From owner-chemistry@ccl.net Tue Sep 13 06:16:01 2011 From: "Steve Hillier Stephen.Hillier[a]ciktn.co.uk" To: CCL Subject: CCL: EVENT:Commercialisation of Nanomaterials,Overcoming Scale-Up Challenge Message-Id: <-45435-110913055440-28960-E9OM7LeUwjWzo8ZqEhpuSg~~server.ccl.net> X-Original-From: "Steve Hillier" Date: Tue, 13 Sep 2011 05:54:38 -0400 Sent to CCL by: "Steve Hillier" [Stephen.Hillier[]ciktn.co.uk] Commercialisation of Nanomaterials Overcoming the Scale-Up Challenge Wed 19 Oct 2011 - Leeds, UK Background Strong investment into nanomaterials and the nanotechnology sector has seeded the development of many new technologies and approaches, but difficulties with process scale-up can slow down the commercialisation of these technologies into viable commercial products. Modelling is emerging as a powerful, cost-effective tool to de-risk aspects of scale-up and to enable this technology translation to occur and realise considerable value for nanotechnology based products. Why Attend? This one-day Seminar will allow experts in modelling to meet with those seeking to commercialise nanotechnology based products to share their mutual experience and their needs. This is an opportunity to learn more about what modelling can do for large and small companies to accelerate the process of scale-up and commercialisation of these products More information For more information please follow this link https://ktn.innovateuk.org/web/4317436 This event is being run by the NanoKTN, Chemistry Innovation KTN and Nanofactory to drive collaborative work in this area Cost A small charge of 60 +VAT is made to cover costs From owner-chemistry@ccl.net Tue Sep 13 08:13:00 2011 From: "VS Kumar Neelamraju nvskumar123(_)gmail.com" To: CCL Subject: CCL:G: microsolvation Message-Id: <-45436-110913003356-25590-OuRVGla+UnjWOzBfzWcJqQ:server.ccl.net> X-Original-From: "VS Kumar Neelamraju" Date: Tue, 13 Sep 2011 00:33:54 -0400 Sent to CCL by: "VS Kumar Neelamraju" [nvskumar123*|*gmail.com] Dear CCL members, I working with cyclic tripeptides. Can any body suggest a systematic procedure to do microsolvation of the peptide with aectronitrile. I am currently using Gaussian03 version for calculations. Many Thanks to all suresh email: nvskuamr123=gmail.com From owner-chemistry@ccl.net Tue Sep 13 10:43:00 2011 From: "psavita psavita ~ crlindia.com" To: CCL Subject: CCL: Ligand Protein docking Message-Id: <-45437-110913064621-11645-nQ4x/dPAAMz9i77JT9yEYw*server.ccl.net> X-Original-From: "psavita" Content-Transfer-Encoding: quoted-printable Content-Type: text/html; charset=ISO-8859-1 Date: Tue, 13 Sep 2011 16:22:32 +0530 MIME-Version: 1.0 MIME-Version: 1.0 Sent to CCL by: "psavita" [psavita : crlindia.com]
Hello Kaamini,

Following is the response from my colleag= ue Arundhati in the Life Sciences team.
Kindly get in touch with her for= more details.

Hi There,

I am not sure if you are interested = in AutoDock4 or =0DAutoDock4.1. I am not able to find AutoDock 4.1 on offic= ial download =0Dpage of the community. 
=0DUsing AutoDock4 the tas= k of protein-ligand docking is little difficult =0Dfor beginners. There are= tutorials available for the same at http://autodock.scripps.edu/faqs-help/tutorial/. =
=0DIt involves step wise execution of following task.
1. Preparation= of ligand and protein molecule as per AutoDock format.
2. Preparation o= f grid and docking parameters files.
3. Executing autogrid as par the pa= rameters to build energy maps for atoms within grid.
=0D4. Performing do= cking using the executable autodock.
5. Analysis of =0Dresults that may= involve building docked pose, extracting energy and =0DRMSD information an= d getting h-bond information.

One has to take =0Dcare of file format= he/she is using before starting the process. Also it=0D needs to tweek the= grid and docking parameters for better results.

You can try the aut= omated protein-ligand docking workflow provided by CRL (www.crlindia.com).=0D This workflow keeps you free fr= om the trouble of spending time in =0Dunderstanding the =0Dtool. This workf= low performs all the steps by itself and give you =0Dresults and detailed a= nalysis of docked poses. I will be happy to know =0Dmore about your require= ment if you are interested in commercial workflow=0D for protein-ligand doc= king.



Regards,

Dr. Arundhati Saraph
arundhati+*+cr= lindia.com


Savita Pundlik
Computational Materials Applied Research Group
C= omputational Research Laboratories Ltd.,
= Taco House, Damle Path, Off Law College Road
Pune - 411004, India.

