From owner-chemistry@ccl.net Tue Oct 16 00:42:00 2012 From: "Shinaj Rajagopal k shinaj/./iisertvm.ac.in" To: CCL Subject: CCL: Maestro: Desmond MD simulation Message-Id: <-47767-121016004030-13807-4skGL+qcXTiWB/6PPj0oCw,server.ccl.net> X-Original-From: "Shinaj Rajagopal k" Date: Tue, 16 Oct 2012 00:40:29 -0400 Sent to CCL by: "Shinaj Rajagopal k" [shinaj[*]iisertvm.ac.in] Hi, How can i embed a minimized structure of a DNA in a membrane of 10 angstrom for the DESMOND MD simulation. I will be thankful for your valuable advice From owner-chemistry@ccl.net Tue Oct 16 07:25:01 2012 From: "meishway linkon meishwaylinkon=yahoo.com" To: CCL Subject: CCL: transfer integral Message-Id: <-47768-121016072345-21401-eVSsykVV6fwoYB7zBlM3Ug[-]server.ccl.net> X-Original-From: "meishway linkon" Date: Tue, 16 Oct 2012 07:23:44 -0400 Sent to CCL by: "meishway linkon" [meishwaylinkon() yahoo.com] hello everybody! i have calculated for the first time crystal state calculations to know about charge carrier properties, but am unable to understand results too much can some one help me to understand it well . V h (eV) V e (eV) 1.06 10 -9 6.62 10 -2 -3.44 10 -12 -1.14 10 -13 -5.17 10 -8 -7.10 10 -8 1.13 10 -7 1.53 10 -10 3.95 10 -7 8.77 10 -9 3.80 10 -10 -3.20 10 -7 -8.07 10 -7 -1.18 10 -10 -3.09 10 -7 -1.74 10 -10 -1.66 10 -7 -2.66 10 -9 -4.17 10 -7 -4.10 10 -8 -2.94 10 -8 1.23 10 -10 2.44 10 -9 -5.98 10 -7 h = 1.51485e-010 (cm 2 /Vs) e = 9.01099e-016 (cm 2 /Vs) like for these pathways what can deduce , is it best electron transporter or hole transporter for solar cells materials.V is interral while is mobility . please explaine me about it , thanks alotttttttttttttt. From owner-chemistry@ccl.net Tue Oct 16 08:36:00 2012 From: "Kevin Theisen kevin-x-ichemlabs.com" To: CCL Subject: CCL: Announcing ChemDoodle 5 Message-Id: <-47769-121016075649-1915-PMHidxmoh1ORZpaU4oLamg*|*server.ccl.net> X-Original-From: "Kevin Theisen" Date: Tue, 16 Oct 2012 07:56:48 -0400 Sent to CCL by: "Kevin Theisen" [kevin * ichemlabs.com] We are pleased to announce that ChemDoodle 5 is now available. ChemDoodle 5 includes significant new features and improvements, including: 1. Round-trip editing on Windows via OLE. (Round-trip editing is already provided on Mac OS X) 2. Round-trip editing on Linux! 3. A revamped shape system for much easier and more precise manipulation of shapes, especially in crowded figures. 4. Also a new quick colors button to now quickly change colors of objects. 5. Bezier curves for complex shapes and mechanisms. 6. Fragmentation tools. 7. More functions for handling chemical data on the clipboard. 8. File chooser previews. 9. 77 new glassware templates! 10. Hundreds of other features and improvements. Upgrade options are available, and a free trial can be obtained at http://www.chemdoodle.com . ChemDoodle has a growing userbase and is used by thousands of institutions in over 70 countries. We actively listen to our users and work hard to produce leading chemical publishing software on all platforms, including desktops, web browsers and mobile devices. Thank you for your time. Sincerely, Kevin Theisen President, iChemLabs kevin . ichemlabs.com http://www.ichemlabs.com iChemLabs LLC. 458 Elizabeth Ave. Suite 5, Box #392 Somerset, NJ 08873 From owner-chemistry@ccl.net Tue Oct 16 14:13:01 2012 From: "Rachelle Bienstock rachelleb1()gmail.com" To: CCL Subject: CCL: Computational de novo ("rational") design of proteins/peptides Message-Id: <-47770-121016140052-26349-3Bnb3hT/gN+1MDQz5EXzkg{}server.ccl.net> X-Original-From: "Rachelle Bienstock" Date: Tue, 16 Oct 2012 14:00:51 -0400 Sent to CCL by: "Rachelle Bienstock" [rachelleb1!^!gmail.com] This is a final reminder of the submission deadline. Announcing A Symposium organized by the ACS CINF (Division of Chemical Information): The deadline was Monday, but we will accept abstracts until Friday Oct 19th. "Computational de novo ("rational") design of proteins/peptides" at the ACS Spring 2013 Meeting to be held in New Orleans, April 7-11,2013: Topics to be included: Computational de novo protein and peptide design for specific functionality; De novo enzymes from computational design; Computationally identifying mutations to confer specific functionality and properties (i.e. additional stability or interaction specificity); Directed enzyme evolution; Designing proteins from simple motifs; Applications of database-driven tools in computational protein design. ABSTRACT SUBMISSION DEADLINE: OCTOBER 19, 2012 Please submit abstracts through the ACS (American Chemical Society) online system https://portal.acs.org/portal/acs/corg/memberapp?_nfpb=true&_pageLabel=mapp_marathon_login_page&toURL=http%3A%2F%2Fabstracts.acs.org%2Findex2.php?frm=1 See (http://portal.acs.org/portal/acs/corg/content?_nfpb=true&_pageLabel=PP_SUPERARTICLE&node_id=879&use_sec=false&sec_url_var=region1&__uuid=ede7763f-5cb3-484e-bba1-79ecac8a1545) for additional information regarding the meeting. From owner-chemistry@ccl.net Tue Oct 16 16:20:00 2012 From: "CARLOS SIMMERLING carlos.simmerling(0)stonybrook.edu" To: CCL Subject: CCL: Oct 23 deadline for ACS COMP division awards Message-Id: <-47771-121016100643-29337-XA2paLI/m9kvG7tlGdeNdg^server.ccl.net> X-Original-From: "CARLOS SIMMERLING" Date: Tue, 16 Oct 2012 10:06:42 -0400 Sent to CCL by: "CARLOS SIMMERLING" [carlos.simmerling*|*stonybrook.edu] Applications are open for 3 types of awards from the ACS Division of Computers in Chemistry, to be awarded at the Spring 2013 national meeting in New Orleans. The deadline is 5pm EDT Tuesday, October 23, 2012. 