From owner-chemistry@ccl.net Thu Mar 30 02:02:00 2006 From: "Gopakumar gopakumar!A!chem.kuleuven.be" To: CCL Subject: CCL: Ghemical and Fedora3 Message-Id: <-31361-060330015923-15321-Vv8/lDI8lg6si7vU9T00wg]![server.ccl.net> X-Original-From: Gopakumar Content-Transfer-Encoding: 8bit Content-Type: TEXT/PLAIN; charset=X-UNKNOWN Date: Thu, 30 Mar 2006 08:59:11 +0200 (CEST) MIME-Version: 1.0 Sent to CCL by: Gopakumar [gopakumar _ chem.kuleuven.be] Dear Goncalo, Many thanks for your help. I've managed to install it under cygwin. I will try to get it done under fedora :-( Thanks again for your help -Gopa On Wed, 29 Mar 2006, [iso-8859-1] Gonçalo Deira Duarte de Campos Justino goncalo.justino.[a].zmail.pt wrote: > Sent to CCL by: =?iso-8859-1?Q?Gon=E7alo_Deira_Duarte_de_Campos_Justino?= [goncalo.justino-.-zmail.pt] > Dear Gopa, I tried a few months ago to compile ghemical under fedora and > under suse. Both required several libraries to be present, and sometimes > each of those libraries required another few libraries. This using the full > install CD's. The "problem" is that Ghemical requires several libraries that > were developed within a scientific frame that are common in suse and fedora. > After a few weeks of the make / make install tango it got to work, albeit at > the same speed as using cygwin under WinXP Pro :(. Persisitence is what it > takes ... > > Good luck > > Gonçalo > > _________________________________ > Gonçalo C. Justino > Molecule Chiseler and Radical Tinderer > http://depoisdos25.blogspot.com > -----Original Message----- > > From: owner-chemistry]_[ccl.net [mailto:owner-chemistry]_[ccl.net] > Sent: quarta-feira, 29 de Março de 2006 16:02 > To: Justino, Gonçalo > Subject: CCL: Ghemical and Fedora3 > > Sent to CCL by: Gopakumar [gopakumar%chem.kuleuven.be] > Hello members, > > I was trying to compile ghemical-1.02 under fedora core 3. And when I > run configure script I am getting an error message > > checking for gdk_gl_query in -lgtkgl... no > configure: error: Cannot find gtkgl library > > Any help is highly appreciated > > -Gopa > Disclaimer: http://www.kuleuven.be/cwis/email_disclaimer.htm From owner-chemistry@ccl.net Thu Mar 30 02:36:00 2006 From: "Jerome Pansanel j.pansanel=pansanel.net" To: CCL Subject: CCL: Ghemical and Fedora3 Message-Id: <-31362-060329105047-31989-hmBQyYzyn33IWQ2ywAWb+g===server.ccl.net> X-Original-From: Jerome Pansanel Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1 Date: Wed, 29 Mar 2006 17:50:33 +0200 MIME-Version: 1.0 Sent to CCL by: Jerome Pansanel [j.pansanel[a]pansanel.net] Hi Gopa, Is the following package installed on your machine ? gtkglext-devel You can find it here : http://rpmfind.net/linux/RPM/fedora/extras/3/i386/gtkglext-devel-1.0.6-1.i386.html Jerome Pansanel Le Mercredi 29 Mars 2006 17:01, Gopakumar gopakumar++chem.kuleuven.be a écrit : > Sent to CCL by: Gopakumar [gopakumar%chem.kuleuven.be] > Hello members, > > I was trying to compile ghemical-1.02 under fedora core 3. And when I > run configure script I am getting an error message > > checking for gdk_gl_query in -lgtkgl... no > configure: error: Cannot find gtkgl library > > Any help is highly appreciated > > -Gopa > > > Disclaimer: http://www.kuleuven.be/cwis/email_disclaimer.htm > > > -------------------------------------------- Mail sent through IMP: http://horde.org/imp/ From owner-chemistry@ccl.net Thu Mar 30 03:11:00 2006 From: "Mgr. Lubos Vrbka lubos.vrbka^^uochb.cas.cz" To: CCL Subject: CCL: free monte carlo code Message-Id: <-31363-060330024725-9464-o2me5X82r6JwgOxWqD42tA++server.ccl.net> X-Original-From: "Mgr. Lubos Vrbka" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-2 Date: Thu, 30 Mar 2006 