From owner-chemistry@ccl.net Sun Mar 6 07:15:00 2011 From: "Jinsong Zhao jszhao!A!yeah.net" To: CCL Subject: CCL: open source software for molecular graph Message-Id: <-44056-110306070418-15188-0Oua38rbQh4imOlDcufFfA^^server.ccl.net> X-Original-From: Jinsong Zhao Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Sun, 06 Mar 2011 20:04:16 +0800 MIME-Version: 1.0 Sent to CCL by: Jinsong Zhao [jszhao^^^yeah.net] Hi there, I hope to convert a molecular structure in XYZ format (or any other format) to a graph or an adjacency matrix. I have to use a open source software to do such conversion, however, I find nothing by google. Would please to give me a hand? Any suggestions or comments will be really appreciated. Regards, Jinsong From owner-chemistry@ccl.net Sun Mar 6 10:11:01 2011 From: "Igor Filippov igor.v.filippov\a/gmail.com" To: CCL Subject: CCL: open source software for molecular graph Message-Id: <-44057-110306095346-17254-ZhcOyNEMt7ZcUhuppo7I5w!A!server.ccl.net> X-Original-From: Igor Filippov Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="UTF-8" Date: Sun, 06 Mar 2011 09:53:33 -0500 Mime-Version: 1.0 Sent to CCL by: Igor Filippov [igor.v.filippov++gmail.com] You can use OpenBabel to create a small perl or python script to read in a structure in xyz format and create an adjacency matrix out of the resulting molecular object. It's open source. Igor On Sun, 2011-03-06 at 07:04 -0500, Jinsong Zhao jszhao!A!yeah.net wrote: > Sent to CCL by: Jinsong Zhao [jszhao^^^yeah.net] > Hi there, > > I hope to convert a molecular structure in XYZ format (or any other > format) to a graph or an adjacency matrix. I have to use a open source > software to do such conversion, however, I find nothing by google. > > Would please to give me a hand? Any suggestions or comments will be > really appreciated. > > Regards, > Jinsong> > From owner-chemistry@ccl.net Sun Mar 6 22:00:00 2011 From: "Carlos Simmerling carlos.simmerling!=!gmail.com" To: CCL Subject: CCL: ACS COMP Division awards applications for Fall 2011 meeting Message-Id: <-44058-110305103054-15032-2Qergr/O4i9bYJNCuk4H3w : server.ccl.net> X-Original-From: "Carlos Simmerling" Date: Sat, 5 Mar 2011 10:30:52 -0500 Sent to CCL by: "Carlos Simmerling" [carlos.simmerling]*[gmail.com] Applications are open for 3 types of awards from the ACS Division of Computers in Chemistry, to be awarded at the Fall 2011 national meeting in Denver. The deadline is 5pm EDT March 28, 2011. 1) CCG Research Excellence award (graduate students) 2) HP Outstanding Junior Faculty Award (tenure-track Assistant Professors) 3) Peter Kollman Graduate Award in Supercomputing CCG Graduate student award CCG Research Excellence student travel award stipends are available for the Fall 2011 Denver 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 (PI). Previous winners are not eligible. To apply for an award for the ACS National Meeting in Denver, CO August 28-September 1, 2011, an extended abstract of the work (no more than 2 pages), a two page CV along with a letter of support from the research advisor, and a personal statement (no more than 1 page) should be sent as a SINGLE pdf or text file to carlos.simmerling-.-gmail.com. You must include your last name in the file name. Letters of support can be sent separately from the other materials. The application deadline is 5pm EDT on March 28, 2011. Applicants will receive email confirmation of receipt of materials. If you do not receive confirmation by March 30, please contact the organizer immediately by telephone (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 631-632-1336 carlos.simmerling-.-gmail.com HP Junior Faculty Award The ACS COMP HP 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 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 Denver, CO August 28-September 1, 2011, an extended abstract of the work (no more than 2 pages), a CV and the letter of departmental support should be sent as a SINGLE pdf or text file to carlos.simmerling-.-gmail.com. The departmental support letter can be sent separately if desired. You must include your last name in the file name. The application deadline is 5pm EDT on March 28. Applicants will receive email confirmation of receipt of materials. If you do not receive confirmation by March 30, please contact the organizer immediately by telephone (see below). 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 HP 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). 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 631-632-1336 carlos.simmerling-.-gmail.com Supercomputing Peter Kollman Graduate Award in Supercomputing to be awarded at the Fall 2011 Denver ACS National Meeting. The ACS Peter Kollman Graduate Award in Supercomputing 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, potential impact on the project of additional supercomputer resources, 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 will likely not be competitive. Application requirements include an 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 page detailed computational plan indicating: computational resources already available for the project, the types of calculations to be performed, 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-.-gmail.com as a SINGLE pdf or text file, and include your last name in the file name. There is a limit of one Supercomputing Award application per research lab (PI). Previous winners are not eligible. The application deadline is 5pm EDT on March 28, 2011. Applicants will receive email confirmation of receipt of materials. If you do not receive confirmation by March 30, please contact the organizer immediately by telephone (see below). 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 631-632-1336 carlos.simmerling-.-gmail.com