Kevin div>

__________________________________________________
Do You > Yahoo!?
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http://mail.yahoo.com > --0-147654940-1147098689=:16061-- > > > > -= This is automatically added to each message by the mailing > script =- > To recover the email address of the author of the message, please > change> Conferences: http://server.ccl.net/chemistry/announcements/ > conferences/ > > Search Messages: http://www.ccl.net/htdig (login: ccl, Password: > search)> > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+- > +-+-+ > Jason D. Thompson, Ph.D. Molecular Pharmacology and Experimental Therapeutics Mayo Clinic Guggenheim 6-93 200 First Street SW Rochester, MN 55905 http://pollux.chem.umn.edu/~thompson --Apple-Mail-24--778235113 Content-Transfer-Encoding: quoted-printable Content-Type: text/html; charset=ISO-8859-1 This may not be what you are = looking for, but you may want to check out:

Kelly, C. P.; Cramer, C. = J.; Truhlar, D. G. J. Phys. Chem. A 2006, 2493

Their methods are = implemented in the free programs GAMESSPLUS (http://comp.chem.umn.edu/game= ssplus), and add-on module to the free GAMESS program, HONDOPLUS (http://comp.chem.umn.edu/hondo= plus), a standalone program based on the HONDO program, and SMxGauss = (http://comp.chem.umn.edu/smxgau= ss), a (relatively) user-friendly front-end to HONDOPLUS that can be = used in conjunction with Gaussian03 and its "External" = command.

On May 9, 2006, at 3:25 AM, kevin abbot = kevanabbot]![yahoo.com wrote:

Sent to CCL by: kevin abbot = [kevanabbot=3D-=3Dyahoo.com]

Content-Type: = text/plain; charset=3Diso-8859-1

Hi folks,
=A0 My = question is really simple: are there some programs (free of charge) that = permit to calculate pka of a determinated compound?

=A0 Any help is = appreciated

=A0 = Kevin

Do You Yahoo!?
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<div>Hi = folks,</div>=A0 = <div>My question is really simple: are there some programs = (free of charge) that permit to calculate pka of a determinated = compound?</div>=A0 = <div> </div>=A0 <div>Any help is = appreciated</div>=A0 = <div> </div>=A0 = <div>Kevin</div><p>______________________________= ____________________<br>Do You Yahoo!?<br>Tired of = spam?=A0 Yahoo! Mail has = the best spam protection around <br>http://mail.yahoo.com=A0

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=

Jason D. Thompson, Ph.D.

