From chemistry-request@ccl.net Mon Mar 14 07:25:29 2005 Received: from pc15547.Chemie.Uni-Marburg.DE (pc15547.Chemie.Uni-Marburg.DE [137.248.152.10]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j2ECPTlm013406 for ; Mon, 14 Mar 2005 07:25:29 -0500 Received: by pc15547.Chemie.Uni-Marburg.DE (Postfix, from userid 500) id AA2A333A59; Mon, 14 Mar 2005 11:35:18 +0100 (CET) From: Ralf Tonner To: "Subbotina Julia" Subject: Re: CCL:Gaussian03W+NBO (direct search) Date: Mon, 14 Mar 2005 11:35:18 +0100 User-Agent: KMail/1.5.1 References: <002a01c52707$940cd350$3ca0320a@tos03> In-Reply-To: <002a01c52707$940cd350$3ca0320a@tos03> Cc: MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Disposition: inline Message-Id: <200503141135.18193.Tonner * chemie.uni-marburg.de> Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id j2ECPTlm013411 Hello Julia, I got the same problem a few weeks ago and could figure out the mistake in the NBO-Tutorial. The input should be: > $CHOOSE LONE 2 2 4 1 5 1 END BOND T 5 1 S 1 2 S 2 3 T 3 4 END $END > The mistake in the manual is the new line after "LONE": Something like > LONE 2 2 4 1 ... > is not allowed. Hope this helps. Cheers Ralf On Saturday 12 March 2005 14:29, Subbotina Julia wrote: > Dear CCLers, > > I have a little problem with Gaussian03W and NBO in it. > > I tried to perform direct NBO search via $CHOOSE. And in > output I got an error:" NATURAL BOND ORBITAL ANALYSIS: > > > > Error in input of bond orbitals: > > Keyword for orbital type is not LONE, BOND, or 3CBOND > (read `4 ')" > > > > So I decided to try the test file on NBO web page > (http://www.chem.wisc.edu/~nbo5/tut_ch.htm) and > unfortunately I got the same error: > > > > Did somebody have the same problem and what is the way to > solve it? > > > > My best regards, > > Julia Subbotina > > Urals State Technical University > > Chemistry Department > > TOSLab > > Ekaterinburg, Russia -- Ralf Tonner Philipps Universitdt Marburg Fachbereich Chemie AK Frenking Hans-Meerwein-Stra_e 35032 Marburg Germany Tel.: +49-6421/28-27030 Tonner * chemie.uni-marburg.de From chemistry-request@ccl.net Mon Mar 14 11:55:36 2005 Received: from server.ccl.net (ccl [127.0.0.1]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j2EGtatZ008664 for ; Mon, 14 Mar 2005 11:55:36 -0500 Received: (from apache@localhost) by server.ccl.net (8.13.1/8.13.1/Submit) id j2EGtaRL008663 for chemistry :: ccl.net; Mon, 14 Mar 2005 11:55:36 -0500 Date: Mon, 14 Mar 2005 11:55:36 -0500 Message-Id: <200503141655.j2EGtaRL008663 :: server.ccl.net> X-Authentication-Warning: server.ccl.net: apache set sender to chemistry-request :: ccl.net using -f From: "Ozgur, , Yazaydin" To: chemistry :: ccl.net X-Web-Message-Number: 050314115451-8612 Subject: W:Mean square displacement and self diffusion coefficient Dear CCL users I am trying to write a fortran code to calculate the mean square displacement and thus self diffusion coefficient. I examined several resources and also the previous discussion here in CCL. With my algorith the diffusion coefficient is siginificantly overestimated although I considered the 3D periodic BC and unfolded the trajectory. I suspect that I truly understand the idea of " time avarage" or "multiple time origins". I appreciate if you could post any useful reference or an available algorithm. Thanks From chemistry-request@ccl.net Mon Mar 14 11:40:49 2005 Received: from web30804.mail.mud.yahoo.com (web30804.mail.mud.yahoo.com [68.142.200.147]) by server.ccl.net (8.13.1/8.13.1) with SMTP id j2EGem9C007565 for ; Mon, 14 Mar 2005 11:40:48 -0500 Received: (qmail 79736 invoked by uid 60001); 14 Mar 2005 15:40:47 -0000 Comment: DomainKeys? See http://antispam.yahoo.com/domainkeys DomainKey-Signature: a=rsa-sha1; q=dns; c=nofws; s=s1024; d=yahoo.com; b=HfYhuEgLpKcBa8e4k97NPuoPFIvZd+csqmvZY0UxOkRknWr1jG+mCLJW2Vd1uXUSkLbeGH/wDq/cqdW8tUcRpq9AWrjrVhQqxkGkmpuoa0mt+JTKd3/U6Cengbib59NPJSvLmmT20h//yrqfgKkVDpl2J2ET8aEwkr6g7t6FDjU= ; Message-ID: <20050314154047.79734.qmail #%# web30804.mail.mud.yahoo.com> Received: from [67.110.18.100] by web30804.mail.mud.yahoo.com via HTTP; Mon, 14 Mar 2005 07:40:47 PST Date: Mon, 14 Mar 2005 07:40:47 -0800 (PST) From: Guosheng Wu Subject: Request for ASA parameters To: chemistry #%# ccl.net MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Hi there, I wonder if anyone could please help me with typical ASA (accessible surface area) parameters, for most protein and ligand atomic types. At my hand, I only have a paper by A. L. Lomize et al(Protein Science, 2002, 11, 1984). They provided some ASA parameters for C/S/N/O atoms: 19 cal/(mole A^2) for aliphatic C, 7 for aromatic C, -1 for S, -21 for N, and -66 for O. I guess there must be many other kinds of data, and for more atomic types(such as metal and halogens). Any information such as numerical data or literature (recent will be better) will be very appreaciated. -Guosheng Wu __________________________________ Do you Yahoo!? Make Yahoo! your home page http://www.yahoo.com/r/hs From chemistry-request@ccl.net Mon Mar 14 13:12:02 2005 Received: from penguin.dq.fct.unl.pt (penguin.dq.fct.unl.pt [193.136.125.112]) by server.ccl.net (8.13.1/8.13.1) with SMTP id j2EIC2Tn011792 for ; Mon, 14 Mar 2005 13:12:02 -0500 Received: from fct.unl.pt (srt1.dq.fct.unl.pt [193.136.125.97]) by penguin.dq.fct.unl.pt (Postfix) with ESMTP id DCDE1E7457 for ; Mon, 14 Mar 2005 16:08:48 +0000 (WET) Message-ID: <4235B717.7010505 -()- fct.unl.pt> Date: Mon, 14 Mar 2005 16:08:55 +0000 From: "J.Aires de Sousa" User-Agent: Mozilla/5.0 (Windows; U; Windows NT 5.1; en-US; rv:1.0.2) Gecko/20030208 Netscape/7.02 X-Accept-Language: en-us, en MIME-Version: 1.0 To: chemistry -()- ccl.net Subject: Neural network QSAR/QSPR of inorganic compounds Content-Type: text/plain; charset=us-ascii; format=flowed Content-Transfer-Encoding: 7bit Hi, I'm looking for nice examples of neural network QSAR / QSPR of inorganic or organometallic compounds, to include in a course. Suggestions? Thanks in advance, Joao Aires de Sousa -- Dr. Joao Aires de Sousa Departamento de Quimica, Faculdade de Ciencias e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal From chemistry-request@ccl.net Mon Mar 14 12:57:09 2005 Received: from server.ccl.net (ccl [127.0.0.1]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j2EHv9xR011144 for ; Mon, 14 Mar 2005 12:57:09 -0500 Received: (from apache@localhost) by server.ccl.net (8.13.1/8.13.1/Submit) id j2EHv91p011143 for chemistry -()- ccl.net; Mon, 14 Mar 2005 12:57:09 -0500 Date: Mon, 14 Mar 2005 12:57:09 -0500 Message-Id: <200503141757.j2EHv91p011143 -()- server.ccl.net> X-Authentication-Warning: server.ccl.net: apache set sender to chemistry-request -()- ccl.net using -f From: "girish, s, suravajhula" To: chemistry -()- ccl.net X-Web-Message-Number: 050314014430-11302 Subject: W:problem with solvent effect calculations Dear all, I was trying to perform solvent effect calculations on calix[4]arene crown-6 interaction with cesium in chcl3 as solvent. For that I placed cesium inside the crown structure did the PCM calculations But guassian gave me an error. What its actually doing is counting the number if bonds cesium is formin with all the surrounding atoms. And since cesium is very close to many atoms its showing errors like Hydrogen has two bonds. could any one suggenst me how to correct this error. I would be glad if any one can suggest me any other method how I should perform a solvent effect on calix[4]arene crown-6 and cesium with chcl3 as the solvent. Regards. Girish Suravajhula. From chemistry-request@ccl.net Mon Mar 14 14:51:34 2005 Received: from mx5.net.nih.gov (mailfwd.nih.gov [165.112.130.36]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j2EJpX1k017100 for ; Mon, 14 Mar 2005 14:51:34 -0500 Received: from mx5.net.nih.gov (localhost [127.0.0.1]) by mx5.net.nih.gov (8.12.10/8.11.6) with ESMTP id j2EIl0C5029703 for ; Mon, 14 Mar 2005 13:47:00 -0500 Received: from