09:47:13 +0200 MIME-Version: 1.0 Sent to CCL by: "Mgr. Lubos Vrbka" [lubos.vrbka_-_uochb.cas.cz] hi guys, could someone point me to free monte carlo code supporting core-shell and buckingham potentials? thanks in advance, lubos -- ..................................................... Mgr. Lubos Vrbka Center for Biomolecules and Complex Molecular Systems Institute of Organic Chemistry and Biochemistry Academy of Sciences of the Czech Republic Prague, Czech Republic http://www.molecular.cz/~vrbka ..................................................... From owner-chemistry@ccl.net Thu Mar 30 04:25:00 2006 From: "David van der Spoel spoel_-_xray.bmc.uu.se" To: CCL Subject: CCL: free monte carlo code Message-Id: <-31364-060330040435-14612-O4RShB0BzUy61YVrC2/BZg^server.ccl.net> X-Original-From: David van der Spoel Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Thu, 30 Mar 2006 11:04:15 +0200 MIME-Version: 1.0 Sent to CCL by: David van der Spoel [spoel#,#xray.bmc.uu.se] Mgr. Lubos Vrbka lubos.vrbka^^uochb.cas.cz wrote: > Sent to CCL by: "Mgr. Lubos Vrbka" [lubos.vrbka_-_uochb.cas.cz] > hi guys, > > could someone point me to free monte carlo code supporting core-shell > and buckingham potentials? > > thanks in advance, > lubos > gromacs does MD with these things, it wouldn't be too hard to implement Monte Carlo with that either. www.gromacs.org -- David. ________________________________________________________________________ David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 spoel*xray.bmc.uu.se spoel*gromacs.org http://folding.bmc.uu.se ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ From owner-chemistry@ccl.net Thu Mar 30 06:00:00 2006 From: "Reinaldo Pis Diez pis_diez,yahoo.com.ar" To: CCL Subject: CCL: Ghemical and Fedora3 Message-Id: <-31365-060329154844-25020-Ar+5wkegaBH8qwMO+FLgoA{}server.ccl.net> X-Original-From: Reinaldo Pis Diez Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Wed, 29 Mar 2006 13:45:46 -0300 MIME-Version: 1.0 Sent to CCL by: Reinaldo Pis Diez [pis_diez ~~ yahoo.com.ar] Dear Gopa, > > checking for gdk_gl_query in -lgtkgl... no > configure: error: Cannot find gtkgl library > You need the libgtkgl library to compile ghemical. Use yum to find packages and/or update your system -> "yum provides libgtkgl" will tell you what package to install. Regards, Reinaldo __________________________________________________ Correo Yahoo! Espacio para todos tus mensajes, antivirus y antispam ¡gratis! ¡Abrí tu cuenta ya! - http://correo.yahoo.com.ar From owner-chemistry@ccl.net Thu Mar 30 08:28:00 2006 From: "Marhoefer, R \(Richard\) Richard.Marhoefer^intervet.com" To: CCL Subject: CCL: Free software for drug design? ..and flexibility descriptors Message-Id: <-31366-060329123519-11463-Wj2ykyNMMpuF02CQVNH1yA]*[server.ccl.net> X-Original-From: "Marhoefer, R \(Richard\)" Content-class: urn:content-classes:message Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="iso-8859-1" Date: Wed, 29 Mar 2006 18:49:18 +0200 MIME-Version: 1.0 Sent to CCL by: "Marhoefer, R \(Richard\)" [Richard.Marhoefer_+_intervet.com] Dear Marc, a number of free programs and/or open source programs for some of the desired application areas are listed in: J.W. Geldenhuys, K.E. Gaasch, M. Watson, D. Allen, C.J. van der Schyf (2006) Optimizing the use of open-source software applications in drug discovery. DDT 11, 127-132. Richard ________________________________ Dr. Richard J. Marhöfer BioChemInformatics Scientist Intervet Innovation GmbH Drug Discovery / BioChemInformatics Zur Propstei, 55270 Schwabenheim, Germany E-mail: richard.marhoefer(~)intervet.com Phone: +49 6130 948-204 Fax: +49 6130 948-517 Intervet is an Akzo Nobel Company > -----Original