From owner-chemistry@ccl.net Wed Jan 14 07:34:00 2009 From: "Val Gillet v.gillet-x-sheffield.ac.uk" To: CCL Subject: CCL: Chemoinformatics Short Course: Sheffield Message-Id: <-38423-090114073206-515-GOO3pYR1AGcA8nbTm+hM3A\a/server.ccl.net> X-Original-From: "Val Gillet" Date: Wed, 14 Jan 2009 07:32:02 -0500 Sent to CCL by: "Val Gillet" [v.gillet^sheffield.ac.uk] "A Practical Introduction to Chemoinformatics" June 16th-19th 2009 University of Sheffield, UK The University of Sheffield will be hosting the above short course which is supported by the Chemical Structure Association Trust (CSAT) and the Molecular Graphics and Modelling Society (MGMS). This intensive short course, which has been run on an annual basis since 2000, provides an introduction to the major aspects of Chemoinformatics, with particular emphasis on applications in modern drug discovery. The course will comprise a mixture of hands-on workshops using state-of-the-art software, lectures, and informal discussions and will be delivered by world leaders in the field > from academia and industry. Please note that due to its intensive nature places on the course are limited to 18. For further details see: http://cisrg.shef.ac.uk/chemcourse or contact Val Gillet (v.gillet at sheffield.ac.uk) From owner-chemistry@ccl.net Wed Jan 14 10:02:00 2009 From: "amine amine m-22#,#hotmail.fr" To: CCL Subject: CCL: molecular mechanic energy minimisation with amber Message-Id: <-38424-090114100043-18262-2I38GdkHabJumuhrOs1j7A++server.ccl.net> X-Original-From: "amine amine" Date: Wed, 14 Jan 2009 10:00:39 -0500 Sent to CCL by: "amine amine" [m-22-,-hotmail.fr] Hi I want to do a Molecular Mechanic Energy minimisation using amber: is it correct like this?? sander -O -i sander.in -o sander.out -p prmtop -c inpcrd -r restrt with this sander.in initial minimisation prior to MD &cntrl imin = 1, maxcyc = 10000, ncyc = 5000, ntb = 0, igb = 0, ntc = 2, ntf = 2, cut = 12, / else? why i can do this? Thanks From owner-chemistry@ccl.net Wed Jan 14 11:19:01 2009 From: "Joaquin Barroso Flores joaco_barroso- -yahoo.com" To: CCL Subject: CCL: population inversion-resonance Message-Id: <-38425-090114091740-15428-k9O1BPVCf1+lObylc3KCPg###server.ccl.net> X-Original-From: Joaquin Barroso Flores Content-Type: multipart/alternative; boundary="0-726587704-1231939046=:9188" Date: Wed, 14 Jan 2009 05:17:26 -0800 (PST) MIME-Version: 1.0 Sent to CCL by: Joaquin Barroso Flores [joaco_barroso]^[yahoo.com] --0-726587704-1231939046=:9188 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: quoted-printable Hi V ronique According to the NBO site by its creators, this warning is displayed if the= occupancy and energy ordering do not coincide, that is, if the aufbau prin= ciple is not quite obeyed.=20 Check this link http://www.chem.wisc.edu/~nbo5/tutorial.html Hope it helps. ******************************************************************** Dr. J= oaquin Barroso-Flores, Ph. D.=C2=A0=20 Facultatea de Chimie Universitatea Babes-Bolyai Cluj-Napoca, Romania http://joaquinbarroso.com Correo alterno: joaquin.barroso+*+gmail.com=20 "Blogastronom=C3=ADa": http://joaquinbarroso.blogspot.com ***************= *****************************************************=0A=0A________________= __________________________________=0ACorreo Yahoo!=0AEspacio para todos tus= mensajes, antivirus y antispam =C2=A1gratis! =0AReg=C3=ADstrate ya - http:= //correo.yahoo.com.mx/ --0-726587704-1231939046=:9188 Content-Type: text/html; charset=utf-8 Content-Transfer-Encoding: quoted-printable
Hi V ronique

According to the NBO site= by its creators, this warning is displayed if the occupancy and energy ord= ering do not coincide, that is, if the aufbau principle is not quite obeyed= .
Check this link
http://www.chem.wisc.edu/~nbo5/tutorial.html
Hope it helps.