pollux.cber.nih.gov (pollux.cber.nih.gov [128.231.52.5]) by mx5.net.nih.gov (8.12.10/8.11.6) with ESMTP id j2EIkx8Z029700; Mon, 14 Mar 2005 13:46:59 -0500 Date: Mon, 14 Mar 2005 13:17:06 -0500 From: Rick Venable To: Guosheng Wu cc: chemistry[at]ccl.net Subject: Re: CCL:Request for ASA parameters In-Reply-To: <20050314154047.79734.qmail[at]web30804.mail.mud.yahoo.com> Message-ID: References: <20050314154047.79734.qmail[at]web30804.mail.mud.yahoo.com> ReplyTo: Rick_Venable[at]nih.gov MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII On Mon, 14 Mar 2005, Guosheng Wu wrote: > I wonder if anyone could please help me with typical ASA (accessible > surface area) parameters, for most protein and ligand atomic types. > > At my hand, I only have a paper by A. L. Lomize et al(Protein Science, > 2002, 11, 1984). They provided some ASA parameters for C/S/N/O atoms: > 19 cal/(mole A^2) for aliphatic C, 7 for aromatic C, -1 for S, -21 for > N, and -66 for O. > > I guess there must be many other kinds of data, and for more atomic > types(such as metal and halogens). Any information such as numerical > data or literature (recent will be better) will be very appreaciated. These types of ASA scale factors are sometimes referred to as atomic solvation parameters (ASP); David Eisenberg has done some work in this area, and a quick search on PubMed* turned up these 5 papers: * http://www.ncbi.nlm.nih.gov/PubMed Mallick P, Weiss R, Eisenberg D. The directional atomic solvation energy: an atom-based potential for the assignment of protein sequences to known folds. Proc Natl Acad Sci U S A. 2002 Dec 10;99(25):16041-6. Das B, Meirovitch H. Optimization of solvation models for predicting the structure of surface loops in proteins. Proteins. 2001 May 15;43(3):303-14. Wimley WC, Creamer TP, White SH. Solvation energies of amino acid side chains and backbone in a family of host-guest pentapeptides. Biochemistry. 1996 Apr 23;35(16):5109-24. Wesson L, Eisenberg D. Atomic solvation parameters applied to molecular dynamics of proteins in solution. Protein Sci. 1992 Feb;1(2):227-35. Yamashita MM, Wesson L, Eisenman G, Eisenberg D. Where metal ions bind in proteins. Proc Natl Acad Sci U S A. 1990 Aug;87(15):5648-52. =+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+= 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 =+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+= From chemistry-request@ccl.net Mon Mar 14 14:53:32 2005 Received: from ppsw-4.csi.cam.ac.uk (ppsw-4.csi.cam.ac.uk [131.111.8.134]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j2EJrUhn017218 for ; Mon, 14 Mar 2005 14:53:31 -0500 Received: from hermes-1.csi.cam.ac.uk ([131.111.8.51]:36960) by ppsw-4.csi.cam.ac.uk (smtp.hermes.cam.ac.uk [131.111.8.154]:25) with esmtpa (EXTERNAL:ab454) id 1DAuXi-0005ba-FI (Exim 4.44) (return-path ); Mon, 14 Mar 2005 18:43:54 +0000 Received: from prayer by hermes-1.csi.cam.ac.uk (hermes.cam.ac.uk) with local (PRAYER:ab454) id 1DAuXi-00082W-LQ (Exim 4.43) (return-path ); Mon, 14 Mar 2005 18:43:54 +0000 From: Andreas Bender To: CHMINF-L[at]LISTSERV.INDIANA.EDU, chemistry[at]ccl.net Cc: boyd[at]CHEM.IUPUI.EDU Subject: Re: molecular similarity Date: 14 Mar 2005 18:43:54 +0000 X-Mailer: Prayer v1.0.13 X-Originating-IP: [131.111.121.25] In-Reply-To: <423079CD.268012AA[at]chem.iupui.edu> Message-ID: References: <423079CD.268012AA[at]chem.iupui.edu> Mime-Version: 1.0 Content-Type: text/plain; format=flowed; charset=ISO-8859-1 Sender: ab454[at]hermes.cam.ac.uk X-Cam-ScannerInfo: http://www.cam.ac.uk/cs/email/scanner/ X-Cam-AntiVirus: No virus found X-Cam-SpamDetails: Not scanned > Hi, Is there a web server where one can submit SMILES or molfiles > and have a Tanimoto similarity score computed? Thanks, Don Hi Don and everyone interested, I just set up a web form for similarity searching at the following URL: http://cheminformatics.org/simsearch/ You can upload a query and a library (restricted to 1000 structures for traffic