Message----- > From: owner-chemistry(~)ccl.net [mailto:owner-chemistry(~)ccl.net] > Sent: Montag, 27. März 2006 12:15 > To: Marhoefer, R (Richard) > Subject: CCL: Free software for drug design? ..and > flexibility descriptors > > > Sent to CCL by: Marc Baaden [baaden%x%smplinux.de] > > Dear All, > > concerning techniques like molecular dynamics, Monte Carlo or > implementations of ab initio approaches there are a number of > freely available programs for the academic community. I > wonder whether similar 'free' (non-commercial) software > exists for drug design? In particular for the following tasks: > - virtual screening > - pharmacophore modeling > - receptor mapping > - QSAR and 3D-QSAR > - Shape alignments > - ComFa-like methods > My focus would be more on exploring these approaches then on > applying them in a production environment on huge projects. > I'd be very grateful for suggestions and comments. > > One more specific request: what type of molecular or atomic > descriptors do exist for conformational flexibility? > > Thank you very much in advance, > Marc Baaden > > -- > Dr. Marc Baaden - Institut de Biologie Physico-Chimique, Paris > mailto:baaden|a|smplinux.de - http://www.baaden.ibpc.fr > FAX: +33 15841 5026 - Tel: +33 15841 5176 ou +33 609 843217 > > > > -= This is automatically added to each message by the mailing > script =- To recover the email address of the author of the > message, please change the strange characters on the top line > to the (~) sign. You can also look up the X-Original-From: line > in the mail header.> Conferences: > http://server.ccl.net/chemistry/announcements/conferences/ > > Search Messages: http://www.ccl.net/htdig (login: ccl, > Password: search)> > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ > -+-+-+-+-+ > > > > -------------------------------------- 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 Thu Mar 30 09:03:00 2006 From: "Sanjoy Bandyopadhyay sanjoy]^[chem.iitkgp.ernet.in" To: CCL Subject: CCL: Forcefield parameters for beta-cyclodextrin Message-Id: <-31367-060330035141-10499-6osOIYks6qFdJ0ALuMpjXQ%a%server.ccl.net> X-Original-From: Sanjoy Bandyopadhyay Content-Type: TEXT/PLAIN; charset=US-ASCII Date: Thu, 30 Mar 2006 13:08:23 +0530 (IST) MIME-Version: 1.0 Sent to CCL by: Sanjoy Bandyopadhyay [sanjoy- -chem.iitkgp.ernet.in] Dear All, I am looking for the topology and forcefield parameters for beta-cyclodextrin. Any help will be appreciated. Thanks. Sanjoy -- -------------------------------------------------------------------- Dr. Sanjoy Bandyopadhyay E-mail: sanjoy{=}chem.iitkgp.ernet.in Assistant Professor Molecular Modeling Laboratory Phone: 91-3222-283344 (Work) Department of Chemistry 91-3222-283345, 279938 (Home) Indian Institute of Technology Fax : 91-3222-255303, 282252 Kharagpur 721 302 West Bengal, India. http://www.chem.iitkgp.ernet.in/faculty/SB/ -------------------------------------------------------------------- From owner-chemistry@ccl.net Thu Mar 30 09:38:00 2006 From: "jacquie cawthray jacqueline.cawthray\a/adelaide.edu.au" To: CCL Subject: CCL: aimpac vs aim2000 Message-Id: <-31368-060330052925-11259-wqbBvo1KvyyKDN6vxFYqyQ*server.ccl.net> X-Original-From: "jacquie cawthray" Date: Thu, 30 Mar 2006 05:29:24 -0500 Sent to CCL by: "jacquie cawthray" [jacqueline.cawthray#%#adelaide.edu.au] Can anyone tell me what the differences are between aimpac and aim2000. I'm looking at intramolecular hydrogen bonds and only have access to the free aimpac suite of programs but not to aim2000. Thanks From owner-chemistry@ccl.net Thu Mar 30 10:12:00 2006 From: "C. Garoufalis garoufal/./physics.upatras.gr" To: CCL Subject: CCL: Silicon clusters: Problems, challenges and,perspectives Message-Id: <-31369-060330041313-12345-hdmZkoUux/sNt3uqlXp7mw|server.ccl.net> X-Original-From: "C. Garoufalis" Date: Thu, 30 Mar 2006 13:56:20 +0300 MIME-Version: 1.0 Sent to CCL by: "C. Garoufalis" [garoufal-.