From owner-chemistry@ccl.net Wed Apr 5 01:30:00 2017 From: "Thomas Exner texner#%#gmx.net" To: CCL Subject: CCL: eChemInfo Training and Innovation Course in Drug Design Message-Id: <-52718-170404055551-64710-Iq8/BGbLfevSgKDF7XSO8g,+,server.ccl.net> X-Original-From: "Thomas Exner" Date: Tue, 4 Apr 2017 05:55:50 -0400 Sent to CCL by: "Thomas Exner" [texner^^gmx.net] 2nd Announcement for the eChemInfo Training and Innovation Course in Drug Design 2017 in Milano Dear CCLers: This is a reminder that the Training and Innovation Course in Drug Design will take place at the Department of Pharmaceutical Sciences, University of Milano from Mon, 17 Jul. to Fri, 21 Jul. 2017. The final program is available at http://www.echeminfo.com/events/drug-design-euro-2017 We will have three exiting key notes: Malaria Drug Discovery Methods, Donatella Taramelli, University of Milan Aspects of Industrial Drug Design, Anna Maria Capelli, Chiesi Design of Cyclopeptidic Drugs, Laura Belvisi / Monica Civera, University of Milan We are also very happy to be able this year to strongly integrate experimental techniques into the workshop. Stefan Jehle from Bruker BioSpin AG, the leading company in biomolecular NMR spectroscopy, will give a session on NMR-driven Fragment Based Drug Design. And we have Anthony Bradley from the Diamond Light Source's XChem project, which provides services for complex structure determination using medium- to high-throughput X-ray. He will give a presentation together with Tim Dudgeon (Informatics Matters) on Moving from Individual Tools to Complete Workflows. And just to remind you on our special setup of the workshop: Use the bring your own problems option to directly apply your newly acquired knowledge to your own research, profit from specific advice by the experts and other participants and contribute to innovative approaches for all case studies. You can also present a poster of your work to give the other attendees an overview of your work and foster discussions within the groups. Bursary Awards are available; deadline was extended until 30 April at http://www.echeminfo.com/bursary-awards Early-bird reduced rates are now also available until 30 April. For further information and questions on these and other eChemInfo workshops, please visit http://www.echeminfo.com/events or contact us. Alessandro Contini, University of Milano (alessandro.contini^_^unimi.it) Thomas Exner, Douglas Connect (thomas.exner^_^douglasconnect.com) P.S.: We would highly appreciate if you could showcase the workshop poster (http://www.echeminfo.com/Milano2017_Poster.pdf) on your notice boards. From owner-chemistry@ccl.net Wed Apr 5 11:35:01 2017 From: "Vidya Kaipanchery vidyak.clt-.-gmail.com" To: CCL Subject: CCL: Difficulty extracting pdb information form output file Message-Id: <-52719-170405085622-7302-D/wDNcmQzw0otTpO9dOALw/./server.ccl.net> X-Original-From: "Vidya Kaipanchery" Date: Wed, 5 Apr 2017 08:56:21 -0400 Sent to CCL by: "Vidya Kaipanchery" [vidyak.clt**gmail.com] I have done a ONIOM calculation in G09 and got my optimized structure. It does not contain any of the pdb (protein data base) information which I require for further calculation(frequency analysis). I tried extracting it form chk file using "newzmat" command and it failed. I also tried to convert the chk to fchk and it didnt work. Can you please help me how to extract my optimized geometry with pdb information from my chk file or even log file? Kind regards, Vidya From owner-chemistry@ccl.net Wed Apr 5 12:10:01 2017 From: "Jan Labanowski jkl-*-wowway.biz" To: CCL Subject: CCL: The CCL mail did not work since March 25 Message-Id: <-52720-170405114738-19538-awHiMKLvLoVDXS5HZNHwzA(-)server.ccl.net> X-Original-From: "Jan Labanowski" Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=UTF-8 Date: Wed, 05 