From owner-chemistry@ccl.net Sat Jun 7 00:21:00 2008 From: "Antonio G. De Crisci antonio.decrisci:+:utoronto.ca" To: CCL Subject: CCL: Relativistic treatment for transition metals in PC GAMESS Message-Id: <-37106-080607001558-20609-VGIoWEyQAZjpBy9opOqbJw .. server.ccl.net> X-Original-From: "Antonio G. De Crisci" Date: Sat, 7 Jun 2008 00:15:54 -0400 Sent to CCL by: "Antonio G. De Crisci" [antonio.decrisci/./utoronto.ca] Hello All, Does anybody know what basis set in PC GAMESS gives partial (or full) relativistic treatment for calculations on molecules that contain late transition metals? Thanks, Antonio De Crisci University of Toronto From owner-chemistry@ccl.net Sat Jun 7 03:00:00 2008 From: "John Hearns john.hearns ~~ streamline-computing.com" To: CCL Subject: CCL: Paralleling computers help Message-Id: <-37107-080606200732-24486-ej/BuVQa6K54IBtIFaa5CQ+/-server.ccl.net> X-Original-From: John Hearns Content-Transfer-Encoding: 7bit Content-Type: text/plain Date: Sat, 07 Jun 2008 00:15:02 +0100 Mime-Version: 1.0 Sent to CCL by: John Hearns [john.hearns[a]streamline-computing.com] On Fri, 2008-06-06 at 23:46 +0330, Amin Ordikhani a.ordikhani{:}gmail.com wrote: > Sent to CCL by: "Amin Ordikhani" [a.ordikhani[-]gmail.com] > Hi dear CCLers, > Could someone give of some information about paralleling computers so > that have higher speed for calculations? > Any information would help me. Sure. These webpages might help: http://www.clustermonkey.net/ http://www.beowulf.org/ You could also have a look at this book: http://tinyurl.com/63wlkz From owner-chemistry@ccl.net Sat Jun 7 08:33:01 2008 From: "Frank Neese neese(a)thch.uni-bonn.de" To: CCL Subject: CCL: Relativistic treatment for transition metals in PC GAMESS Message-Id: <-37108-080607083150-19150-sSf71vWAguoQUUQXXAHEzw,,server.ccl.net> X-Original-From: Frank Neese Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-15; format=flowed Date: Sat, 07 Jun 2008 14:31:28 +0200 MIME-Version: 1.0 Sent to CCL by: Frank Neese [neese%a%thch.uni-bonn.de] > Sent to CCL by: "Antonio G. De Crisci" [antonio.decrisci/./utoronto.ca] > Hello All, > > Does anybody know what basis set in PC GAMESS gives partial (or full) relativistic treatment for calculations on molecules that contain late transition metals? > > Thanks, > Antonio De Crisci > University of Toronto > Dear Antonio, We have just published a series of affordable segmented basis sets for up to the third transition row that can be used together with ZORA or DKH. The reference is: All-Electron Scalar Relativistic Basis Sets for Third-Row Transition Metal Atoms Pantazis, D. A.; Chen, X.-Y.; Landis, C. R.; Neese, F. J. Chem. Theory and Comput.; 2008; ASAP Article; DOI: 10.1021/ct800047t The basis sets are available with ORCA but should work, of course, also with other programs. Best regards, Frank -- --------------------------------------------------------------- Prof. Dr. Frank Neese Lehrstuhl fuer Theoretische Chemie Universitaet Bonn Wegelerstr. 12 D-53115 Bonn, Germany neese(-)thch.uni-bonn.de Phone: +49-28-732351 FAX: +49-(0)228-739064 --------------------------------------------------------------- From owner-chemistry@ccl.net Sat Jun 7 13:57:01 2008 From: "Antonio G De Crisci antonio.decrisci _ utoronto.ca" To: CCL Subject: CCL: Relativistic treatment for transition metals in PC GAMESS Message-Id: <-37109-080607135435-22547-cQh0tjDwxnUX350HDx7A/w===server.ccl.net> X-Original-From: "Antonio G De Crisci" Date: Sat, 7 Jun 2008 13:54:31 -0400 Sent to CCL by: "Antonio G De Crisci" [antonio.decrisci\a/utoronto.ca] Thank You Frank. I have looked at you supporting information, which contains the full listings of the basis sets for the heavy metals. Thank you. I presume I would need to know a certain keyword in the input file to implement this into my calculation, however, im not very familiar with the syntax of PC GAMESS as I have just recently become familiar with some its capabilities. Would you (or anyone on the list) know what syntax and keyword I would need to input to augment any existing basis set? With regards, Antonio > "Frank Neese neese(a)thch.uni-bonn.de" wrote: > > Sent to CCL by: Frank Neese [neese%a%thch.uni-bonn.de] > > > Sent to CCL by: "Antonio G. De Crisci" [antonio.decrisci/./utoronto.ca] > > Hello All, > > > > Does anybody know what basis set in PC GAMESS gives partial (or full) relativistic treatment for calculations on molecules that contain late transition metals? > > > > Thanks, > > Antonio De Crisci > > University of Toronto > > > Dear Antonio, > > We have just published a series of affordable segmented basis sets for > up to the third transition row that can be used together with ZORA or DKH. > The reference is: > > All-Electron Scalar Relativistic Basis Sets for Third-Row Transition > Metal Atoms > Pantazis, D. A.; Chen, X.-Y.; Landis, C. R.; Neese, F. > J. Chem. Theory and Comput.; 2008; ASAP Article; DOI: 10.1021/ct800047t > > > The basis sets are available with ORCA but should work, of course, also > with other programs. > > Best regards, > Frank > > > -- > --------------------------------------------------------------- > Prof. Dr. Frank Neese > Lehrstuhl fuer Theoretische Chemie > Universitaet Bonn > Wegelerstr. 12 > D-53115 Bonn, Germany > neese(-)thch.uni-bonn.de > Phone: +49-28-732351 > FAX: +49-(0)228-739064 > --------------------------------------------------------------- > > From owner-chemistry@ccl.net Sat Jun 7 17:41:01 2008 From: "Iain Wallace iain.m.wallace*gmail.com" To: CCL Subject: CCL: Comparing Chemical Libraries Message-Id: <-37110-080607174004-14805-uW8tJsodiG5mKwm9lWnHFA*server.ccl.net> X-Original-From: "Iain Wallace" Content-Type: multipart/alternative; boundary="----=_Part_11268_2159748.1212874794052" Date: Sat, 7 Jun 2008 17:39:54 -0400 MIME-Version: 1.0 Sent to CCL by: "Iain Wallace" [iain.m.wallace ~ gmail.com] ------=_Part_11268_2159748.1212874794052 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline Hi all, I have built a model (using Pipeline pilot and ECFP_4 fingerprints ) to predict inhibition and I was wondering if anybody could give me some pointers on how I could figure out how widely applicable my model is, or how I could use it to find other molecules to screen, from outside of the library that we have purchased and screened. I could only look at molecules that are similar (i.e. within 70%?) to the molecules I used to build the model. I guess I am wondering what approaches other people take, Thanks for your time, Iain ------=_Part_11268_2159748.1212874794052 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline Hi all,