=


= From owner-chemistry@ccl.net Tue Sep 13 11:18:00 2011 From: "Angel Fernandez angel_dfer|-|hotmail.com" To: CCL Subject: CCL:G: Gaussian 09: Operation out of range (l122.exe) Message-Id: <-45438-110913100614-14380-KUl+2FlAUOCwXBlyGSh45Q(-)server.ccl.net> X-Original-From: "Angel Fernandez" Date: Tue, 13 Sep 2011 10:06:07 -0400 Sent to CCL by: "Angel Fernandez" [angel_dfer{:}hotmail.com] In case someone else has this problem, the solution is to use Unrestricted functions (UB3LYP) when calculations with fragments are done. With B3LYP it may work, but Gaussian 09 is not prepared for it, so unrestricted must be set always with Guess=Fragment > "Angel Fernandez angel_dfer{=}hotmail.com" wrote: > > Sent to CCL by: "Angel Fernandez" [angel_dfer###hotmail.com] > Hello. I am trying to run DFT calculations on a system with one less electron > than I have already calculated. With the same input words (only different > charge and multiplicity), everything works ok for original system but not > now. > > I have checked free space and usual causes of this ending. I appreciate some > help, since I've tried different bases or options, and I can't get it done. > > Input commands: > > #P B3LYP/gen pseudo=read Guess=(Fragment=2,only) pop=none Charge > > I put some lines of the error output: > > > (Enter /util/software/G09RevA02/g09/l122.exe) > Operation on file out of range. > FileIO: IOper= 2 IFilNo(1)= -522 Len= 4591 IPos= 4591 > Q=***************** > > > dumping /fiocom/, unit = 1 NFiles = 57 SizExt = 524288 WInBlk = > 8192 > defal = T LstWrd = 364085248 FType=2 FMxFil=10000 > > Number 0 0 501 502 503 507 > 508 512 > Base 109731840 363560960 90112 417792 262144 270336 > 516096 434176 > End 130744320 364085248 91112 428783 265718 275506 > 516126 443455 > End1 130744320 364085248 98304 434176 270336 278528 > 524288 450560 > Wr Pntr 109666304 172924928 90112 417792 262144 270336 > 516096 434176 > Rd Pntr 109666304 172924928 90159 417792 262144 270336 > 516096 443455 > Length 21012480 524288 1000 10991 3574 5170 > 30 9279 > > .. (More things like these go in the middle). > > > dumping /fiocom/, unit = 3 NFiles = 1 SizExt = 524288 WInBlk = > 8192 > defal = T LstWrd = 65536 FType=2 FMxFil=10000 > > Number 0 > Base 40960 > End 65536 > End1 65536 > Wr Pntr 40960 > Rd Pntr 40960 > Length 24576 > Error termination in NtrErr: > NtrErr Called from FileIO. > > From owner-chemistry@ccl.net Tue Sep 13 11:52:00 2011 From: "EMRYS THOMAS ddolgam+/-live.co.uk" To: CCL Subject: CCL:G: microsolvation Message-Id: <-45439-110913111024-11496-wWkWeZORACMkKWilqg8T0g%%server.ccl.net> X-Original-From: "EMRYS THOMAS" Date: Tue, 13 Sep 2011 11:10:17 -0400 Sent to CCL by: "EMRYS THOMAS" [ddolgam%x%live.co.uk] > "VS Kumar Neelamraju nvskumar123(_)gmail.com" wrote: > > Sent to CCL by: "VS Kumar Neelamraju" [nvskumar123*|*gmail.com] > Dear CCL members, > > I working with cyclic tripeptides. Can any body suggest a systematic procedure to do microsolvation of the peptide with aectronitrile. I am currently using Gaussian03 version for calculations. > > Many Thanks to all > > suresh > email: nvskuamr123=gmail.com > > See: JPC(A) 108 10794-10800(2004)for amide-acetonitrile modelling. Emrys Thomas From owner-chemistry@ccl.net Tue Sep 13 13:20:00 2011 From: "Billy McCann bwm0005^tigermail.auburn.edu" To: CCL Subject: CCL: Pseudopotentials theory Message-Id: <-45440-110913105653-25082-mpnnPQq8pbjI8iPlhYI9kA__server.ccl.net> X-Original-From: Billy McCann Content-Language: en-US Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="iso-8859-1" Date: Tue, 13 Sep 2011 14:56:23 +0000 MIME-Version: 1.0 Sent to CCL by: Billy McCann [bwm0005%%tigermail.auburn.edu] Here are a few references which I came across when recently when looking into pseudopotentials. Hope they help. Feel free to send me an email if you can't acquire them. 1. A New Approximation Method in the Problem of Many Electrons. Hellmann, H. J. Chem. Phys., 1935, 3, 61. 2. Ab Initio effective core potentials for molecular calculations. Potentials for the transition metal atoms Sc to Hg. P. Jeffrey Hay and Willard R. Wadt. J. Chem. Phys. 82 (1) 1 January 1985 3. Effective Core Potentials. Michael Dolg. published in Modern Methods and Algorithms of Quantum Chemistry, Proceedings, Second Edition, J. Grotendorst (Ed.), John von Neumann Institute for Computing, J¨ulich, NIC Series, Vol. 3 , ISBN 3-00-005834-6, pp. 507-540, 2000. 4. Relativistic effective core potentials. Michael Dolg. published in Relativistic Electronic Structure Theory, Part I: Fundamentals. Theoretical and Computational Chemistry. Volume 11. Chapter 14. P. Schwerdtfeger (Ed.). Elsevier Science. 2002. ---------------- Billy Wayne McCann Acevedo Research Group Auburn University, Alabama United States -----Original Message----- > From: owner-chemistry+bwm0005==auburn.edu.__.ccl.net [mailto:owner-chemistry+bwm0005==auburn.edu.