-physics.upatras.gr] Papers are invited for a special issue of the new magazine on scientific computing, “Computing Letters” (COLE). This special issue with the general title «Silicon clusters: Problems, challenges and perspectives» with guest editors Professor George Maroulis and me (Aristides Zdetsis). The special issue will be published promptly (in electronic and hard copy form) well before the end of 2006, after peer review. It could also be published as a separate volume by Brill Academic publishers, Netherlands. For a few selected papers there will be also the possibility of further oral presentation in a special symposium of the forthcoming international conference on Computational Methods in Science and Engineering, ICCMSE 2006, to be held between October 27 and November 1, 2006 in Chania Crete, Greece. If you are interested you can send your manuscript or your inquires for further information directly to one of the co-editors, professor Maroulis or me. e-mail:zdetsis]|[upatras.gr , or Maroulis]|[upatras.gr -- ------------------------------------------------- Dr. Christos S. Garoufalis Dept. of Physics, Univ. of Patras, Greece email: garoufal]|[physics.upatras.gr Tel. +30 2610 997729 ------------------------------------------------- [The MS-Word Attachment removed by CCL Admin] From owner-chemistry@ccl.net Thu Mar 30 11:57:00 2006 From: "Sergio Emanuel Galembeck segalemb##usp.br" To: CCL Subject: CCL: aimpac vs aim2000 Message-Id: <-31370-060330115411-24167-02uYUYMEdxl9IV8LaaCfyw * server.ccl.net> X-Original-From: Sergio Emanuel Galembeck Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1 Date: Thu, 30 Mar 2006 13:54:00 -0300 MIME-Version: 1.0 Sent to CCL by: Sergio Emanuel Galembeck [segalemb^usp.br] Dear Jacquie, There are three software public available that do AIM calculations, AIM2000, Morphy98 and AIMPAC. AIMPAC is free and is a very good program, but do not have a good graphical interface. For the other hand, AIM2000 is much easier to use than AIMPAC and has a very good graphical interface, but there are only a version for Windows. Morphy is also very good and very stable, specially for difficult integrations, and the operation can be fully automated. It has versions for Windows and Linux. I my lab I use AIM2000 and Morphy, mainly AIM2000 for visualization of molecular graphics and Morphy for the determination of critical points parameters and integrated properties. OK! But if you have access only to AIMPAC, I can obtain all results from AIM theory. Hope this help you, Sergio Citando "jacquie cawthray jacqueline.cawthray\\a/adelaide.edu.au" : > Sent to CCL by: "jacquie cawthray" [jacqueline.cawthray#%#adelaide.edu.au] > Can anyone tell me what the differences are between aimpac and aim2000. I'm > looking at intramolecular hydrogen bonds and only have access to the free > aimpac suite of programs but not to aim2000. > Thanks> > > > From owner-chemistry@ccl.net Thu Mar 30 22:37:01 2006 From: "Sue L chsue2004++yahoo.com" To: CCL Subject: CCL: TDDFT with CPCM Message-Id: <-31371-060330222800-20044-IvxeRX2QB0zTrKllGqyAwg^_^server.ccl.net> X-Original-From: "Sue L" Date: Thu, 30 Mar 2006 22:27:56 -0500 Sent to CCL by: "Sue L" [chsue2004,yahoo.com] Hi In Gaussain03, is following input line correct for studying the solvent effect (CPCM) on the singlet-singlet transition energies calculated by TDDFT? n B3LYP/6-31g* td(singlets, nstates=10) scrf(cpcm, solvent=ch2cl2) Thank you very much Sue