Apr 2017 11:47:31 -0400 MIME-Version: 1.0 Sent to CCL by: "Jan Labanowski" [jkl:_:wowway.biz] Dear CCL, After I updated my CCL server on March 25 everything looked fine only the CCL mail was not being sent to subscribers. It went to a proverbial black hole due to some security weirdness. If you sent a message to CCL after March 25 it was not sent. Sorry... I have all the copies of your emails in my logs, but it probably is easier if you just get your copy from your "Sent" folder and resend it. Some messages may not be relevant any more. You can see at http://www.ccl.net/cgi-bin/ccl/month-index.cgi?2017+03 that until today no messages are archived. Yes, it is my fault, and I am sorry, but what can I say... S... happens and I was very busy lately. > From what I see, the job postings worked OK. I am still reviewing what happened and why, but it should be fine to post messages to CCL now. Jan -- Jan Labanowski CCL Administrator jkl!=!ccl.net   From owner-chemistry@ccl.net Wed Apr 5 15:40:36 2017 From: "Close, David M. CLOSED..mail.etsu.edu" To: CCL Subject: CCL:G: Difficulty extracting pdb information form output file Message-Id: <-52721-170405134721-12943-bP80qyjeyaNQQXdqqsnzsg===server.ccl.net> X-Original-From: "Close, David M." Content-Language: en-US Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="us-ascii" Date: Wed, 5 Apr 2017 17:47:13 +0000 MIME-Version: 1.0 Sent to CCL by: "Close, David M." [CLOSED:+:mail.etsu.edu] Vidya: Not sure what you mean by pdb information? The Protein Data Bank lists the structure of proteins determined by x-ray crystallography. They list the xyz coordinates of these structures. Surely the Gaussian out also lists the xyz coordinates in the output file. Are you trying to convert one set of data to another? If so there is the old utility called BABEL that will do just that. Regards, Dave Close -----Original Message----- > From: owner-chemistry+closed==etsu.edu__ccl.net [mailto:owner-chemistry+closed==etsu.edu__ccl.net] On Behalf Of Vidya Kaipanchery vidyak.clt-.-gmail.com Sent: Wednesday, April 05, 2017 8:56 AM To: Close, David M. Subject: CCL: Difficulty extracting pdb information form output file Sent to CCL by: "Vidya Kaipanchery" [vidyak.clt**gmail.com] I have done a ONIOM calculation in G09 and got my optimized structure. It does not contain any of the pdb (protein data base) information which I require for further calculation(frequency analysis). I tried extracting it form chk file using "newzmat" command and it failed. I also tried to convert the chk to fchk and it didnt work. Can you please help me how to extract my optimized geometry with pdb information from my chk file or even log file? Kind regards, Vidyahttp://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 Wed Apr 5 15:42:18 2017 From: "Oliver Koch oliver.koch[-]tu-dortmund.de" To: CCL Subject: CCL: Call for papers - 13th German Conference on Chemoinformatics Message-Id: <-52722-170405142957-18927-2UomeKMT/d65wo4fdU7gsA]*[server.ccl.net> X-Original-From: "Oliver Koch" Date: Wed, 5 Apr 2017 14:29:55 -0400 Sent to CCL by: "Oliver Koch" [oliver.koch*|*tu-dortmund.de] Dear colleagues and friends, the division Chemistry-Information-Computer (CIC) of the German Chemical Society cordially invites you to participate in the 13th German Conference on Chemoinformatics. The conference will take place November 7- 10, 2017 in Mainz, Germany. The aim of the conference is to reflect and highlight the new role of cheminformatics in the modern information world. It will span a wide range of subjects related to the use of computers in chemistry, pharmacy, materials science and biology; from chem- and bioinformatics to explicit modelling and from industrial applications to fundamental academic research. Confirmed Speakers: * Evan Bolton (NCBI, USA) * David Case (Rutgers