From owner-chemistry@ccl.net Mon May 8 08:10:00 2006 From: "Rene Thomsen rt#molegro.com" To: CCL Subject: CCL: Molegro releases Molegro Virtual Docker 2006 v1.1 Message-Id: <-31702-060508080701-27259-2NbaQmdzjXHCm+8GjNpz2w]=[server.ccl.net> X-Original-From: "Rene Thomsen" Date: Mon, 8 May 2006 08:06:56 -0400 Sent to CCL by: "Rene Thomsen" [rt.:.molegro.com] Aarhus, Denmark, May 8th, 2006 - Molegro is pleased to announce a new release of Molegro Virtual Docker 2006, an integrated platform for predicting protein-ligand interactions. Molegro Virtual Docker handles all aspects of the docking process from preparation of the molecules to determination of the potential binding sites of the target protein, and prediction of the binding modes of the ligands. Molegro Virtual Docker offers high-quality docking based on a novel optimization technique combined with a user interface experience focusing on usability and productivity. Molegro Virtual Docker runs on Windows, Linux, and Mac OS X. A journal paper comparing Molegro Virtual Docker with other state-of-the-art docking programs is available from Journal of Medicinal Chemistry: http://dx.doi.org/10.1021/jm051197e New features in version 1.1: * Support for scripting (e.g. batch job execution). * The Pose Organizer has been redesigned to handle large docking runs more easily. * Python wrapper for controlling MVD using Python scripts. For more information, or to download a trial version, please visit our company website at: http://www.molegro.com or contact: Rene Thomsen, CEO Molegro Hoegh-Guldbergs Gade 10, Bldg. 1090 DK-8000 Aarhus Denmark E-mail: rt:molegro.com Phone: (+45) 8942-3165 About Molegro Molegro is a Danish company founded in 2005. Our company concentrates on developing high-performance drug discovery solutions leading to a faster drug-development process. Our goal is to provide scientifically superior products focusing on both state-of-the-art algorithms and an intuitive graphical user interface experience. From owner-chemistry@ccl.net Mon May 8 09:07:00 2006 From: "Gerard Pujadas gerard.pujadas-.-urv.cat" To: CCL Subject: CCL: Energy minimization protocol for protein structures? Message-Id: <-31703-060508083535-6352-pFYDUCW3WKkLhxegxQ9suA..server.ccl.net> X-Original-From: "Gerard Pujadas" Date: Mon, 8 May 2006 08:35:34 -0400 Sent to CCL by: "Gerard Pujadas" [gerard.pujadas,,urv.cat] Dear CCL list subscribers, I wonder if there is any standard protocol to follow when doing an energy minimization of a protein structure. I would like to know also if there is a free (or low cost for non commercial or academic) and easy-to-use software that can do this kind of energy minimization With many thanks in advances. Yours sincerely, Gerard From owner-chemistry@ccl.net Mon May 8 09:42:00 2006 From: "Gerard Pujadas gerard.pujadas=urv.cat" To: CCL Subject: CCL: Energy minimization protocol for protein structures? Message-Id: <-31704-060508085814-20506-kt2YMBDyE0MtFOL8fZ67Ng_+_server.ccl.net> X-Original-From: "Gerard Pujadas" Date: Mon, 8 May 2006 08:58:13 -0400 Sent to CCL by: "Gerard Pujadas" [gerard.pujadas()urv.cat] Dear CCL list subscribers, I wonder if there is any standard protocol to follow when doing an energy minimization of a protein structure. I would like to know also if there is a free (or low cost for non commercial or academic) and easy-to-use software that can do this kind of energy minimization With many thanks in advances. Yours sincerely, Gerard From owner-chemistry@ccl.net Mon May 8 10:17:01 2006 From: "Karl Irikura karl.irikura:-:nist.gov" To: CCL Subject: CCL: Gas phase aciditiy and basicity of various organic acides and bases! Message-Id: <-31705-060508084455-11656-zLrP9BhtLs7d5nt59tzycA!A!server.ccl.net> X-Original-From: Karl Irikura Content-Type: text/plain; charset="us-ascii"; format=flowed Date: Mon, 08 May 2006 08:36:49 -0400 Mime-Version: 1.0 Sent to CCL by: Karl Irikura [karl.irikura(~)nist.gov] Hi. Here are two sites: http://webbook.nist.gov/chemistry/ ("Ion energetics") http://web.utk.edu/~bartmess/negdoc.htm (not actually a website) Good luck, Karl At 12:13 AM 5/6/2006, you wrote: >Sent to CCL by: yorth kos [yortama2003=yahoo.ca] >--0-725951840-1146843206=:26692 >Content-Type: text/plain; charset=iso-8859-1 >Content-Transfer-Encoding: 8bit > >Dear all CCL'ers > > I'm looking for a website related to the gas phase acidity and > basicity of a huge number of organic molecules.I would really > appreciate if somebody could kindly provide me any information! > > My best wishes in advance > Hossein > > > >--------------------------------- >Now you can have a huge leap forward in email: get the new Yahoo! Mail. >--0-725951840-1146843206=:26692 >Content-Type: text/html; charset=iso-8859-1 >Content-Transfer-Encoding: 8bit > >
Dear all CCL'ers
 
I'm looking for >a website  related to the gas phase acidity and basicity of a >huge number of organic molecules.I would really appreciate if >somebody could kindly provide me any >information!
