From owner-chemistry@ccl.net Sat May 20 14:48:00 2006 From: "MIRICA, LIVIU liviu : berkeley.edu" To: CCL Subject: CCL: AutoDock's parameters for cooper? Message-Id: <-31798-060520040101-628-L6/squ2cTO7JKhqREP/lDA,+,server.ccl.net> X-Original-From: "MIRICA, LIVIU" Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="ISO-8859-1"; format="flowed" Date: Sat, 20 May 2006 01:00:51 -0700 MIME-Version: 1.0 Sent to CCL by: "MIRICA, LIVIU" [liviu###berkeley.edu] Hi all, Related to Gerard's question, I am also interested in finding out where would one find the parameters for Fe to be used in Autodock. I am interested mainly in non-heme iron systems, although the Fe parameters for heme systems may be a good start. Thanks, Liviu Mirica On Thu, 18 May 2006 14:05:52 -0400 "D.BIO- Gerard Pujadas gerard.pujadas!=!urv.cat" wrote: > Sent to CCL by: "D.BIO- Gerard Pujadas" [gerard.pujadas-.-urv.cat] > > > Dear CCL list members, > > we would like to dock some ligands into a > receptor that has cooper has a cofactor. Then, I > wonder if any of you have the Rij and epsij > parameters for Cu-Cu that are suitable for their > use with AutoDock v3.05 > > With many thanks in advances for your help > > Gerard > > > -- > ============================= NOTE: NEW E-MAIL ============================ > Dr. Gerard Pujadas > Grup de recerca en Nutrigenòmica > Dept. Bioquímica i Biotecnologia room 106 > Campus de Sant Pere Sescelades e-mail: gerard.pujadas=-=urv.cat > Univ. Rovira i Virgili phone: 34-977 559565 > C/ Marcel·lí Domingo fax: 34-977 558232 > 43007 Tarragona (CATALONIA) > State: Spain (European Union) > ===========================================================================> > > From owner-chemistry@ccl.net Sat May 20 16:31:01 2006 From: "=?ISO-8859-1?Q?Carlos_Javier_Nu=F1ez_Aguero?= carlosjn]^[ce.fis.unam.mx" To: CCL Subject: CCL: Conformational Changes - Animation Message-Id: <-31799-060519165847-23764-MQgnC8FCWPDyEi4SXEjAGQ=server.ccl.net> X-Original-From: =?ISO-8859-1?Q?Carlos_Javier_Nu=F1ez_Aguero?= Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Fri, 19 May 2006 15:13:14 -0500 Mime-Version: 1.0 Sent to CCL by: =?ISO-8859-1?Q?Carlos_Javier_Nu=F1ez_Aguero?= [carlosjn ~~ ce.fis.unam.mx] Hi all, You can make a nice movie with o gOpenMol: http://www.gopenmol.com/ o Chimera http://www.cgl.ucsf.edu/chimera/ o VMD http://www.ks.uiuc.edu/Research/vmd/ all the molecular viewers can manipule the trayectory files of CHARMM, AMBER, GROMOS, GROMACS, and, maybe, NAMD Hasta la proxima vez Carlos N. SANDEEP KUMAR skumar23 ~~ jhem.jhu.edu wrote: >Sent to CCL by: SANDEEP KUMAR [skumar23###jhem.jhu.edu] > >Hello Veer: > >If you have different frames/pictures/conformations of your protein on a PC with Windows, then you can use Windows Movie Maker to arrange them in any sequence you like and make a movie out of it. > >Sincerely, >Sandeep >------------------------------------------------------------------- >Dr. Sandeep Kumar, >Associate Research Scientist, >Johns Hopkins University Department of Biology, >106 Mudd Hall, 3400 N. Charles Street, >Baltimore, MD 21218, USA. >Phone: 410-516-8433, >Email: kumarsan(a)jhu.edu. >URL: http://myprofile.cos.com/Kumarsan. >or https://jshare.johnshopkins.edu/skumar23/public_html/ > > >----- Original Message ----- > > >>From: "Veer Shanmugasundaram Veerabahu.Shanmugasundaram]=[pfizer.com" >> >> >Date: Friday, May 19, 2006 10:41 am >Subject: CCL: Conformational Changes - Animation > > > >>Sent to CCL by: "Veer Shanmugasundaram" >>[Veerabahu.Shanmugasundaram()pfizer.com] >>Dear CCL'ers: >> >>What are some nice tools that you have used to take multiple >>conformational states of say a protein structure/model and show >>conformational changes between these states as an animated movie in >>a presentation. >> >>Thanks in advance, >>Veer >>---- >>Veer Shanmugasundaram, Ph.D >>Computer-Assisted Drug Discovery, >>Pfizer Global Research & Development, >>2800 Plymouth Road, >>Ann Arbor, MI 48105. >>Tel:(734)622-7131 >>Fax:(734)622-2782 >>Email:Veerabahu.Shanmugasundaram-x-pfizer.com >> >> >> >>-= This is automatically added to each message by the mailing >>script =- >>To recover the email address of the author of the message, please >>changethe strange characters on the top line to the (a) sign. You can >>also> Conferences: >>http://server.ccl.net/chemistry/announcements/conferences/ >>Search Messages: http://www.ccl.net/htdig (login: ccl, Password: >>search)> >>-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+- >>+-+-+> > > > > > -- No virus found in this outgoing message. Checked by AVG Free Edition. Version: 7.1.392 / Virus Database: 268.6.1/344 - Release Date: 5/19/2006