1) CCG Research Excellence award (graduate students) 2) OPENEYE Outstanding Junior Faculty Award (tenure-track Assistant Professors) 3) Peter Kollman Graduate Award in High Performance Computing CCG Research Excellence student travel award stipends are available for the Spring 2013 New Orleans ACS National Meeting. The CCG Excellence Awards have been created to stimulate graduate student participation in ACS COMP Division activities (symposia and poster sessions) at ACS National Meetings. Those eligible for a CCG Excellence Award are graduate students in good standing who present work within the COMP program, either in oral or poster format. Winners receive $1,150 to offset their travel expenses, as well as a copy of CCG's MOE (Molecular Operating Environment) software with a one-year license. They are also honored during a ceremony at the COMP Division Poster Session. Up to 5 awardees will be chosen on the basis of the quality and significance of the research to be presented, as well as the strength of the supporting letter and other materials. All graduate students of the Americas (North, South or Central) are encouraged to submit applications. Awards will be given only to those individuals making presentations, not co-authors. There is a limit of one CCG award application per research lab. Previous winners are not eligible. To apply for an award for the ACS National Meeting in New Orleans, LA, April 7-11 2013, a title and extended abstract of the work (no more than 2 pages), a two page CV, a personal statement (no more than 1 page) and a letter of support from the research advisor should be sent as a SINGLE pdf or text file to carlos.simmerling , stonybrook.edu. Use the subject ACS CCG AWARD APPLICATION. You must use your last name as the beginning of the file name ("yourname.CCG.application.pdf"). Letters of support can be sent separately > from the other materials but must still arrive by the deadline. The application deadline is 5pm EDT on Tuesday, October 23. Applicants will receive email confirmation of receipt of materials. If you do not receive confirmation by midnight Oct 25, please contact the organizer immediately by email (see below). In addition, you must submit your normal poster abstract to the "Chemical Computing Group Excellence Award" symposium on the ACS PACS system prior to the PACS deadline. Note that you MUST APPLY TWICE: email your application, and submit an abstract to PACS. Both must be submitted before their respective deadlines. Do not submit your PACS abstract to the standard poster session- it must be submitted for the CCG session or your application will not be considered. More information on awards offered by the ACS COMP division can be found on the web site at http://www.acscomp.org/Awards/index.html Carlos Simmerling Chair, ACS COMP Division Awards Committee Professor, Department of Chemistry Stony Brook University, Stony Brook, NY 11794-3400 carlos.simmerling , stonybrook.edu OPENEYE Junior Faculty Award The ACS COMP OPENEYE Outstanding Junior Faculty Award program provides $1,000 to up to four outstanding tenure-track junior faculty members to present their work in COMP symposia at ACS National Meetings. The Awards are designed to assist new faculty members in gaining visibility within the COMP community. Award certificates and $1,000 prizes will be presented at the COMP Poster session. While special consideration will be given to Assistant Professors presenting work in the area of algorithm and methods development, applications for Outstanding Junior Faculty Awards are invited from all current tenure-track junior/untenured faculty (or equivalent positions in other institution types) who are members of ACS and the ACS Division of Computers in Chemistry. Postdoctoral researchers in transition to faculty appointments may also be considered. Selection criteria will include the novelty and importance of the work to be presented, CV of the applicant, as well as the level of Departmental support as indicated by the applicant's department Chair or Chair designee. To apply for an award for the ACS National Meeting in New Orleans, LA, April 7-11 2013, a title and extended abstract of the work (no more than 2 pages), a complete CV (including ACS member number) and the letter of departmental support should be sent as a SINGLE pdf or text file to carlos.simmerling , stonybrook.edu. Use the subject ACS OPENEYE AWARD APPLICATION. You must use your last name as the beginning of the file name ("yourname.OPENEYE.application.pdf"). The departmental support letter can be sent separately if desired but must arrive by the deadline. You must include your last name at the start of the file name. The application deadline is 5pm EDT on Tuesday, October 23. Applicants will receive email confirmation of receipt of materials. If you do not receive confirmation by midnight Oct 25, please contact the organizer immediately by email. In