Molecular Pharmacology and Experimental = Therapeutics

Mayo Clinic

Guggenheim 6-93

200 First Street SW

Rochester, MN 55905

http://pollux.chem.umn.edu/~= thompson

= --Apple-Mail-24--778235113-- From owner-chemistry@ccl.net Tue May 9 10:33:03 2006 From: "Heribert Reis hreis:+:eie.gr" To: CCL Subject: CCL: Combined Molecular Dynamics and Semiempirical Methods Message-Id: <-31721-060509093813-32306-OBtMms360IT1noGRDqvxNw]-[server.ccl.net> X-Original-From: "Heribert Reis" Date: Tue, 9 May 2006 09:38:09 -0400 Sent to CCL by: "Heribert Reis" [hreis|-|eie.gr] Hello, I'm looking for a way to do a classical molecular dynamics simulation of a liquid (ideally with a polarizable Force Field), but with one molecule treated by semiempirical methods (PM3 or similar), so basically a QM/MM calculation. I know that there is the GAMESS-Tinker combination, but it seems that it does not allow to compute trajectories (also the version of Tinker used seems to be a bit old). Anyone knows a possibility to do this? A bit of additional programming would not be an unsurmountable hurdle. Thanks for any suggestion. Heribert Reis From owner-chemistry@ccl.net Tue May 9 11:08:00 2006 From: "Darryl Reid darryl.reid,gmail.com" To: CCL Subject: CCL: Docking program for metalloenzymes Message-Id: <-31722-060509080724-6676-gaOP29srW/7rZgIXnEq9eQ---server.ccl.net> X-Original-From: "Darryl Reid" Content-Disposition: inline Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Tue, 9 May 2006 07:08:20 -0400 MIME-Version: 1.0 Sent to CCL by: "Darryl Reid" [darryl.reid(a)gmail.com] The eHiTS docking program has been successfully used to dock ligands to metalloenzymes and it is free for academics. You can find out more at: www.simbiosys.ca/ehits/ Darryl On 5/8/06, MIRICA, LIVIU liviu]*[berkeley.edu wrote: > 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 Tue May 9 12:31:00 2006 From: "Ross Walker ross_-_rosswalker.co.uk" To: CCL Subject: CCL: Combined Molecular Dynamics and Semiempirical Methods Message-Id: <-31723-060509121231-15848-Resn48DJ0cTAGIuSoT3MXg~~server.ccl.net> X-Original-From: "Ross Walker" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="us-ascii" Date: Tue, 9 May 2006 09:12:17 -0700 MIME-Version: 1.0 Sent to CCL by: "Ross Walker" [ross .. rosswalker.co.uk] Dear Heribert, > I'm looking for a way to do a classical molecular dynamics simulation > of a liquid (ideally with a polarizable Force Field), but with one > molecule treated by semiempirical methods (PM3 or similar), so > basically a QM/MM calculation. I know that there is the GAMESS-Tinker > combination, but it seems that it does not allow to compute > trajectories (also the version of Tinker used seems to be a bit old). > > Anyone knows a possibility to do this? A bit of additional > programming > would not be an unsurmountable hurdle. Amber 9 has full support for QM/MM MD simulations that can combine a number of different semi-empirical Hamiltonians with any of the Amber force fields. It also supports a full treatment of long range electrostatics using a Particle Mesh Ewald approach for the QM/MM calculation and also supports QM/MM with Generalized Born implicit solvent. The implementation is also very simple so that if you have a simulation setup to run classically in Amber already you only need to change a couple of entires in your input file and you are good to go. Details on amber are at http://amber.scripps.edu A tutorial on AMBER 9 QM/MM is at http://www.rosswalker.co.uk/tutorials/amber_workshop/Tutorial_Six_amber9/ind ex.htm All the best Ross /\ \/ |\oss Walker | HPC Consultant and Staff Scientist | | San Diego Supercomputer Center | | Tel: +1 858 822 0854 | EMail:- ross:rosswalker.co.uk | | http://www.rosswalker.co.uk | PGP Key available on request | Note: Electronic Mail is not secure, has no guarantee of delivery, may not be read every day, and should not be used for urgent or sensitive issues. From owner-chemistry@ccl.net Tue May 9 13:35:01 2006 From: "Jozsef Csontos jozsefcsontos{=}creighton.edu" To: CCL Subject: CCL:G: g03 CCSD(T) Message-Id: <-31724-060509130917-9940-yYkV2SNAfK89jSw11g4Tog%a%server.ccl.net> X-Original-From: Jozsef Csontos Content-Transfer-Encoding: 7bit Content-Type: text/plain Date: Tue, 09 May 2006 12:09:09 -0500 Mime-Version: 1.0 Sent to CCL by: Jozsef Csontos [jozsefcsontos:-:creighton.edu] Dear List Members, is there any chance to restart (I mean continue) a crashed CCSD(T) calculation in g03? Best regards, Jozsef -- Jozsef Csontos, Ph.D. Department of Biomedical Sciences Creighton University, Omaha, NE From owner-chemistry@ccl.net Tue May 9 14:10:01 2006 From: "james vivian jamestvivian- -msn.com" To: CCL