__.ccl.net] On Behalf Of Carlos Andres Jimenez qcarlos04[A]gmail.com Sent: Saturday, September 10, 2011 10:53 AM To: Billy McCann Subject: CCL: Pseudopotentials theory Sent to CCL by: "Carlos Andres Jimenez" [qcarlos04-,-gmail.com] Dear all Im working with pseudopotentials in transition metals and I would like to know the theory related beyond computational calculations, specially for LANL2DZ and STUTTGART pseudopotentials. Can someone tell or send me any references (articles, e-textbooks, etc) in which theoretical explanations are given? Thank you very much for your help. Kind regards Carlos Jimenez Chemistry student QUIREMA research laboratory Universidad de Antioquia Colombiahttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt From owner-chemistry@ccl.net Tue Sep 13 14:58:00 2011 From: "Carlos Simmerling carlos.simmerling%gmail.com" To: CCL Subject: CCL: October 20 deadline for ACS COMP division awards for junior faculty an Message-Id: <-45441-110913134559-4931-DKwUDmLUpsr5uDvFVFM7BQ%x%server.ccl.net> X-Original-From: "Carlos Simmerling" Date: Tue, 13 Sep 2011 13:45:54 -0400 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 Spring 2012 national meeting in San Diego. The deadline is 5pm EDT Thursday, October 20, 2012. 1) CCG Research Excellence award (graduate students) 2) HP Outstanding Junior Faculty Award (tenure-track Assistant Professors) 3) Peter Kollman Graduate Award in High Performance Computing CCG Graduate student award CCG Research Excellence student travel award stipends are available for the Spring 2012 San Diego 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 San Diego, CA March 25- 29, 2012, 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%gmail.com. Use the subject ACS CCG AWARD APPLICATION. You must include your last name at the beginning of the file name. 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 Thursday, October 20. Applicants will receive email confirmation of receipt of materials. If you do not receive confirmation by 1pm on October 21, 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 (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 San Diego, CA March 25- 29, 2012, 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%gmail.com. Use the subject ACS HP AWARD APPLICATION. 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 Thursday, October 20. Applicants will receive email confirmation of receipt of materials. If you do not receive confirmation by 1pm on October 21, 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 High Perfomance Computing Peter Kollman Graduate Award in High Performance Computing to be awarded at the Spring 2012 San Diego 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 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%gmail.com 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. There is a limit of one Kollman Award application per research lab (PI). Previous winners are not eligible. The application deadline is 5pm EDT on Thursday, October 20. Applicants will receive email confirmation of receipt of materials. If you do not receive confirmation by 1pm on October 21, 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 From owner-chemistry@ccl.net Tue Sep 13 20:23:00 2011 From: "Haibin Scopus lihb734_-_yahoo.com" To: CCL Subject: CCL:G: ask for help about solvation in Gaussian09 Message-Id: <-45442-110913201951-4822-qyZaunM+//1Cjl062C2xTA ~ server.ccl.net> X-Original-From: Haibin Scopus Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=utf-8 Date: Tue, 13 Sep 2011 17:19:43 -0700 (PDT) MIME-Version: 1.0 Sent to CCL by: Haibin Scopus [lihb734.:.yahoo.com] Dear CCLers,     I need your help about solvation model in Gaussian09. In our work, we stuied the absorption spectra of some dyes, also the spectra change upon the dyes adsorbed onto TiO2 nanoparticle by means of CPCM implemented in Gaussian 09. As for spectra, the referee give us two clues to improve our manuscript, however, I can not follow his/her kind suggestion. So, could you help me out of these puzzle?   Suggestion given by Referee: Q1: For solvation calculations (CPCM), it appears that only single points have been done, but this is not entirely clear from the computational details. Please clarify.   My understanding for Q1: The referee thinked that we did not give a clear description on computational details, so we should rewrite computational details to clarify this ambiguous description.   Q2: I am not sure whether TiO2–dye models have been used with CPCM solvation, and if so, how the authors deal with the fact that a spurious part of the solvation energy arises from their model, i.e. the solvation of (backside of) the Ti cluster. Please comment on this aspect. My understanding for Q2: Sorry, I can not follow the referee, in particular "a spurious part of the solvation energy arises from their model, i.e. the solvation of (backside of) the Ti cluster." I really need your help to understand exactly the meaning of this senctence and what I should do to figure out this suggestion.          Thank you very much for your suggestion. Looking forward to your reply.          your sincerely,     Haibin Li Institute of Functional Material Chemistry, Faculty of Chemistry Northeast Normal University changchun, Jilin, 130024 PR CHINA E-mail: lihb734|-|nenu.edu.cn; lihb734|-|yahoo.com http://www.nenu.edu.cn