From owner-chemistry@ccl.net Tue Mar 15 03:41:01 2011 From: "vincent zoete vincent.zoete()gmail.com" To: CCL Subject: CCL: software or script to visualize chemical evolution tree Message-Id: <-44135-110315033840-28583-VGIoWEyQAZjpBy9opOqbJw .. server.ccl.net> X-Original-From: vincent zoete Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1 Date: Tue, 15 Mar 2011 08:38:33 +0100 MIME-Version: 1.0 Sent to CCL by: vincent zoete [vincent.zoete_+_gmail.com] Dear Andrew, You might also want to have a look at "Stripper". This program extracts scaffolds from organic drug-like molecules by stripping away sidechains and representing the remaining structure in a condensed form. It's an open source software distributed by Silicos that could be useful for what you want to do. Have a nice day! Vincent www.click2drug.org On Mon, Mar 14, 2011 at 12:18 PM, Andrew Voronkov drugdesign##yandex.ru wrote: > > Sent to CCL by: Andrew Voronkov [drugdesign~!~yandex.ru] > I have a desire to depict process of hit-to lead development and lead optimization in a tree-like manner. But I became curious if there are  any tools which may assist to visualize such an evolution - for example I enter the initial hit and then a number of derivatives, then some of these derivatives have other derivatives etc. Something like phylogenetic tree, but with taking into account the chemical similarity. If you are aware of any of such tools or approaches, please give the name of software, or links to some publications or algorithms. Probably there is some special term for this field of chemoinformatics. This is nothing to do with PCA and diversity selection, this is something between data management and workflow description from one side and similarity evaluation from another. > > > Best regards, > Andrew>      http://www.ccl.net/cgi-bin/ccl/send_ccl_message>      http://www.ccl.net/cgi-bin/ccl/send_ccl_message>      http://www.ccl.net/chemistry/sub_unsub.shtml>      http://www.ccl.net/spammers.txt> > > From owner-chemistry@ccl.net Tue Mar 15 12:22:00 2011 From: "Roby Kurian Roby_Kurian*umit.maine.edu" To: CCL Subject: CCL:G: Installing g03 and g09 on the same machine Message-Id: <-44136-110315095829-25651-qJrEoFBxocpog82paPG/BQ{}server.ccl.net> X-Original-From: "Roby Kurian" Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1 Date: Tue, 15 Mar 2011 09:58:03 -0400 MIME-Version: 1.0 Sent to CCL by: "Roby Kurian" [Roby_Kurian{=}umit.maine.edu] I have been trying to do QST3 - ONIOM calculations in Gaussian 09. Since the calculations were failing all the time with strange error messages, I browsed through CCL and learned that Gaussian 03 is much more stable than Gaussian 09 when it comes to QST3-ONIOM jobs. So I tried running the same calculation on one of the older machines here having Gaussian 03 on it. This time the calculation failed due to insufficient memory. So I installed g03 on the same machine where I was running g09 (its a quadcore mac, with 4 X 2GB memory) and after that machine is having serious memory issues. Previously I was able to do calculations requiring 8000MW, now after installing g03, I cannot even do a 400MW calculation. The system fails to allocate memory. I have installed both g03 and g09 to the same directory. I would like to know if anybody installed two different versions of Gaussian on the same machine with out any issue? Thanks, Roby Kurian Graduate student Dept of Chemistry University of Maine From owner-chemistry@ccl.net Tue Mar 15 13:05:01 2011 From: "Herbert Fruchtl herbert.fruchtl===st-andrews.ac.uk" To: CCL Subject: CCL:G: Installing g03 and g09 on the same machine Message-Id: <-44137-110315130316-20241-r1xM0PObESvsYnftDmXmiw _ server.ccl.net> X-Original-From: Herbert Fruchtl Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Tue, 15 Mar 2011 17:02:51 +0000 MIME-Version: 1.0 Sent to CCL by: Herbert Fruchtl [herbert.fruchtl^st-andrews.ac.uk] We are running both without problem. Of course they should be in different directories. You can't mix the "link* executables from different versions. If a program crashes and you can't allocate memory anymore, look if there are orphaned shared memory