I see no harm in giving this advance notice of this forthcoming item. regards, eric scerri >Hello Netters... > >Someone knows a dictionary definition >for the following terms: > >Quantum Chemistry >Theoretical Chemistry >Computational Chemistry > > >Also I will thank if someone send me >a reference where are defined these terms > >Thanks in advance.... > > >Antonio Buljan > > > >-= This is automatically added to each message by mailing script =- >To send e-mail to subscribers of CCL put the string CCL: on your Subject: line >and send your message to: CHEMISTRY~at~ccl.net > >Send your subscription/unsubscription requests to: >CHEMISTRY-REQUEST~at~ccl.net HOME Page: http://www.ccl.net | Jobs >Page: http://www.ccl.net/jobs >If your mail is bouncing from CCL.NET domain send it to the maintainer: >Jan Labanowski, jkl~at~ccl.net (read about it on CCL Home Page) >-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ -- Dr. Eric Scerri , UCLA, Department of Chemistry & Biochemistry, 607 Charles E. Young Drive East, Los Angeles, CA 90095-1569 USA E-mail : scerri~at~chem.ucla.edu tel: 310 206 7443 fax: 310 206 2061 Web Page: http://www.chem.ucla.edu/dept/Faculty/scerri/index.html Editor of Foundations of Chemistry http://www.kluweronline.com/issn/1386-4238 Also see International Society for the Philosophy of Chemistry http://www.georgetown.edu/earleyj/ISPC.html From chemistry-request@ccl.net Tue Jun 10 04:48:26 2003 Received: from mail4.hitachi.co.jp (mail4.hitachi.co.jp [133.145.228.5]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h5A8mOkr031744 for ; Tue, 10 Jun 2003 04:48:25 -0400 Received: from mc2.mcg.hitachi.co.jp by mail4.hitachi.co.jp (8.9.3p2/3.7W-mail4) id RAA29337; Tue, 10 Jun 2003 17:48:22 +0900 (JST) Received: (from root@localhost) by mc2.mcg.hitachi.co.jp (8.11.6+Sun/8.11.6) id h5A8mLH15190 for ; Tue, 10 Jun 2003 17:48:21 +0900 (JST) Received: from unknown [192.168.2.1] by mc2.mcg.hitachi.co.jp with SMTP id TAA15186 ; Tue, 10 Jun 2003 17:48:21 +0900 Received: from navsg2.hitachi.co.jp by navsg2.hitachi.co.jp (8.9.3/3.7W-navsg2) id RAA09086; Tue, 10 Jun 2003 17:48:20 +0900 (JST) Received: from hul3.hitachi-ul.co.jp ([158.211.190.2]) by navsg2.hitachi.co.jp (NAVGW 2.5.2.17) with SMTP id M2003061017482027005 for ; Tue, 10 Jun 2003 17:48:20 +0900 Received: by hul3.hitachi-ul.co.jp (8.11.6+Sun/3.7W-hitachi-ul) id h5A8iE408219; Tue, 10 Jun 2003 17:44:14 +0900 (JST) Received: from hul2.hitachi-ul.co.jp [158.211.18.118] by hul3.hitachi-ul.co.jp with SMTP id TAA08214 ; Tue, 10 Jun 2003 17:44:14 +0900 Received: from k5jk-ux-09.hitachi-ul.co.jp (localhost [127.0.0.1]) by hul2.hitachi-ul.co.jp (8.8.8+Sun/3.6W-hul2) with ESMTP id RAA13316 for ; Tue, 10 Jun 2003 17:48:19 +0900 (JST) Received: from hitachi-ul.co.jp ([202.19.63.88]) by k5jk-ux-09.hitachi-ul.co.jp (8.11.4/8.11.4) with ESMTP id h5A8mFc20444 for ; Tue, 10 Jun 2003 17:48:15 +0900 (JST) Message-ID: <3EE59AE7.74135E06~at~hitachi-ul.co.jp> Date: Tue, 10 Jun 2003 17:46:45 +0900 From: "k.watanabe" X-Mailer: Mozilla 4.7 (Macintosh; I; PPC) X-Accept-Language: ja,en MIME-Version: 1.0 To: chemistry~at~ccl.net Subject: molecular conformer Content-Type: text/plain; charset=iso-2022-jp Content-Transfer-Encoding: 7bit Hi, Now, we search conformer that can change a bond, angle and torsion in molecule and generate many structures (like DS ViewerPro Conformer). Does anyone know this? Freeware is better for us. K. Watanabe From chemistry-request@ccl.net Tue Jun 10 09:36:46 2003 Received: from histidine.utmb.edu (histidine.utmb.edu [129.109.59.80]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h5ADajkr005567 for ; Tue, 10 Jun 2003 09:36:45 -0400 Received: from histidine.utmb.edu (localhost [127.0.0.1]) by histidine.utmb.edu (8.12.9/8.12.9) with ESMTP id h5ADaiUJ046213; Tue, 10 Jun 2003 08:36:44 -0500 (CDT) (envelope-from bdodson=at=histidine.utmb.edu) Received: (from bdodson@localhost) by histidine.utmb.edu (8.12.9/8.12.9/Submit) id h5ADaiVP046210; Tue, 10 Jun 2003 08:36:44 -0500 (CDT) From: "M. L. Dodson" MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Message-ID: <16101.57068.467886.313240=at=histidine.utmb.edu> Date: Tue, 10 Jun 2003 08:36:44 -0500 To: Vlad Cojocaru Cc: CCL , amber , VMD Subject: Re: helix axis for A-RNA In-Reply-To: <3EE5CE25.9070700=at=mpi-bpc.mpg.de> References: <3EE5CE25.9070700=at=mpi-bpc.mpg.de> X-Mailer: VM 7.14 under 21.1 (patch 14) "Cuyahoga Valley" XEmacs Lucid Reply-To: bdodson=at=scms.utmb.EDU Vlad Cojocaru writes: > Dear coleagues, > I have an RNA molecule that comprises two helical regions and one > loop and I would like to follow the agle between the 2 helices during an > MD trajectory. I was thinking to represent the helical axis of the two > helices and then calculate the angle between the 2 axis. I was trying > with VMD to represent the helical axis but yet I didnt have a lot of > success. If somebody knows how coould one define and represent the > helical axis of an A type RNA helix within VMD or other software I would > kindly appreciate any suggestions. > Best wishes, > vlad > > -- > Vlad Cojocaru > Max Planck Institute for Biophysical Chemistry > Department: 060 > Am Fassberg 11, 37077 Goettingen, Germany > tel: ++49-551-201.1327 > e-mail: Vlad.Cojocaru=at=mpi-bpc.mpg.de > home tel: ++49-551-9963204 I have had good luck using nab from the Case laboratory for these kinds of one-off computations (and for many other molecular modeling activities, as well). http://www.scripps.edu/case/ Bud Dodson -- M. L. Dodson bdodson=at=scms.utmb.edu 409-772-2178 FAX: 409-772-1790 From chemistry-request@ccl.net Tue Jun 10 10:21:39 2003 Received: from pantheon-po03.its.yale.edu (pantheon-po03.its.yale.edu [130.132.50.19]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h5AELdkr006988 for ; Tue, 10 Jun 2003 10:21:39 -0400 Received: from eros.pquim.unam.mx (lexa.chem.yale.edu [130.132.24.6]) by pantheon-po03.its.yale.edu (8.11.6p2/8.11.6) with ESMTP id h5AELcS02397 for ; Tue, 10 Jun 2003 10:21:38 -0400 (EDT) Message-ID: <3EE5E972.4020607{at}eros.pquim.unam.mx> Date: Tue, 10 Jun 2003 10:21:38 -0400 From: Ivan Tubert-Brohman User-Agent: Mozilla/5.0 (Windows; U; Windows NT 5.0; en-US; rv:1.1) Gecko/20020826 X-Accept-Language: en-us, en MIME-Version: 1.0 To: chemistry{at}ccl.net Subject: Re: CCL:Theoretical, Quantum & Computational Chemistry References: <3EE51450.5060200{at}udec.cl> Content-Type: text/plain; charset=us-ascii; format=flowed Content-Transfer-Encoding: 7bit X-YaleITSMailFilter: Version 1.0c (attachment(s) not renamed) See http://server.ccl.net/cgi-bin/ccl/message.cgi?2002+11+14+020 for a definition given during a recent discussion in this list. Ivan Dr. Antonio Buljan wrote: > Hello Netters... > > Someone knows a dictionary definition > for the following terms: > > Quantum Chemistry > Theoretical Chemistry > Computational Chemistry > > > Also I will thank if someone send me > a reference where are defined these terms > > Thanks in advance.... > > > Antonio Buljan > From chemistry-request@ccl.net Tue Jun 10 13:18:44 2003 Received: from aleph.net.uniovi.es (aleph.net.uniovi.es [156.35.11.1]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h5AHIikr012348 for ; Tue, 10 Jun 2003 13:18:44 -0400 Received: from CONVERSION-DAEMON.aleph.net.uniovi.es by aleph.net.uniovi.es (PMDF V6.1 #39514) id <01KWXVDEQ84W017L28.-at-.aleph.net.uniovi.es> for chemistry.-at-.ccl.net; Tue, 10 Jun 2003 19:18:40 +0200 (MET) Received: from Debug (ercina.si.uniovi.es [156.35.14.3]) by aleph.net.uniovi.es (PMDF V6.1 #39514) with SMTP id <01KWXVDDMVKW016LHN.-at-.aleph.net.uniovi.es> for chemistry.-at-.ccl.net; Tue, 10 Jun 2003 19:18:39 +0200 (MET) Date: Tue, 10 Jun 2003 19:18:39 +0000 (MET-1METDST) From: hvg.-at-.correo.uniovi.es Subject: To: chemistry.-at-.ccl.net Message-id: <01KWXVDDN0AA016LHN.