addition, you must submit your normal poster abstract to the "Outstanding Junior Faculty Award" symposium on the ACS PACS system prior to the PACS deadline. Note that you MUST APPLY TWICE: email your application, and submit an abstract to PACS. Both must be submitted before their respective deadlines. Do not submit your PACS abstract to the standard poster session- it must be submitted for the OPENEYE session or your application will not be considered. Note that the award application is for the poster session. If you want to also give an oral presentation, you must submit a separate abstract to PACS for an oral presentation in a relevant session, in addition to the poster abstract in the award section (note that acceptance into the oral sessions is not guaranteed). Use a somewhat different title for the talk and poster. More information on awards offered by the ACS COMP division can be found on the web site at http://www.acscomp.org/Awards/index.html Carlos Simmerling Chair, ACS COMP Division Awards Committee Professor, Department of Chemistry Stony Brook University Stony Brook, NY 11794-3400 carlos.simmerling , stonybrook.edu Peter Kollman Graduate Award in High Performance Computing to be awarded at the Spring 2013 New Orleans ACS National Meeting. The ACS Peter Kollman Graduate Award in High Performance Computing has been created to provide supercomputer resources to outstanding students in the early stages of their graduate career, particularly for projects that need high performance computing resources for their chemistry-related project. Those eligible for the award are graduate students in good standing who are carrying out research in the broadly defined area of computational chemistry. Winners (or their adviser, if necessary) will be the Principal Investigator of a new account on the kraken Cray XT5 supercomputer at the National Institute of Computational Sciences (NICS), with an allocation of computing time to support the project. For information about kraken, see http://www.nics.tennessee.edu/computing-resources/kraken. Allocations will be determined based on the requested amount and consideration of resource availability. Up to 2 awardees will be chosen on the basis of: the significance of the project plan, the potential impact on the project of obtaining additional supercomputer resources, the qualifications of the student, and the strength of the supporting letter and other materials. Projects with modest computational needs that can be performed on individual machines or small clusters are not likely to be competitive. Application requirements include a title and extended abstract of the work (no more than 1 page), a two page CV, a brief letter of support from the research advisor, and a 1-2 page detailed computational plan indicating: computational resources already available for the project, the types of calculations to be performed, experience of the applicant with high performance computing, availability of software, justification of number and length of runs, parallel scaling data, and an estimate of the total time needed. Submit the application to carlos.simmerling , stonybrook.edu as a SINGLE pdf or text file, and include your last name at the start of the file name. Use the subject ACS Kollman AWARD APPLICATION. You must use your last name as the beginning of the file name ("yourname.KOLLMAN.application.pdf").There is a limit of one Peter Kollman Award application per research lab (PI). Previous winners are not eligible. The application deadline is 5pm EDT on Tuesday, October 23. Applicants will receive email confirmation of receipt of materials. If you do not receive confirmation by midnight Oct 25, please contact the organizer immediately by email. Winners are encouraged but not required to present their work within the COMP program at the meeting, either in oral or poster format. If you want to present your work in an oral or poster presentation, you must also submit your abstract using the ACS PACS system, prior to the PACS deadline. Application for the supercomputing award does not constitute an application for a presentation. More information on awards offered by the ACS COMP division can be found on the web site at http://www.acscomp.org/Awards/index.html Carlos Simmerling Chair, ACS COMP Division Awards Committee Professor, Department of Chemistry Stony Brook University Stony Brook, NY 11794-3400 carlos.simmerling , stonybrook.edu From owner-chemistry@ccl.net Tue Oct 16 16:55:00 2012 From: "David Andr Cornil david.andre.cornil#,#gmail.com" To: CCL Subject: CCL: Dipole correction in Crystal09 Message-Id: <-47772-121016100933-29750-0g5mx2hleO7IR4CVkNFxww .. server.ccl.net> X-Original-From: "David Andr Cornil" Date: Tue, 16 Oct 2012 10:09:29 -0400 Sent to CCL by: "David Andr Cornil" [david.andre.cornil.:.gmail.com] Dear CCL users, Has anyone of you used the CRYSTAL09 package for interface calculations ? More particulary, I wonder if the packahe can deal with dipole correction (as in VASP or SIESTA for example). I checked the manual about this option but without any success. Regards, David "Pocket" CORNIL, PhD Laboratory for Chemistry of Novel Materials (CMN) University of Mons 20 Place du Parc 7000 MONS (BELGIUM) David.Cornil{:}umons.ac.be