*******************************= *************************************
Dr. Joaquin = Barroso-Flores, Ph. D. 
=
Facultatea de Chimie
Universitatea Babes-Bolyai
C= luj-Napoca, Romania

http://joaquinbarroso.com

Correo alterno:=
=
*****************************************************= ***************

________________________________= __________________
Correo Yahoo!
Espacio para todos tus mensajes, ant= ivirus y antispam =C2=A1gratis!
Reg=C3=ADstrate ya - http://correo.yaho= o.com.mx/ --0-726587704-1231939046=:9188-- From owner-chemistry@ccl.net Wed Jan 14 16:10:01 2009 From: "Ross Walker ross[-]rosswalker.co.uk" To: CCL Subject: CCL: Postdoc Position Available at SDSC/UCSD Message-Id: <-38426-090114160659-21420-bAxbLDssIDRZca5nF5VRVA::server.ccl.net> X-Original-From: "Ross Walker" Content-Language: en-us Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="Windows-1252" Date: Wed, 14 Jan 2009 13:06:37 -0800 MIME-Version: 1.0 Sent to CCL by: "Ross Walker" [ross{:}rosswalker.co.uk] Dear All, I apologize for this slightly off topic message but I thought you might have interest, or know somebody who might be interested, in the following postdoc position that I currently have available: ------------------------ Postdoctoral Researcher University of California Campus: San Diego Academic Department/Research Unit: San Diego Supercomputer Center Research Discipline: Computational Molecular Biology/Chemistry, High Performance Computing Description: A postdoctoral position in computational molecular biology is available within the group of Ross Walker at the San Diego Supercomputer Center. This will involve close collaboration with UCSD and Lawrence Livermore National Laboratory to carry out research in the field of Molecular Dynamics Simulations. The research focus of the group is advanced Molecular Dynamics (MD) simulations. It includes the development of efficient algorithms for accurate and parallel computation of Quantum Mechanical and hybrid Quantum/Molecular Mechanical (QM/MM) MD simulations; improved sampling techniques for classical and QM/MM MD simulations; the development of novel approaches for analysis of large scale and long time length MD simulation trajectories; approaches to parallel post-processing and on the fly MD analysis as well as the use of MD simulation techniques for studying protein reactivity including elucidation of the activation pathways of adenovirus proteases and studies of cellulose degrading enzymes for use in bio-fuel production. The successful candidate will interact with the developers of the AMBER software package. The incumbent will have access to SDSC and LLNL supercomputer resources including some of the world's most powerful machines. Occasional travel may be required including visits to the LLNL site approximately once every 3 to 4 months. Location: Nestled along the Pacific Ocean on 1,200 acres of coastal woodland, just steps from the beach and minutes from beautiful downtown La Jolla, UC San Diego (http://www.ucsd.edu/) is a preeminent university in the country providing an excellent environment for research in computational biology, computer science, biochemistry, bioengineering, medicine, as well as interdisciplinary research. The successful candidate will reside in the new building of San Diego Supercomputer Center (http://www.sdsc.edu/) on the main campus of UCSD. Salary/Stipend Information: Commensurate with NIH Guidelines. Benefits: This position qualifies for Full Postdoctoral Benefits - see http://research.ucsd.edu/postdoc/benefits.aspx for further information. Procedure to Apply: Interested individuals should e-mail their curriculum vitae, a cover letter stating research interests and career goals and the names, telephone numbers, and e-mail addresses of three references to Dr. Ross C. Walker at rcw=-=sdsc.edu. Skills and Knowledge Required: The applicant should have, or expect to shortly receive, a Ph.D. in Computational Biology, Computational Chemistry, Computational Life Sciences or relevant disciplines as well as research experience in computational molecular biology, computer programming skills, including Fortran 95 and C/C++, and knowledge of molecular biology, protein structure and molecular dynamics. Applicants with Ph.D.'s in Computer Science backgrounds will also be considered if they have experience in molecular dynamics simulations or related disciplines. Experience in high performance computing, molecular dynamics and parallel programming (MPI) is also desirable. Applicants should enjoy working on challenging and exciting projects together with a team of international experts. Position Closing Date: Open Until Filled. Appointment Length/Period: One year, with possibility of renewals. For more information or to apply, please contact: Ross C. Walker, Phd rcw=-=sdsc.edu Telephone: (858) 822-0854 ------------------------ From owner-chemistry@ccl.net Wed Jan 14 16:55:00 2009 From: "Sachin Tyagi styagi2|a|uic.edu" To: CCL Subject: CCL:G: how to calc. BDE Message-Id: <-38427-090113145213-20218-ETc9kVj+VqHwexQEb/3djg-.