From owner-chemistry@ccl.net Tue Jul 3 03:15:01 2007 From: "St phane Vellay stephane.vellay=free.fr" To: CCL Subject: CCL: Managing downloaded reference pdf files Message-Id: <-34623-070703030626-1579-9T+6zVdGjObpWNsfrNtXYg~!~server.ccl.net> X-Original-From: "St phane Vellay" Date: Tue, 3 Jul 2007 03:06:22 -0400 Sent to CCL by: "St phane Vellay" [stephane.vellay++free.fr] Dear Mallik, I suggest you to use BibTeX. it "is a tool for formatting lists of references. The BibTeX tool is typically used together with the LaTeX document preparation system." Have a look at the free softwares available at the bottom of the page. http://en.wikipedia.org/wiki/BibTeX Use it in addition with the powerful TeXMed, to export PubMed to BibTeX: http://www.sbg.bio.ic.ac.uk/~mueller/TeXMed/ I recommend BibDesk (only for MacOSX) with which you can link to any files (including .pdf): http://bibdesk.sourceforge.net/ Kind regards Stephane | Dr Stephane VELLAY, PharmD | stephane.vellay() free.fr | http://stephane.vellay.free.fr From owner-chemistry@ccl.net Tue Jul 3 03:49:00 2007 From: "Simmie, John john.simmie::nuigalway.ie" To: CCL Subject: CCL:G: Rate of reaction Message-Id: <-34624-070703033854-14529-xGtLIQT6b/Yr9gJL8XCGEg!=!server.ccl.net> X-Original-From: "Simmie, John" Content-class: urn:content-classes:message Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="US-ASCII" Date: Tue, 3 Jul 2007 08:04:38 +0100 MIME-Version: 1.0 Sent to CCL by: "Simmie, John" [john.simmie*|*nuigalway.ie] You use Gaussian, etc to compute the barrier height (activation energy) and then Transition state theory to compute the rate constant k not as in you post the rate r which is a different quantity. Once you have k as a function of T then you can fit the data to the modified Arrhenius equation k = A T^n exp(-E/RT) John Simmie//National University of Ireland Galway -----Original Message----- > From: owner-chemistry**ccl.net [mailto:owner-chemistry**ccl.net] Sent: 02 July 2007 19:31 To: Simmie, John Subject: CCL: Rate of reaction Sent to CCL by: "Yousef Sharifi" [ysharifi^-^gmail.com] I am trying to use TST to estimate the activation energy for Ch3+H2->Ch4+H. If you consider the reaction rate as r= A*T^n*exp(-E/RT), how do you calculate the activation energy for various temperature ranges? for example 700k-1500k? How do you calculate the temperature power--n? Thanks From owner-chemistry@ccl.net Tue Jul 3 06:41:01 2007 From: "Oellien, F (Frank) Frank.Oellien],[Intervet.com" To: CCL Subject: CCL: 3. German Conference on Chemoinformatics Message-Id: <-34625-070703063903-4711-UBYGUH3eSeYoR1xe8OMhUQ#server.ccl.net> X-Original-From: "Oellien, F (Frank)" Content-class: urn:content-classes:message Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="iso-8859-1" Date: Tue, 3 Jul 2007 11:41:19 +0200 MIME-Version: 1.0 Sent to CCL by: "Oellien, F (Frank)" [Frank.Oellien-.-Intervet.com] Dear Colleagues, the CIC division of the German Chemical Society is proud to announce the 3. German Conference on Chemoinformatics (http://www.gdch.de/gcc2007) to be held in Goslar, Germany, November 11-13, 2007. This international symposium will address a broad range of modern research topics in the field of Computers and Chemistry. Focus will be on recent developments and trends in the fields of * Chemoinformatics and Drug Development * Chemical Information * Molecular Modelling * Computational Material Science and