Subject: CCL: Combined Molecular Dynamics and Semiempirical Methods Message-Id: <-31725-060509134902-25759-gDBwKSJ/+K4BQaT3ehQnYg+*+server.ccl.net> X-Original-From: "james vivian" Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="us-ascii" Date: Tue, 9 May 2006 13:02:35 -0400 MIME-Version: 1.0 Sent to CCL by: "james vivian" [jamestvivian|msn.com] CHARMM + semiempirial is a nice way to fly if you want to generate the trajectories. You can pass charges via the "usersb" subroutine option, feeding the charges back into CHARMM at increments along the trajectory. If you are only doing a ground state calculation, it's reasonably straightforward. > -----Original Message----- > > I'm looking for a way to do a classical molecular dynamics simulation > > of a liquid (ideally with a polarizable Force Field), but with one > > molecule treated by semiempirical methods (PM3 or similar), so > > basically a QM/MM calculation. I know that there is the GAMESS-Tinker > > combination, but it seems that it does not allow to compute > > trajectories (also the version of Tinker used seems to be a bit old). > > From owner-chemistry@ccl.net Tue May 9 14:45:01 2006 From: "Dale Braden genghis]~[schrodinger.com" To: CCL Subject: CCL: Calculation of pka Message-Id: <-31726-060509130421-8665-xkixCz7+9YOc6dDPF7goJA+/-server.ccl.net> X-Original-From: Dale Braden Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed Date: Tue, 9 May 2006 09:22:44 -0700 (PDT) MIME-Version: 1.0 Sent to CCL by: Dale Braden [genghis+/-schrodinger.com] Hi, Schrodinger has two products for calculating pKas: Jaguar and Epik. Jaguar employs a quantum-mechanics-based protocol for predicting the pKa of a molecule. The ab initio result is adjusted to account for errors in the continuum solvation model by using simple empirical factors which depend upon the functional group undergoing ionization. The protocol is described in the following article: J. J. Klicic, R. A. Friesner, S.-Y. Liu, W. C. Guida; J. Phys. Chem. A 106 (2002) 1327-1335. The protocol can be extended by the user. More information on Jaguar can be found at: http://www.schrodinger.com/ProductDescription.php?mID=6&sID=9&cID=0 Epik uses empirical equations to rapidly predict pKas. It also can be used to generate the most important structures consistent with a specified pH. Epik has been carefully vetted on drug-like molecules whose chemistry can be quite challenging. More information on Epik can be found at: http://www.schrodinger.com/ProductDescription.php?mID=6&sID=25&cID=0 John Shelley, Epik Product Manager Dale Braden, Jaguar Product Manager Schrodinger, Inc. From owner-chemistry@ccl.net Tue May 9 15:20:00 2006 From: "Chandrika J Moudgal moudgal.chandrika++epa.gov" To: CCL Subject: CCL: EPA QSAR/VFAR worshop annoucement; June 20 and 21, Cincinnati, OH Message-Id: <-31727-060509141842-7931-0UrvqLVww0Je50yNyrV84Q-$-server.ccl.net> X-Original-From: "Chandrika J Moudgal" Date: Tue, 9 May 2006 14:18:39 -0400 Sent to CCL by: "Chandrika J Moudgal" [moudgal.chandrika||epa.gov] Hello All, EPA is pleased to announce a workshop on Quantitative Structure Activity Relationship (QSAR) models and a new and evolving methodology called Virulence Factor Activity Relationship (VFAR). Workshop details appear on http://www.epa.gov/nhsrc/. The workshop will be conducted on June 20th and 21st at the Hilton Netherland Hotel in Cincinnati, OH. Registration is free. This workshop is sponsored by the National Homeland Security Research Center (NHSRC) and National Risk Management Research Laboratory (NRMRL), both parts of EPAs Office of Research and Development. NHSRC seeks to develop effective technologies and methods for quantifying, assessing, and addressing the risks posed by chemical, biological, and radiological agents that might be released during an emergency event. NRMRLs mission is to develop ways to prevent and reduce pollution of air, land, and water, which also includes quantifying the potential environmental harm and toxicity of chemical releases. Please check the web page in a couple of weeks for both QSAR and VFAR related charge questions. Registration details are provided on the web site. EPA encourages all interested parties to register and participate in the workshop. For any questions, please feel free to contact me at moudgal.chandrika a epa.gov. Thank you. Chandrika --------------------------------------------------------------------- Chandrika J. Moudgal Threat and Consequence Assessment Division National Homeland Security Research Center Office of Research and Development, US EPA Phone: 503-326-3541 Fax: 503-326-4005 Mailing Address: 1001 SW 5th Avenue Suite 1510 Portland, OR 97204