segments. The commands you need are ipcs and ipcrm. Herbert On 03/15/2011 01:58 PM, Roby Kurian Roby_Kurian*umit.maine.edu wrote: > > Sent to CCL by: "Roby Kurian" [Roby_Kurian{=}umit.maine.edu] > I have been trying to do QST3 - ONIOM calculations in Gaussian 09. Since the calculations were failing all the time with strange error messages, I browsed through CCL and learned that Gaussian 03 is much more stable than Gaussian 09 when it comes to > QST3-ONIOM jobs. So I tried running the same calculation on one of the older machines here having Gaussian 03 on it. This time the calculation failed due to insufficient memory. > > So I installed g03 on the same machine where I was running g09 (its a quadcore mac, with 4 X 2GB memory) and after that machine is having serious memory issues. Previously I was able to do calculations requiring 8000MW, now after installing g03, I > cannot even do a 400MW calculation. The system fails to allocate memory. > > I have installed both g03 and g09 to the same directory. I would like to know if anybody installed two different versions of Gaussian on the same machine with out any issue? > > Thanks, > > Roby Kurian > Graduate student > Dept of Chemistry > University of Maine> > -- Herbert Fruchtl Senior Scientific Computing Officer School of Chemistry, School of Mathematics and Statistics University of St Andrews -- The University of St Andrews is a charity registered in Scotland: No SC013532 From owner-chemistry@ccl.net Tue Mar 15 14:20:00 2011 From: "Serge Gorelsky gorelsky() gmail.com" To: CCL Subject: CCL:G: Gaussian09 and NBO analysis problems Message-Id: <-44138-110315141911-21593-85SrheIaI6XdYE4GVF//aA^_^server.ccl.net> X-Original-From: Serge Gorelsky Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=UTF-8 Date: Tue, 15 Mar 2011 14:18:44 -0400 MIME-Version: 1.0 Sent to CCL by: Serge Gorelsky [gorelsky||gmail.com] Hello, > Sorry to say but for our calculations we have found the NBO implementation > in g09 to be broken for the complexes we study, for us it broke around the > g03e1 version, as in the results for the atom charges were wildly different > to the previous g03b/c/d cahrges. I do not think that "broken" is a proper word - the default NBO charges in G09 use a different set of valence orbitals for metal atoms than, say, G03c1 version: For example, in the older versions, a Cu atom in the NBO analysis would show up with 3d and 4s valence orbitals while 4p orbitals were included in the Rydberg set of orbitals. In the new versions, the same Cu atom would include 3s, 4s and 4p orbitals in the valence shell... Thus, NBO populations from two calculations using G03c1 and G09a1 would contain different NPA charges for atoms... See Maseras and Morokuma, CHEMICAL PHYSICS LETTERS (1992) v. 195, p 500 for more detail. Apparently, by adding IOp(6/90=2), one can force Gaussian 09 (revision Rev.B.01 and later) to go back to the old NBO scheme for transition metals. Which definition works "better" (in all possible chemical/physical senses) is still an open question. -- Best regards,   Serge Gorelsky From owner-chemistry@ccl.net Tue Mar 15 15:36:00 2011 From: "John McKelvey jmmckel**gmail.com" To: CCL Subject: CCL: Multiple drawings for publication Message-Id: <-44139-110315134826-25030-6H8L5eEAL3mq4Z4vtBwC3Q::server.ccl.net> X-Original-From: John McKelvey Content-Type: text/plain; charset=ISO-8859-1 Date: Tue, 15 Mar 2011 13:48:17 -0400 MIME-Version: 1.0 Sent to CCL by: John McKelvey [jmmckel=gmail.com] Folks, I have a collection of ab 50 molecules in either cartesian or internal coordinates for which I need stick figures. There needs to be an index in one corner for each molecule, i.e. 1,2 3 4,.. I would appreciate suggestions as how to do this. Many thanks, John -- John McKelvey 10819 Middleford Pl Ft Wayne, IN 46818 260-489-2160 jmmckel^-^gmail.com From owner-chemistry@ccl.net Tue Mar 15 16:11:00 2011 From: "eurisco1[A]pochta.ru" To: CCL Subject: CCL:G: Installing g03 and g09 on the same machine Message-Id: <-44140-110315154512-15992-caMxUKXQUELKTmESORtyLQ---server.ccl.net> X-Original-From: Content-Transfer-Encoding: 8bit Content-Type: text/plain; format=flowed; charset="UTF-8"; reply-type=original Date: Tue, 15 Mar 2011 22:43:56 +0300 MIME-Version: 1.0 Sent to CCL by: [eurisco1\a/pochta.ru] Dear Roby Kurian, > installing g03, I >cannot even do a 400MW calculation. The system fails to allocate memory. It is very likely that your g03 is for x86 architecture. >I have installed both g03 and g09 to the same directory. Did you replace executable files of g09 by files of g03? If yes, it makes some problems. It is better to install g03 and g09 in different directories something like /home/user1/g03 and /home/user1/g09. Sincerely, Ol Ga -----ИÑходное Ñообщение----- > From: Roby Kurian Roby_Kurian*umit.maine.edu Sent: Tuesday, March 15, 2011 4:58 PM To: Ga, Ol Subject: CCL:G: Installing g03 and g09 on the same machine Sent to CCL by: "Roby Kurian" [Roby_Kurian{=}umit.maine.edu] I have been trying to do QST3 - ONIOM calculations in Gaussian 09. Since the calculations were failing all the time with strange error messages, I browsed through CCL and learned that Gaussian 03 is much more stable than Gaussian 09 when it comes to QST3-ONIOM jobs. So I tried running the same calculation on one of the older machines here having Gaussian 03 on it. This time the calculation failed due to insufficient memory. So I installed g03 on the same machine where I was running g09 (its a quadcore mac, with 4 X 2GB memory) and after that machine is having serious memory issues. Previously I was able to do calculations requiring 8000MW, now after installing g03, I cannot even do a 400MW calculation. The system fails to allocate memory. I have installed both g03 and g09 to the same directory. I would like to know if anybody installed two different versions of Gaussian on the same machine with out any issue? Thanks, Roby Kurian Graduate student Dept of Chemistry University of Mainehttp://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 Mar 15 16:46:00 2011 From: "Victor Rosas Garcia rosas.victor**gmail.com" To: CCL Subject: CCL: Multiple drawings for publication Message-Id: <-44141-110315162358-27461-3Nj2zZwvCfCCfgRczsR8PQ~!~server.ccl.net> X-Original-From: Victor Rosas Garcia Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1 Date: Tue, 15 Mar 2011 14:23:48 -0600 MIME-Version: 1.0 Sent to CCL by: Victor Rosas Garcia [rosas.victor _ gmail.com] BKChem (http://bkchem.zirael.org/) can import an XYZ structure and render it as a line drawing. You can even rotate it in 3D and then export as PNG or PDF. Don't know about a way to run this in batch mode. Hope this helps. Victor 2011/3/15 John McKelvey jmmckel**gmail.com : > > Sent to CCL by: John McKelvey [jmmckel=gmail.com] > Folks, > > I have a collection of ab 50 molecules in either cartesian or internal > coordinates for which I need stick figures.  There needs to be an > index in one corner for each molecule, i.e. 1,2 3 4,.. > > I would appreciate suggestions as how to do this. > > Many thanks, > > John > > -- > John McKelvey > 10819 Middleford Pl > Ft Wayne, IN 46818 > 260-489-2160 > jmmckel~~gmail.com>      http://www.ccl.net/cgi-bin/ccl/send_ccl_message>      http://www.ccl.net/cgi-bin/ccl/send_ccl_message>      http://www.ccl.net/chemistry/sub_unsub.shtml>      http://www.ccl.net/spammers.txt> > > From owner-chemistry@ccl.net Tue Mar 15 17:21:00 2011 From: "Andreas W Goetz agoetz{=}sdsc.edu" To: CCL Subject: CCL: AMBER Workshop in Shanghai, China, August 22-26 2011 Message-Id: <-44142-110315163229-2071-KLwTQe4+ELzLK9je4SJdDg ~~ server.ccl.net> X-Original-From: "Andreas W Goetz" Date: Tue, 15 Mar 2011 16:32:26 -0400 Sent to CCL by: "Andreas W Goetz" [agoetz-#-sdsc.edu] Dear all, We would like to draw your attention to the first AMBER workshop in Asia, which will take place in late August 2011. The workshop will be held at the ECNU (East China Normal University) campus, which is nicely located in the city of Shanghai, China. More details, including the provisional program and how to apply will be provided shortly. We expect to open registration on June 01, 2011. For the moment if you are interested please take note of the following dates. DATES: Monday August 22, 2011 to Friday August 26, 2011 LOCATION: Shanghai, China HOST: Prof. John Zhang (East China Normal University) INSTRUCTORS: Prof. Ross Walker, Dr. Andreas Goetz (San Diego Supercomputer Center) TARGET AUDIENCE: Graduate students, postdocs and young faculty who have limited experience in Molecular Dynamics and/or the AMBER software and would benefit from an introductory workshop that also covers advanced topics and the latest features in the AMBER software, including GPU acceleration. AVAILABLE SPACES: 50 COST: Registration and attendance of the workshop is free. However, participants are expected to pay for their own travel and accomodation. RESTRICTION ON ATTENDEES: The workshop will be open to any student or academic from around the world although preference will be given to those studying or working in Asia. As soon as we have the website with provisional program, travel/lodging information and application instructions completed I will post the details here. In the meantime, please forward this announcement to anybody you think may be interested in this workshop. Thanks. All the best, Andy -- Dr. Andreas W. Goetz San Diego Supercomputer Center Tel : +1-858-822-4771 Email: agoetz]=[sdsc.edu Web : www.awgoetz.de From owner-chemistry@ccl.net Tue Mar 15 21:22:01 2011 From: "Rajarshi Guha rajarshi.guha!^!gmail.com" To: CCL Subject: CCL: =?windows-1252?Q?Call_for_Papers=3A_High_Content_Screening=3A_Exploring_R?= =?windows-1252?Q?elationships_Between_Small_Molecules_and_Phenotypic_Results=2E?= =?windows-1252?Q?_242nd_ACS_National_Meeting_Denver=2C_Aug_28_=96_Sept_1=2C_2011?= Message-Id: <-44143-110315212034-4730-vE5vVC/jTzyqaj0QwLJVZQ!A!server.ccl.net> X-Original-From: Rajarshi Guha Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=windows-1252 Date: Tue, 15 Mar 2011 21:20:24 -0400 MIME-Version: 1.0 Sent to CCL by: Rajarshi Guha [rajarshi.guha=gmail.com] High Content Screening: Exploring Relationships Between Small Molecules and Phenotypic Results. 242nd ACS National Meeting Denver, Aug 28 – Sept 1, 2011 CINF Division Dear Colleagues, we are organizing an ACS symposium, focusing on the use of High Content Screening (HCS) for small molecule applications. High content screens, while resource intensive, are capable of providing a detailed view of the phenotypic effects of small molecules. Traditional reporter based screens are characterized by a one-dimensional signal. In contrast, high content screens generate rich, multi-dimensional datasets that allow for wide-ranging and in-depth analysis of various aspects of chemical biology including mechanisms of action, target identification and so on. Recent developments in high-throughput HCS pose significant challenges throughout the screening pipeline ranging from assay design and miniaturization to data management and analysis. Underlying all of this is the desire to connect chemical structure to phenotypic effects. We invite you to submit contributions highlighting novel work and new developments in High Content Screening (HCS), High Content Analysis (HCA), and data exploration as it relates to the field of small molecules. Topics of interest include but are not limited to * Compound & in silico screening for drug discovery * Compound profiling by high content analysis * Chemistry & probes in imaging * Lead discovery strategies – one size fits all or horses for courses? * Application of HCA in discovering toxicology screening strategies * Novel data mining approaches for HCS data that link phenotypes to chemical structures * Software & informatics for HCS data management and integration In addition to these topics special consideration will be given to contributions that present contributions in in-silico exploration based on HCS data. We would also like to point out that sponsorship opportunities are available. The deadline for abstract submissions is April 1, 2011. All abstracts should be submitted via PACS at http://abstracts.acs.org. If you have any questions feel free to contact Tim or myself. Tim Moran Accelrys tmoran*accelrys.com +1 858 799 5609 Rajarshi Guha NIH Chemical Genomics Center guhar*mail.nih.gov +1 814 404 5449 -- Rajarshi Guha NIH Chemical Genomics Center