University, USA) * Bettina Keller (FU Berlin, Germany) * Frank Kertscher (IBM Watson, Munich, Germany) * Nadine Schneider (Novartis, Switzerland) * Walter Thiel (MPI Mlheim, Germany) * Jrg K. Wegener (Janssen Pharmaceutica, Belgium) There will be sessions on: * Big Data and Deep Learning * Chemical Information * Chemoinformatics and Drug Discovery * Databases and Data Handling * Material Sciences * Molecular Modelling * Protein Modelling * Simulations * Structure Determination * Target and ADMETox prediction The scientific programme will include plenary and contributed lectures, posters and software presentations. The deadline for submissions of oral contributions and research telegrams is May 31, 2017. The deadline for poster submissions is August 30, 2017. See more details at http://www.gdch.de/gcc2017 Registration will open in May 2017 at: http://www.gdch.de/gcc2017 Hope to see you in Mainz, The organizers From owner-chemistry@ccl.net Wed Apr 5 21:19:13 2017 From: "Kaushik Hatua kaushikhatua!=!yahoo.in" To: CCL Subject: CCL: Electric field in g09 Message-Id: <-52723-170405201754-11268-NM+zviJIZc73rzhPZw5xfg_._server.ccl.net> X-Original-From: Kaushik Hatua Content-Type: multipart/alternative; boundary="----=_Part_40272_1487032065.1491437865809" Date: Thu, 6 Apr 2017 00:17:45 +0000 (UTC) MIME-Version: 1.0 Sent to CCL by: Kaushik Hatua [kaushikhatua===yahoo.in] ------=_Part_40272_1487032065.1491437865809 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 7bit Can anybody suggest me how to add two different electric field from different directions using g09. Field keyword has only example along a particular direction. I need to optimize molecule with field from different directions say along x and y with field 0.001 a.u Sent from Yahoo Mail on Android ------=_Part_40272_1487032065.1491437865809 Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: 7bit Can anybody suggest me how to add two different electric field from different directions using g09. Field keyword has only example along a particular direction. I need to optimize molecule with field from different directions say along x and y with field 0.001 a.u

------=_Part_40272_1487032065.1491437865809-- From owner-chemistry@ccl.net Wed Apr 5 23:42:00 2017 From: "Carles Bo cbo{=}iciq.es" To: CCL Subject: CCL: 11EuCO-TCC 4-7 September Deadline Abstracts Submission Extended Message-Id: <-52724-170405181057-31203-h5bu5lU5Tjh4OoZKP42g0w%x%server.ccl.net> X-Original-From: "Carles Bo" Date: Wed, 5 Apr 2017 18:10:56 -0400 Sent to CCL by: "Carles Bo" [cbo#,#iciq.es] 11EuCO-TCC Deadline for Abstracts Submission extended till April 16th. The deadline for submitting your abstract for oral communications, posters and applications demos to the 11EuCO-TCC Conference is approaching! Visit the conference website to submit your abstract and to register: http://www.11euco-tcc.org Recent News: - Interested to know about the success of new CompChem based companies? Special Session conducted by Drs. Alfons Nonell (Mindthebyte) and Xavier Barril (Minorix Therapeutics). - Prof. Ursula Roethlisberger (EPFL, Switzerland) will receive the EuCheMS Lecture Award during the closing ceremony of 11EUCO-TCC. Prof. David Cole-Hamilton, EuCheMS President, will present the award. - Communications presented at the conference are invited to submit a paper to the Topical Collection EuCo-TCC kindly provided by The Journal of Molecular Modelling. Associate Editors: Drs. Peter Szalay (Etvs Lornd University) and Ramn Says (Universitat de Barcelona). - Stay in Barcelona the day after and attend the 6th Workshop TCCM on Theoretical Chemistry and Computational Modeling, which is part of European Master TCCM & Join Doctorate TCCM. It will take place on September 8th in the same venue. We look forward to welcoming you in Barcelona next September!