 
My best wishes in >advance
Hossein

>

Now you can have a huge leap forward in > email: href="http://us.rd.yahoo.com/evt=40705/*http://mrd.mail.yahoo.com/try_beta?.intl=ca"> > get the new Yahoo! Mail. >--0-725951840-1146843206=:26692------------------------------------------------ Dr. Karl K. Irikura National Institute of Standards and Technology 100 Bureau Drive, Stop 8380 Gaithersburg, MD 20899-8380 voice: 301-975-2510 fax: 301-869-4020 e-mail: karl.irikura:+:nist.gov http://www.nist.gov/compchem/ ---------------------------------------------- From owner-chemistry@ccl.net Mon May 8 10:51:01 2006 From: "Nuno R. L. Ferreira nunolf]|[ci.uc.pt" To: CCL Subject: CCL: Energy minimization protocol for protein structures? Message-Id: <-31706-060508104208-27040-Iy2XdyyYuzVn9VL/n29VOg**server.ccl.net> X-Original-From: "Nuno R. L. Ferreira" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="iso-8859-1" Date: Mon, 8 May 2006 15:40:35 +0100 MIME-Version: 1.0 Sent to CCL by: "Nuno R. L. Ferreira" [nunolf(_)ci.uc.pt] Hi Gromacs and NAMD are two free software packs you can use to perform molecular dynamics simulations, but there are others. In both these packs you must write a script with the parameters to perform your task. But, there's always tutorials with self-explanatory examples. There's also SwissPDB Viewer, which has a GUI. To start with, this could be a good choice. The choice would rely on your background about the subject and the final goal. Best regards, Nuno ----- Original Message ----- > From: "Gerard Pujadas gerard.pujadas-.-urv.cat" To: "Ferreira, Nuno R. L. " Sent: Monday, May 08, 2006 2:09 PM Subject: CCL: Energy minimization protocol for protein structures? > Sent to CCL by: "Gerard Pujadas" [gerard.pujadas,,urv.cat] > > Dear CCL list subscribers, > > I wonder if there is any standard protocol to follow when doing an energy minimization of a protein structure. > > I would like to know also if there is a free (or low cost for non commercial or academic) and easy-to-use software that can do this kind of energy minimization > > With many thanks in advances. > > Yours sincerely, > > Gerard> > > > > > --- > avast! Antivirus: Inbound message clean. > Virus Database (VPS): 0619-0, 08-05-2006 > Tested on: 08-05-2006 14:18:57 > avast! - copyright (c) 1988-2006 ALWIL Software. > http://www.avast.com > > > --- avast! Antivirus: Outbound message clean. Virus Database (VPS): 0619-0, 08-05-2006 Tested on: 08-05-2006 15:40:37 avast! - copyright (c) 1988-2006 ALWIL Software. http://www.avast.com From owner-chemistry@ccl.net Mon May 8 12:52:01 2006 From: "Pierre Mignon pmignon^-^vub.ac.be" To: CCL Subject: CCL: Periodic plane waves calculations Message-Id: <-31707-060508124349-1026-4GZzXZ6qZicwg2jyhz1nmw..server.ccl.net> X-Original-From: Pierre Mignon Date: Mon, 8 May 2006 18:04:44 +0200 (CEST) Sent to CCL by: Pierre Mignon [pmignon:+:vub.ac.be] Dear All, I am planning to perform theoretical studies on Alumino-Silicates systems, zeolites, using periodic plane waves packages. My question is simple: Which package, VASP, CPMD, CP2K ... is the more efficient to perform calculations on solids such as zeolites ? The aim of the study is to optimize geometries, compute IR frequencies, compute electronic properties such as electronic densities, atomic charges, electrostatic potential, search for transition state geometries ... Thank you in advance, Pierre. Mignon Pierre PhD Free University of Brussel (VUB) Dienst Algemene Chemie (ALGC) Pleinlaan, 2 1050 Brussels Belgium Tel + 32 2 629 37 48 Fax + 32 2 629 33 17 e-mail pmignon,+,vub.ac.be