Nanotechnology and other highlights in the field of Computational Chemistry. The scientific program will include plenary lectures, short lectures as well as poster presentations. Invited Speakers are J. Bajorath, T. Oprea, A. Tropsha, A. Hillisch, T. Frauenheim A special highlight of the conference will be the awarding of the Gmelin-Beilstein-Denkmünze to Dr. Olga Kennard and the handover of the FIZ BERLIN Chemie awards. We will also award the three best poster submissions. Abstracts for oral contributions and posters can still be submitted until July 31. The conference website at http://www.gdch.de/gcc2007 has links to the abstract submission interface, a PDF version of the first circular as well as additional information. Feel free to contact me if you have questions. With kind regards Dr. Frank Oellien Scientist Intervet Innovation GmbH Zur Propstei 55270 Schwabenheim, Germany E-Mail: frank.oellien[*]intervet.com Phone: +49 (6130) 948 365 Fax: +49 (6130) 948 517 Home http://www.intervet.com Intervet Innovation GmbH is an Akzo Nobel company Sitz der Gesellschaft: Schwabenheim Amtsgericht Mainz, HRB 23 166 Geschäftsführer: Dr. Peter Schmid -------------------------------------- This message, including attachments, is confidential and may be privileged. If you are not an intended recipient, please notify the sender then delete and destroy the original message and all copies. You should not copy, forward and/or disclose this message, in whole or in part, without permission of the sender. -------------------------------------- From owner-chemistry@ccl.net Tue Jul 3 07:16:00 2007 From: "Jenniferf Clare Brookes ucapjcb]![ucl.ac.uk" To: CCL Subject: CCL:G: Gaussian input parameters Message-Id: <-34626-070703064919-8472-EAB/jkHCwRf76aUv791/SA|a|server.ccl.net> X-Original-From: "Jenniferf Clare Brookes" Date: Tue, 3 Jul 2007 06:49:14 -0400 Sent to CCL by: "Jenniferf Clare Brookes" [ucapjcb**ucl.ac.uk] Hi all, I have done a potential energy scan of a molecule using Gaussian 03, which gives the structure output at each step with the potential energy eigenvalue. The molecule specifications are in the same format as the input parameters Gaussian lists, so bond lengths, angles and dihedrals between atoms are listed. See below for example. Please can someone tell me if there is a program that will convert this to .xyz cartesian coordinates? I usually use babel to convert file formats, but I do not know what this file format actually is, if it is anything popularly used. Thank you very much. Jenny 11 EIGENVALUES -- -235.72712 R1 1.64747 R2 1.64806 R3 1.08684 R4 1.10655 R5 1.50695 R6 1.68276 R7 1.08974 R8 1.08724 R9 1.50688 R10 1.68262 R11 1.08720 R12 1.08970 R13 1.14086 R14 1.06147 R15 1.09617 R16 1.09634 R17 1.09619 R18 1.09634 A1 106.91803 A2 117.56272 A3 104.13313 A4 117.53447 A5 104.09912 A6 104.85103 A7 86.68473 A8 116.06098 A9 114.83340 A10 110.98164 A11 113.48103 A12 112.34167 A13 86.67196 A14 114.77670 A15 116.12895 A16 113.47913 A17 110.98097 A18 112.34345 A19 110.44036 A20 101.18141 A21 120.91893 A22 101.17311 A23 120.93294 A24 95.84916 A25 110.79656 A26 109.22065 A27 106.62858 A28 110.03778 A29 112.89682 A30 107.10285 A31 110.78728 A32 109.31483 A33 106.56693 A34 110.09651 A35 112.82150 A36 107.09824 D1 52.73206 D2 174.10246 D3 -70.48290 D4 -82.00204 D5 39.36836 D6 154.78300 D7 162.55750 D8 -76.07210 D9 39.34253 D10 -52.90133 D11 -174.40107 D12 70.17556 D13 