I have built a model (using Pipeline pilot and ECFP_4 fingerprints ) to predict inhibition and I was wondering if anybody could give me some pointers on how I could figure out how widely applicable my model is, or how I could use it to find other molecules to screen, from outside of the library that we have purchased and screened. I could only look at molecules that are similar (i.e. within 70%?) to the molecules I used to build the model. I guess I am wondering what approaches other people take,

Thanks for your time,

Iain

------=_Part_11268_2159748.1212874794052-- From owner-chemistry@ccl.net Sat Jun 7 19:01:01 2008 From: "Radoslaw Kaminski rkaminski.rk a gmail.com" To: CCL Subject: CCL: wave_function_optimization Message-Id: <-37111-080607190016-12635-BcdEKFoDuHzNaMyqVsNQCg_._server.ccl.net> X-Original-From: "Radoslaw Kaminski" Date: Sat, 7 Jun 2008 19:00:13 -0400 Sent to CCL by: "Radoslaw Kaminski" [rkaminski.rk()gmail.com] Hello, I found in one of the publications (Eur. J. Inorg. Chem., 2007, 324332) the statement like this: For every nickel complex it was necessary to check the stability of the wave function to see whether any instability existed > from unrestricted contributions. We found instability in every case. After the check, the wave function was optimized to remove the contributions. The structures were then reoptimized using the optimized wave functions, their wave function stabilities rechecked, and frequencies recalculated. I would be very grateful if somebody could tell me how to do it or where I can find some more information about it. I don't know why do we have to check the stability of such function and optimize it and how to do such things... All the best Radoslaw Kaminski From owner-chemistry@ccl.net Sat Jun 7 23:16:01 2008 From: "Henry Martinez hmartine a gmail.com" To: CCL Subject: CCL: nmr=spinspi, readatoms Message-Id: <-37112-080606180659-24781-zuFBt9uH3taLXj6n3FserA^server.ccl.net> X-Original-From: "Henry Martinez" Date: Fri, 6 Jun 2008 18:06:55 -0400 Sent to CCL by: "Henry Martinez" [hmartine.,,.gmail.com] I am trying to set an nmr=spinspin calculation, but I just want to do it for some atoms of the whole structure, I have tried a lot of ways, the last one was # b3lyp/epr-iii nmr=spinspin readatoms IOp(10/48=10), but it did not work, I still do not know how to specify the atoms I want, can any body send me an email me with an example of the input file of how to calculate the coupling constants for specific atoms for a small structure like ethanol, or whatever..... Thanks a lot, I really need this. From owner-chemistry@ccl.net Sat Jun 7 23:51:01 2008 From: "Pradipta Bandyopadhyay pradipta_b-*-mail.jnu.ac.in" To: CCL Subject: CCL: Code for clustering !! Message-Id: <-37113-080606010906-8149-6wKlPeCehOBljORFADvong---server.ccl.net> X-Original-From: "Pradipta Bandyopadhyay" Content-Disposition: inline Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=US-ASCII Date: Fri, 06 Jun 2008 09:57:36 +0530 Mime-Version: 1.0 Sent to CCL by: "Pradipta Bandyopadhyay" [pradipta_b ~ mail.jnu.ac.in] Dear All, I am looking for a fortran code (or 2 codes) for hierarchical clustering = and k-means clustering. I want to use it for=20 clustering molecules based on energy and/or geometrical parameters. I = would appreciate any pointer. thanks, Pradipta Dr. Pradipta Bandyopadhyay Associate Professor Centre for Computational Biology and Bioinformatics School of Information Technology Jawaharlal Nehru University, New Delhi, INDIA