From owner-chemistry@ccl.net Mon May 8 16:30:00 2006 From: "MIRICA, LIVIU liviu]*[berkeley.edu" To: CCL Subject: CCL: Docking program for metalloenzymes Message-Id: <-31708-060508142140-29822-LRbbDWRzzo+25dnwQ0ritg|a|server.ccl.net> X-Original-From: "MIRICA, LIVIU" Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="ISO-8859-1"; format="flowed" Date: Mon, 08 May 2006 10:42:45 -0700 MIME-Version: 1.0 Sent to CCL by: "MIRICA, LIVIU" [liviu()berkeley.edu] Hi, I have a question regarding the application of the different docking programs to metalloenzymes. I am interested in analyzing the docking of small ligands to enzymes that have a metal ion in the active site (and the ligand may or may not bind to the metal). Given the large number of docking programs, what is the state-of-the-art in terms of taking into account the interactions of ligands and proteins with metal ions? Which program would be most successful for docking ligands to metalloenzymes, either for PC (preferred) or Linux platforms? Any advice will be appreciated. Thanks for your help. Liviu Mirica ------------------------------------------------------ Liviu Mirica, PhD Department of Chemistry University of California, Berkeley, CA 94720 From owner-chemistry@ccl.net Mon May 8 17:05:01 2006 From: "MIRICA, LIVIU liviu[-]berkeley.edu" To: CCL Subject: CCL: [CCL] Docking program for metalloenzymes Message-Id: <-31709-060508154155-4328-ju4MYHdnXHJY6q6UkB2TYQ###server.ccl.net> X-Original-From: "MIRICA, LIVIU" Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="ISO-8859-1"; format="flowed" Date: Mon, 08 May 2006 12:41:43 -0700 MIME-Version: 1.0 Sent to CCL by: "MIRICA, LIVIU" [liviu,berkeley.edu] Hi, I have a question regarding the application of the different docking programs to metalloenzymes. I am interested in analyzing the docking of small ligands to enzymes that have a metal ion in the active site (and the ligand may or may not bind to the metal). Given the large number of docking programs, what is the state-of-the-art in terms of taking into account the interactions of ligands and proteins with metal ions? Which program would be most successful for docking ligands to metalloenzymes, either for PC (preferred) or Linux platforms? Any advice will be appreciated. Thanks for your help. Liviu Mirica ---------------------------------------------------- Liviu Mirica, PhD Postdoctoral Scholar - Klinman Lab Department of Chemistry University of California, Berkeley, CA 94720 From owner-chemistry@ccl.net Mon May 8 19:43:00 2006 From: "zjwu zjwu[a]imr.edu" To: CCL Subject: CCL:G: error in frequency calculation Message-Id: <-31710-060508193834-6855-EsNfr6an51/cN72tvjlIVA_+_server.ccl.net> X-Original-From: "zjwu" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="gb2312" Date: Tue, 9 May 2006 07:50:37 +0900 Mime-Version: 1.0 Sent to CCL by: "zjwu" [zjwu(-)imr.edu] Dear All, Recently, I have calculated the electronic properties of molecules containing transition metal (also radioactive) Tc. However, during my calculation, I have found that the geometry optimization was finished perfectly, but the frequency calculation teminated with an error message. Here in the following, I attached an error message from a calculation of diatomic molecule TcC: Defaulting to unpruned grid for atomic number 43. Full mass-weighted force constant matrix: Low frequencies --- -NaNQ -NaNQ -NaNQ -NaNQ -NaNQ -NaNQ Molecule is linear but NTrRo=3. Error termination via Lnk1e in /opt/g03/g03/l716.exe Does anybody know how to solve the problem? Thank you very much. Regards, Zhijian WU