81.84764 D14 -39.65210 D15 -155.07547 D16 -162.75047 D17 75.74979 D18 -39.67358 D19 -62.48486 D20 99.90214 D21 -153.57090 D22 -49.71506 D23 -148.32462 D24 -41.79766 D25 62.05818 D26 -14.48949 D27 92.03747 D28 -164.10669 D29 -5.75440 D30 115.28431 D31 -125.13659 D32 -122.44033 D33 -1.40161 D34 118.17749 D35 109.93559 D36 -129.02570 D37 -9.44659 D38 -100.07896 D39 153.38855 D40 49.53332 D41 14.29615 D42 -92.23634 D43 163.90843 D44 148.14594 D45 41.61345 D46 -62.24178 D47 5.98898 D48 -114.89885 D49 125.50717 D50 -109.63259 D51 129.47958 D52 9.88560 D53 122.74302 D54 1.85520 D55 -117.73878 From owner-chemistry@ccl.net Tue Jul 3 07:51:00 2007 From: "Paulo E. Abreu qtabreu_-_ci.uc.pt" To: CCL Subject: CCL: Managing downloaded reference pdf files Message-Id: <-34627-070703064423-6314-7jmyIM4OC2ZIyu3UGitcZg++server.ccl.net> X-Original-From: "Paulo E. Abreu" Content-Transfer-Encoding: 7bit Content-Type: text/plain Date: Tue, 03 Jul 2007 10:49:52 +0100 Mime-Version: 1.0 Sent to CCL by: "Paulo E. Abreu" [qtabreu^^^ci.uc.pt] Hello Take a look at referencer (http://icculus.org/referencer/) I think it does everything you need. Hope this helps. Paulo E. Abreu On Mon, 2007-07-02 at 09:26 -0400, Bhabani S Mallik mbhabani~!~yahoo.com wrote: > Sent to CCL by: "Bhabani S Mallik" [mbhabani_+_yahoo.com] > Dear All, > > I want to manage all my reference pdf files ( huge number) with a proper way. > I mean is there any software which can convert all my files to browsable > html pages with title, author, year of publication and a link to that pdf file ?> > > -- Departamento de Quimica e-mail:qtabreu\a/ci.uc.pt Faculdade de Ciencias e Tecnologia -o) da Universidade de Coimbra TEL:351 239 852080 / \ 3004-535 Coimbra FAX:351 239 827703 _\_v Portugal =============================================================================== "Independent hackers account for 28% of corporate computers intrusions; 29% of break-ins come from other corporations; 35% are the work of disgruntled employees." (source: Kessler) From owner-chemistry@ccl.net Tue Jul 3 09:54:00 2007 From: "=?ISO-8859-1?Q?=D6d=F6n?= Farkas farkas,,chem.elte.hu" To: CCL Subject: CCL: Gaussian input parameters Message-Id: <-34628-070703095104-27934-cAKo4cL0exNZdJx2Vyy2nQ .. server.ccl.net> X-Original-From: =?ISO-8859-1?Q?=D6d=F6n?= Farkas Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=UTF-8 Date: Tue, 03 Jul 2007 15:42:58 +0200 Mime-Version: 1.0 Sent to CCL by: =?ISO-8859-1?Q?=D6d=F6n?= Farkas [farkas=-=chem.elte.hu] Hi Jenny, I've got a simple script which does something what you need, you can find it at the end of the message. Best wishes, Ödön -- Ödön Farkas Associate professor Deparment of Organic Chemistry and Laboratory of Chemical Informatics, Institute of Chemistry, Eötvös Loránd University, Budapest Address: 1/A Pázmány Péter sétány, H-1117 Budapest, Hungary Phone: +36-1-372-2570 Cell phone: +36-30-255-3111 Fax: +36-1-372-2620 URL: http://organ.elte.hu/farkas #!