-server.ccl.net> X-Original-From: Sachin Tyagi Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Tue, 13 Jan 2009 13:02:50 -0600 MIME-Version: 1.0 Sent to CCL by: Sachin Tyagi [styagi2(0)uic.edu] Thanks John for your help, I will have your suggested book in couple of days.I have couple of additional questions. I am using LanL2DZ basis set for my calculations, do you think this is good basis set to provide close to real (if not real) bond dissociation energies? I am looking for dissociation energy of double bond (carbene precursor), do you think we can use same process in this case? I think this is going to be stepwise process but I am nor sure whether its possible to do to two homolytic cleavage consecutively. Your help is much appreciated. Thanks Regards Sachin Univ. of Illinois at Chicago John M Simmie john.simmie- -nuigalway.ie wrote: > Sent to CCL by: "John M Simmie" [john.simmie*|*nuigalway.ie] > Sachin > A number of different methods & models possible; suppose you want to calculate the BDE of the CH bond in the side-chain methyl group of 2-methylfuran (2MF) then you need to compute the enthalpy of H-atom, 2-methylfuran and the radical as well to get > BDE = H(H-atom) H(radical) H(2MF) > converting atomic units into kJ/mol by multiplying by 2625.5 > > Use the best level of theory compatible with your computational resources and size of molecule often this is the most difficult aspect of the whole problem. For smallish molecules I tend to use CBS-QB3 multilevel theory which is built into Gaussian-03 and is easy to use & capable of good results, but, much depends upon your particular system. Errol Lewar's book "Computational Chemistry" published by Kluwer is a very good guide > > John Simmie::Combustion Chemistry Centre::National University of Ireland, Galway> > > From owner-chemistry@ccl.net Wed Jan 14 18:30:00 2009 From: "Jan Labanowski janl-,-speakeasy.net" To: CCL Subject: CCL: positions advertised on CCL -- reminder about rules Message-Id: <-38428-090114182723-16858-Tixf4Kam84fPqpXBXzr6kg^server.ccl.net> X-Original-From: Jan Labanowski Content-Disposition: inline Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="iso-8859-1" Date: Wed, 14 Jan 2009 18:27:10 EST MIME-Version: 1.0 Sent to CCL by: Jan Labanowski [janl%%speakeasy.net] Dear CCL, Before you post to CCL you have to read the rules: http://www.ccl.net/chemistry/aboutccl/rules/ that are available on the very top of the navigation menu on the CCL Home P= age. There are also instructions that are available at: http://www.ccl.net/chemistry/aboutccl/instructions Recently two positions were advertised on CCL. This is not only about my gr= eed and a zeal to "get rich fast", but the job advertising was not welcome on C= CL since MANY, MANY YEARS, before there was even a case made for supporting th= e CCL in this way. The job ads simply are not the issues that are of general inte= rest. It is hard to believe that someone who advertises the position does not have enough funds for supporting CCL with the fee of a 100 USD. If this is reall= y a case, then please talk to me, and I will post it for you on the Web site fo= r free. I have no recourse, but put the offenders of the CCL rules on the "review" = list. I do it without much enthusiasm, since I have better things to do than cens= oring what you post on the CCL. Yours trully, Jan Labanowski CCL Maintainer From owner-chemistry@ccl.net Wed Jan 14 19:04:00 2009 From: "Brian Masek bmasek%x%tripos.com" To: CCL Subject: CCL: New Software Announcement - Muse(TM) from Tripos Message-Id: <-38429-090114155320-20197-KP3byABLGjB1m/u+mrKnhw-.-server.ccl.net> X-Original-From: "Brian Masek" Date: Wed, 14 Jan 2009 15:53:16 -0500 Sent to CCL by: "Brian Masek" [bmasek+/-tripos.com] Tripos announces the release of Muse. Muse is software designed to accelerate the identification and optimization of lead candidates. Using Muse, CADD scientists and medicinal chemists identify novel structures, scaffolds, or side-chains that meet specific design objectives. Use Muse for lead hopping, scaffold hopping or inventing new R-Groups around a fixed scaffold. Generate ideas that meet multiple design criteria. Easily integrate in-house or 3rd party CADD properties for use as design criteria. Muse addresses issues faced by discovery scientists every day: * How do you generate new ideas that meet many different design objectives? * What do you do when youve searched your existing compounds and youve run out of ideas? * What if filtering virtual screening results leaves you with nothing that meetings your design objectives? Users can: Perform Lead Hopping, Scaffold Hopping or invent New R-Groups around a fixed scaffold Generate ideas that meet multiple design criteria Easily integrate in-house or 3rd party scoring methods for use as design criteria For more information and a free 30 day evaluation visit www.tripos.com/Muse Muse is available for Windows (XP or Vista) and Linux (RHEL 4 or 5; coming soon).