reasons) and the script will score and rank the library structures according to Tanimoto simimilarity to the query. Circular fingerprints ("MOLPRINT 2D") are used for this purpose; mol2 input format is required. (Might include the conversion from other formats in the future if I have time.) The descriptor has been recently validated and published in J. Chem. Inf. Comput. Sci. , 2004, 44, 170-178 ( DOI http://dx.doi.org/10.1021/ci034207y ) and J. Chem. Inf. Comput. Sci. , 2004, 44, 1708-1718 ( DOI http://dx.doi.org/10.1021/ci0498719 ) on several datasets from the MDDR. Source code / binaries for local installation can also be obtained > from me (for Linux and IRIX). Access to the web site as well as the tools themselves are free (feel free to invite me for a pint if you find the tool useful :-) ). And if you are looking for a postdoc in virtual screening or other areas of ligand-based drug design from early next year on - any location worldwide, interesting work more important than pay, you are more than welcome to contact me. Best wishes, Andreas P.S.: I tested the site on Windows and Linux with Netscape, IE and Konqueror - if there are any strange error messages or otherwise unexplicable behaviour please inform me. -- Andreas Kieron Patrick Bender http://www.andreasbender.de From chemistry-request@ccl.net Mon Mar 14 18:39:34 2005 Received: from postfix2-c.free.fr (postfix2-c.free.fr [213.228.0.80]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j2ENdSSE030554 for ; Mon, 14 Mar 2005 18:39:33 -0500 Received: from postfix3-2.free.fr (postfix3-2.free.fr [213.228.0.169]) by postfix2-c.free.fr (Postfix) with ESMTP id 9ED60B317E7 for ; Mon, 14 Mar 2005 23:17:28 +0100 (CET) Received: from [82.66.102.10] (michelet-4-82-66-102-10.fbx.proxad.net [82.66.102.10]) by postfix3-2.free.fr (Postfix) with ESMTP id B9385C048; Mon, 14 Mar 2005 23:17:26 +0100 (CET) In-Reply-To: <200503141655.j2EGtaRL008663 = server.ccl.net> References: <200503141655.j2EGtaRL008663 = server.ccl.net> Mime-Version: 1.0 (Apple Message framework v619.2) Content-Type: text/plain; charset=ISO-8859-1; delsp=yes; format=flowed Message-Id: Cc: ccl (E-mail) From: khinsen = cea.fr Subject: Re: CCL:W:Mean square displacement and self diffusion coefficient Date: Mon, 14 Mar 2005 23:17:20 +0100 To: "Ozgur, , Yazaydin" X-Mailer: Apple Mail (2.619.2) Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id j2ENdYSE030559 On 14.03.2005, at 17:55, Ozgur, , Yazaydin wrote: > I am trying to write a fortran code to calculate the mean square > displacement and thus self diffusion coefficient. I examined several > resources and also the previous discussion here in CCL. With my > algorith the diffusion coefficient is siginificantly overestimated > although I considered the 3D periodic BC and unfolded the trajectory. > I suspect that I truly understand the idea of " time avarage" or > "multiple time origins". I appreciate if you could post any useful > reference or an available algorithm. > The program nMoldyn calculates the mean square displacement (and other dynamical quantities) efficiently using an FFT-based method. You can download it at http://dirac.cnrs-orleans.fr/nMOLDYN/ On that page you can also find the references G.R. Kneller, V. Keiner, M. Kneller, M. Schiller nMOLDYN: A program package for a neutron scattering oriented analysis of Molecular Dynamics simulations Comp. Phys. Comm. 91, 191-214 (1995) T. Rsg, K. Murzyn, K. Hinsen, G. R. Kneller nMOLDYN: A Program Package for a Neutron Scattering Oriented Analysis of Molecular Dynamics Simulations J. Comp. Chem. 24(5), 657-667 (2003) which describe the algorithms and implementations. -- ------------------------------------------------------------------------ ------- Konrad Hinsen Laboratoire Leon Brillouin, CEA Saclay, 91191 Gif-sur-Yvette Cedex, France Tel.: +33-1 69 08 79 25 Fax: +33-1 69 08 82 61 E-Mail: khinsen = cea.fr ------------------------------------------------------------------------ -------