/bin/bash (echo $* ; cat ) | awk ' BEGIN { getline for ( i = 1 ; i <= NF ; i++ ) { ax[i] = "" ax[i] = $(i) } nvar = NF } { if ( $1 == "Charge" && $2 == "=" ) { charge = $3 multiplicity = $6 } if ( $1 == "SCF" && $2 == "Done:" ) { e=$5 } if ( $1 == "Energy=" ) { e=$2 } if ( NF > 1 ) { if ( $(NF-1) == "Energy=" ) { e=$(NF) } } if ( $4 ~ /EUMP/ ) { e=$6 } if ( $3 == "E(Cis)" ) { e=$5 } if ( $1 == "ONIOM:" && $3 == "energy" ) { e=$(NF) } if ( ( $1 == "Input" || $1 == "Standard" || $1 == "Z-Matrix" ) && $2 == "orientation:" ) { getline getline getline getline i = 0 for ( getline ; NF > 1 ; getline ) { i++ NA = $1 IA[i] = $2 cx[i] = $4 cy[i] = $5 cz[i] = $6 } } if ( $2 == "Stationary" || ( $1 == "Optimization" && $2 == "completed." ) ) { print "--Link1--" print "_+_route.inc" getline getline getline getline getline getline for ( getline ; NF > 1 ; getline ) { for ( i = 1 ; i <= nvar ; i++ ) { if ( $2 == ax[i] ) { x[i] = $4 printf(" %15.7f",x[i]) } } } printf(" %15.7f\n",e) printf("\n") printf(" 0 1\n") for ( i = 1 ; i <= NA ; i++ ) { printf("%10d%15.6f%15.6f%15.6f\n",IA[i],cx[i],cy[i],cz[i]) } printf("\n") } } ' From owner-chemistry@ccl.net Tue Jul 3 11:38:00 2007 From: "Francisco Munoz dqufmi0,uib.es" To: CCL Subject: CCL: ESPA2008 Message-Id: <-34629-070703110302-25759-8/uBRLEnlTCrS7r2KxhNfA _ server.ccl.net> X-Original-From: "Francisco Munoz" Date: Tue, 3 Jul 2007 11:02:59 -0400 Sent to CCL by: "Francisco Munoz" [dqufmi0_+_uib.es] ESPA 2008, First announcement Dear Colleagues, We are pleased to inform you that the conference ELECTRONIC STRUCTURE: PRINCIPLES AND APPLICATIONS (ESPA 2008) will be held in Palma de Mallorca (Spain) from September 2-5, 2008. The first meeting of this series was held in Miraflores de la Sierra (Madrid) in 1998. Further editions were held in San Sebastian (2000), Sevilla (2002), Valladolid (2004) and Santiago de Compostela (2006). The conference topics include all aspects of Theoretical and Computational Chemistry as well as other related fields such as Physical, Inorganic and Organic Chemistry, Biochemistry and Drug Design. The conference program will consist of plenary lectures and oral and poster presentations. English will be the official language of the conference. Additional information can be found on the conference web site: www.espa2008.org. If you wish to receive further information, please fill in the Pre-register form or send an e-mail to: dqufmi0++uib.es We would like to encourage you to come to Palma de Mallorca and participate actively with a scientific contribution. We look forward to seeing you in Palma de Mallorca. Best regards The Organising Committee Josefa Donoso, Juan Frau, Bartolom Vilanova, Antoni Salv, Joaquin Ortega, Miquel Adrover and Francisco Munoz Francisco Muoz Professor of Physical Chemistry Department of Chemistry University of Balearic Islands 07112 Palma de Mallorca Tel.: + 34 971 17 32 52 Fax : + 34 971 17 34 26 e-mail: dqufmi0++uib.es http://www.uib.es/depart/dqu/dqf/indexc.htm. http://www.uib.es/depart/dqu/dqf/paco/ From owner-chemistry@ccl.net Tue Jul 3 12:13:00 2007 From: "Eszter Hazai Eszter.Hazai##virtuadrug.com" To: CCL Subject: CCL: Autodock chlorine containing compounds Message-Id: <-34630-070703075524-16974-X1AMlWrp2KSLhTq+Noxoyw . server.ccl.net> X-Original-From: "Eszter Hazai" Date: Tue, 3 Jul 2007 07:55:21 -0400 Sent to CCL by: "Eszter Hazai" [Eszter.Hazai]^[virtuadrug.com] Hi, has anyone any experience with docking chlorine containing compounds using Autodock 3.0 or 4.0? Although I have very good results with most of the compounds I docked, but not the ones containing chlorine. Any ideas? Thanks Eszter Hazai Eszter.Hazai ~ virtuadrug.com From owner-chemistry@ccl.net Tue Jul 3 12:48:01 2007 From: "Andrew Colasanti acolasanti[-]gmail.com" To: CCL Subject: CCL: Managing downloaded reference pdf files Message-Id: <-34631-070702123152-11578-MJHR9TE2ze2CdY2EbeVBug^_^server.ccl.net> X-Original-From: "Andrew Colasanti" Content-Disposition: inline Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Mon, 2 Jul 2007 11:30:08 -0400 MIME-Version: 1.0 Sent to CCL by: "Andrew Colasanti" [acolasanti#,#gmail.com] I have been using JabRef (jabref.sourceforge.net) for 3-4 years now to manage my references/pdfs. Jabref is similar to EndNote. Jabref won't convert all of your pdf's automatically so it will take some time getting everything set but after initial setup is is easy to keep things organized. Andrew On 7/2/07, Bhabani S Mallik mbhabani~!~yahoo.com wrote: > > Sent to CCL by: "Bhabani S Mallik" [mbhabani_+_yahoo.com] > Dear All, > > I want to manage all my reference pdf files ( huge number) with a proper way. > I mean is there any software which can convert all my files to browsable > html pages with title, author, year of publication and a link to that pdf file ?> > > > From owner-chemistry@ccl.net Tue Jul 3 15:29:00 2007 From: "Alejandro Velazquez mesientovivo * hotmail.com" To: CCL Subject: CCL:G: Gaussian input parameters Message-Id: <-34632-070703152522-25127-TAKQx5GY6Ky8UGkokACC/A:+:server.ccl.net> X-Original-From: "Alejandro Velazquez" Date: Tue, 3 Jul 2007 15:25:18 -0400 Sent to CCL by: "Alejandro Velazquez" [mesientovivo(_)hotmail.com] Hi Jenniferf! You can use Molden to visualize input files from Gaussian 03 and with it to obtain xyz coordinates. Molden can be downloaded from: http://www.cmbi.ru.nl/molden/howtoget.html Regards. Alejandro Sent to CCL by: "Jenniferf Clare Brookes" [ucapjcb**ucl.ac.uk] Hi all, I have done a potential energy scan of a molecule using Gaussian 03, which gives the structure output at each step with the potential energy eigenvalue. The molecule specifications are in the same format as the input parameters Gaussian lists, so bond lengths, angles and dihedrals between atoms are listed. See below for example. Please can someone tell me if there is a program that will convert this to .xyz cartesian coordinates? I usually use babel to convert file formats, but I do not know what this file format actually is, if it is anything popularly used. Thank you very much. Jenny From owner-chemistry@ccl.net Tue Jul 3 16:03:01 2007 From: "Fco. Javier Modrego modrego_+_unizar.es" To: CCL Subject: CCL: Managing downloaded reference pdf files Message-Id: <-34633-070703153811-30632-wyHnzV6jNE4KS/7no6CETA : server.ccl.net> X-Original-From: "Fco. Javier Modrego" Content-Type: multipart/alternative; boundary="============_-1028631014==_ma============" Date: Tue, 3 Jul 2007 21:37:54 +0200 Mime-Version: 1.0 Sent to CCL by: "Fco. Javier Modrego" [modrego]![unizar.es] --============_-1028631014==_ma============ Content-Type: text/plain; charset="us-ascii" ; format="flowed" cb2bib that can be found at http://www.molspaces.com/cb2bib/ can help to manage PDF and much more. I think it is worth to try... Hope this helps you F.J. Modrego Dr. F.J. Modrego Department of Inorganic Chemistry Facultad de Ciencias University of Zaragoza 50009 ZARAGOZA SPAIN Tel <34>-976-762288 Fax <34>-976-761187 E-mail: modrego(_)unizar.es --============_-1028631014==_ma============ Content-Type: text/html; charset="us-ascii" Re: CCL: Managing downloaded reference pdf files
cb2bib that can be found at http://www.molspaces.com/cb2bib/ can help to manage PDF and much more. I think it is worth to try...