-at-.aleph.net.uniovi.es> X-Mailer: Endymion MailMan Standard Edition v3.0.17 Content-transfer-encoding: 7BIT Hi, I am trying to run Gaussian under LINUX (Red Hat 8.0) and I find the following problem: When a "scr" large file must be created (for example, running a CCSD(T) calculation with MaxDisk=8GB) the program start extending this file until a size of 2.1GB (2099204 KB). Then, Gaussian aborts (out of disk space). Of course, I can create manually files as large as 8GB in my computer under LINUX with no problems. So it seems that is Gaussian which is generating the problem. I can run the same calculation by defining extensions of 1GB for the "scr" file in the command line. Is there any suggestion to solve the problem? Thanks From chemistry-request@ccl.net Tue Jun 10 21:29:05 2003 Received: from antivirus1.its.rochester.edu (antivirus1.its.rochester.edu [128.151.57.50]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h5B1T4kr021376 for ; Tue, 10 Jun 2003 21:29:04 -0400 Received: from antivirus1.its.rochester.edu (localhost [127.0.0.1]) by antivirus1.its.rochester.edu (8.12.9/8.12.4) with ESMTP id h5B1T4Dx017420 for ; Tue, 10 Jun 2003 21:29:04 -0400 (EDT) Received: from mail.rochester.edu (mail1.ats.rochester.edu [128.151.224.31]) by antivirus1.its.rochester.edu (8.12.9/8.12.4) with SMTP id h5B1T33h017417; Tue, 10 Jun 2003 21:29:03 -0400 (EDT) Received: from mail.rochester.edu (mail.rochester.edu [128.151.224.17]) by mail.rochester.edu (8.12.9/8.12.1) with SMTP id h5B1T23r020789; Tue, 10 Jun 2003 21:29:02 -0400 (EDT) Sender: weiz[at]mail.rochester.edu From: "weiz" Reply-to: weiz[at]mail.rochester.edu To: johns[at]ks.uiuc.edu Cc: chemistry[at]ccl.net Subject: vmd under windows X-Mailer: Quality Web Email v3.0q, http://netwinsite.com/refw.htm Date: Tue, 10 Jun 2003 21:29:02 -0400 Priority: normal Message-id: <3ee685de.5133.27812[at]mail.rochester.edu> Dear Sir: I want to use vmd to make some pictures for my paper, but I only have linux and windows system.when I used vmd under linux and render the picture into ps format, it lost most of the fanzy effect, the picture looks ugly. when I switch to windows machine and render the picture to "snapshot", it looks very good. however, some other problems come, I actually have a trajectory saved in xyz format, in linux, vmd can read all of them and show the movie, but under windows it can not even read one snapshot, the error message is *********************** Invalid switch - "tmp". 'C:\Program' is not recognized as an internal or external command,operable program or batch file. ERROR> Could not read file ...... ************************ can you give me some hint about this? Wei From chemistry-request@ccl.net Tue Jun 10 18:17:58 2003 Received: from web10706.mail.yahoo.com (web10706.mail.yahoo.com [216.136.130.214]) by server.ccl.net (8.12.8/8.12.8) with SMTP id h5AMHwkr017923 for ; Tue, 10 Jun 2003 18:17:58 -0400 Message-ID: <20030610221757.64270.qmail~at~web10706.mail.yahoo.com> Received: from [128.248.174.76] by web10706.mail.yahoo.com via HTTP; Tue, 10 Jun 2003 15:17:57 PDT Date: Tue, 10 Jun 2003 15:17:57 -0700 (PDT) From: Subject: QSAR: difference between regression-only CV r^2 and cross validated r^2? To: chemistry~at~ccl.net MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Dear colleagues: I am a newbie in QSAR. Recently I read several papers talking about the cross validated r^2 which is used for model validation. I get quite confused about the concepts of regression-only cross validated r^2 and cross validated r^2. These articles mentioned they are different but neither of them gave the clear explanation. In my knowledge, the CV r^2 is calculated by using formula q^2=1-PRESS/SD where PRESS is obtained from leave-one-out cross validation and SD is the total sum of squares from the experimentally measured bioactivity data. So can anyone tell me the difference between these two concepts. Thanks. Lei Huang Department of Bioengieering University of Illinois at Chicago Room 218 Science and Engineering Offices 851 S. Morgan St. (M/C 063) Chicago, IL 60607-7052 Email: hxbus~at~yahoo.com __________________________________ Do you Yahoo!? Yahoo! Calendar - Free online calendar with sync to Outlook(TM). http://calendar.yahoo.com