Hope this helps you

        F.J. Modrego


 Dr. F.J. Modrego
 Department of Inorganic Chemistry
 Facultad de Ciencias
 University of Zaragoza
 50009 ZARAGOZA
 SPAIN
 Tel <34>-976-762288
 Fax <34>-976-761187
 E-mail:  modrego(_)unizar.es
--============_-1028631014==_ma============-- From owner-chemistry@ccl.net Tue Jul 3 17:19:00 2007 From: "Adam Tenderholt atenderholt..gmail.com" To: CCL Subject: CCL: Managing downloaded reference pdf files Message-Id: <-34634-070703171121-16979-3FGNnPUlwe5pwOlFssdnsQ . server.ccl.net> X-Original-From: "Adam Tenderholt" Content-Disposition: inline Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Tue, 3 Jul 2007 13:09:56 -0700 MIME-Version: 1.0 Sent to CCL by: "Adam Tenderholt" [atenderholt(-)gmail.com] If you use Mac OS X, you should also check out Papers: http://www.apple.com/downloads/macosx/math_science/papers.html Think iTunes with a built-in PDF viewer. The little bit I've used, it's pretty awesome. It is shareware, however, so you'll have to shell out a bit of money once the trial period expires. Adam From owner-chemistry@ccl.net Tue Jul 3 17:53:00 2007 From: "Manish Sud msud]|[sdsc.edu" To: CCL Subject: CCL: Availability of structure generation tools for lipids Message-Id: <-34635-070703173119-24127-ewLo7Rm734N7K6f3yEZRcA a server.ccl.net> X-Original-From: "Manish Sud" Date: Tue, 3 Jul 2007 17:31:14 -0400 Sent to CCL by: "Manish Sud" [msud|a|sdsc.edu] On behalf of the LIPID Metabolites And Pathways Strategy (LIPID MAPS) consortium, I would like to announce the availability of LipidMapsTools package, a collection of command line Perl scripts to generate structures and ontological data for various lipid categories. The current release of LipidMapsTools package supports structure generation for Fatty acyls, Glycerolipids, Glycerophospholipids, Cardiolipins, Sphingolipids and Sterols. Please visit www.lipidmaps.org/tools/ for further details and to download the package. Manish Sud msud ~ sdsc.edu From owner-chemistry@ccl.net Tue Jul 3 21:17:01 2007 From: "Jian computationalboy-.-gmail.com" To: CCL Subject: CCL: Autodock chlorine containing compounds Message-Id: <-34636-070703211541-29357-BuloySqvP9WxKPB7lDPiSw!^!server.ccl.net> X-Original-From: Jian Content-Type: multipart/alternative; boundary="----=_Part_79093_26257760.1183511734064" Date: Wed, 4 Jul 2007 09:15:34 +0800 MIME-Version: 1.0 Sent to CCL by: Jian [computationalboy]=[gmail.com] ------=_Part_79093_26257760.1183511734064 Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit Content-Disposition: inline You should edit the .pdbq file for the small molecules, in which you should rename chlorine to "c" as mentioned in AutoDock FAQ. Some other elements are as the same, such as iron was renamed to "f", bromine to "b", etc. Regards! On 7/3/07, Eszter Hazai Eszter.Hazai##virtuadrug.com < owner-chemistry]_[ccl.net> wrote: > > > Sent to CCL by: "Eszter Hazai" [Eszter.Hazai]^[virtuadrug.com] > Hi, > has anyone any experience with docking chlorine containing compounds using > Autodock 3.0 or 4.0? Although I have very good results with most of the > compounds I docked, but not the ones containing chlorine. Any ideas? > > Thanks > Eszter Hazai > Eszter.Hazai|*|virtuadrug.com> > > > ------=_Part_79093_26257760.1183511734064 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline You should edit the .pdbq file for the small molecules, in which you should rename chlorine to "c" as mentioned in AutoDock FAQ.
Some other elements are as the same, such as iron was renamed to "f", bromine to "b", etc.
Regards!

On 7/3/07, Eszter Hazai Eszter.Hazai##virtuadrug.com <owner-chemistry]_[ccl.net> wrote:

Sent to CCL by: "Eszter  Hazai" [Eszter.Hazai]^[ virtuadrug.com]
Hi,
has anyone any experience with docking chlorine containing compounds using Autodock 3.0 or 4.0? Although I have very good results with most of the compounds I docked, but not the ones containing chlorine. Any ideas?

Thanks
Eszter Hazai
Eszter.Hazai|*|virtuadrug.com



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------=_Part_79093_26257760.1183511734064-- From owner-chemistry@ccl.net Tue Jul 3 21:52:00 2007 From: "Caleb Carlin cmcarlin_._mtu.edu" To: CCL Subject: CCL: Implementing polarizable models Message-Id: <-34637-070703162851-30855-Foy99yWXeI5Dgco2QUWZUg,server.ccl.net> X-Original-From: "Caleb Carlin" Content-Type: multipart/alternative; boundary="----=_Part_71135_9385454.1183487765311" Date: Tue, 3 Jul 2007 14:36:05 -0400 MIME-Version: 1.0 Sent to CCL by: "Caleb Carlin" [cmcarlin:mtu.edu] ------=_Part_71135_9385454.1183487765311 Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit Content-Disposition: inline Hi all, I am trying to test the various water models to determine the most accurate for use in a larger system. I have run into problems implementing the PPC and SPC/FW models on Gromacs as there seems to be no native support for calculating local electric fields. Is it possible to implement polarizable models in Gromacs? If not, what package is needed to run such a system? Thank you for any help. Caleb Carlin ------=_Part_71135_9385454.1183487765311 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline Hi all,
I am trying to test the various water models to determine the most accurate for use in a larger system.  I have run into problems implementing the PPC and SPC/FW models on Gromacs as there seems to be no native support for calculating local electric fields.  Is it possible to implement polarizable models in Gromacs?  If not, what package is needed to run such a system?

Thank you for any help.
Caleb Carlin
------=_Part_71135_9385454.1183487765311-- From owner-chemistry@ccl.net Tue Jul 3 22:29:01 2007 From: "Rajarshi Guha rguha(a)indiana.edu" To: CCL Subject: CCL: Managing downloaded reference pdf files Message-Id: <-34638-070703142145-17197-iISZevllvk+yX9Trnayj4w##server.ccl.net> X-Original-From: Rajarshi Guha Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed Date: Tue, 3 Jul 2007 14:21:13 -0400 Mime-Version: 1.0 (Apple Message framework v752.3) Sent to CCL by: Rajarshi Guha [rguha**indiana.edu] On Jul 2, 2007, at 9:26 AM, Bhabani S Mallik mbhabani~!~yahoo.com wrote: > > Sent to CCL by: "Bhabani S Mallik" [mbhabani_+_yahoo.com] > Dear All, > > I want to manage all my reference pdf files ( huge number) with a > proper way. > I mean is there any software which can convert all my files to > browsable > html pages with title, author, year of publication and a link to > that pdf file ? If you're on a Mac, BibDesk is a fantastic piece of software. ------------------------------------------------------------------- Rajarshi Guha GPG Fingerprint: 0CCA 8EE2 2EEB 25E2 AB04 06F7 1BB9 E634 9B87 56EE ------------------------------------------------------------------- Despite the high cost of living, it remains popular. From owner-chemistry@ccl.net Tue Jul 3 23:02:01 2007 From: "Arthur G. Cox acox/a\southuniversity.edu" To: CCL Subject: CCL: molecular modeling for pharmacy students Message-Id: <-34639-070703162139-26780-CYNj6Fja6if2tjV+htBsIA^^server.ccl.net> X-Original-From: "Arthur G. Cox" Date: Tue, 3 Jul 2007 16:21:34 -0400 Sent to CCL by: "Arthur G. Cox" [acox%x%southuniversity.edu] I am trying to formulate a 3 hour computer laboratory exercise to illustrate the use of computers in drug design for pharmacy students. Can anyone point me towards recources or software that could be useful in this regard? Thanks -Art Cox