From owner-chemistry@ccl.net Fri Jan 28 03:21:00 2011 From: "Shirin Seifert shirin.seifert!A!gmail.com" To: CCL Subject: CCL:G: gaussian 09W in fedora Message-Id: <-43783-110128031638-23873-mx7/zdeHAjw+cfpaSTCQpQ() server.ccl.net> X-Original-From: Shirin Seifert Content-Type: multipart/alternative; boundary=0016e6dab3cd6cfb90049ae3aeda Date: Fri, 28 Jan 2011 11:46:21 +0330 MIME-Version: 1.0 Sent to CCL by: Shirin Seifert [shirin.seifert-,-gmail.com] --0016e6dab3cd6cfb90049ae3aeda Content-Type: text/plain; charset=ISO-8859-1 Dear meerja, I myself have tested G09 (Linux) in virtual machine, and virtual box. I tried an optimization job in G09(Windows) and in virtualization software( virtual box and VMware). I compared the job ending time. for my case, G09W (with 2 cores) had approximately the same convergence time as G09 (Linux 16 cores) in virtual machine and virtual box. VMware performance was even better. But I got the highest performance when running G09 directly in windows or Linux operating systems. This was my own experience with my multiprocessor computer server. I do not suggest using Virtual machines. Best of luck, SS On Fri, Jan 28, 2011 at 7:42 AM, neeraj misra neerajmisra- -hotmail.com < owner-chemistry-x-ccl.net> wrote: > > Sent to CCL by: "neeraj misra" [neerajmisra..hotmail.com] > DOES ANY ONE SUGGEST ME WHAT THE ERROR # 2066 MEANS ? THIS CAME UP WHEN I > WAS TRYING TO EXECUTE GAUSSIAN 09W VIA WINE PROGRAM LOADER IN FEDORA > CORE14.IS THERE ANY AY OUT TO RUN G09W CALCULATIONS IN FEDORA...I HAVE > ORACLE VIRTUAL BOX INSTALLED TOO.. > > THANKS IN ADVANCE> > > --0016e6dab3cd6cfb90049ae3aeda Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Dear meerja,

I myself have tested G09 (Linux) in virtual machine, an= d virtual box. I tried an optimization job in G09(Windows) and in virtualiz= ation=A0 software( virtual box and VMware). I compared the job ending time.= for my case, G09W (with 2 cores) had approximately the same convergence ti= me as G09 (Linux 16 cores) in virtual machine and virtual box. VMware perfo= rmance was even better. But I got the highest performance when running G09 = directly in windows or Linux operating systems. This was my own experience = with my multiprocessor computer server. I do not suggest using Virtual mach= ines.

Best of luck,
SS

On Fri, Jan 28, 2= 011 at 7:42 AM, neeraj misra neerajmisra- -h= otmail.com <owner-chemistry-x-ccl.net> wrote:

Sent to CCL by: "neeraj =A0misra" [neerajmisra..hotmail.com]
DOES ANY ONE SUGGEST ME WHAT THE =A0ERROR # 2066 MEANS ? THIS CAME UP WHEN = I WAS TRYING TO EXECUTE GAUSSIAN 09W VIA WINE PROGRAM LOADER IN FEDORA CORE14.IS THERE ANY AY OUT T= O RUN G09W CALCULATIONS IN FEDORA...I HAVE ORACLE VIRTUAL BOX INSTALLED TOO= ..

THANKS IN ADVANCE



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--0016e6dab3cd6cfb90049ae3aeda-- From owner-chemistry@ccl.net Fri Jan 28 05:27:00 2011 From: "Anup Shah shahanup86#gmail.com" To: CCL Subject: CCL: How to get 3D structures of FDA approved drugs Message-Id: <-43784-110126234722-16031-b1R86r3yM/BB4IF25Za4sQ-#-server.ccl.net> X-Original-From: "Anup Shah" Date: Wed, 26 Jan 2011 23:47:21 -0500 Sent to CCL by: "Anup Shah" [shahanup86%x%gmail.com] Hello all, Can anybody suggest any source from which we can download 3D structures or crystal structures of FDA approved drugs? Thanking you in anticipation Regards Anup Shah IGIB, New Delhi, India From owner-chemistry@ccl.net Fri Jan 28 06:53:00 2011 From: "Peter Schmidtke pschmidtke#,#mmb.pcb.ub.es" To: CCL Subject: CCL: How to get 3D structures of FDA approved drugs Message-Id: <-43785-110128065127-7702-8mRsMP6oYXw0SzvGhUECgA^server.ccl.net> X-Original-From: Peter Schmidtke Content-transfer-encoding: 7BIT Content-type: text/plain; charset=ISO-8859-1 Date: Fri, 28 Jan 2011 12:52:03 +0100 MIME-version: 1.0 Sent to CCL by: Peter Schmidtke [pschmidtke+/-mmb.pcb.ub.es] Hello Anup, It depends a bit, do you need the 3d structure in it's target? If yes, I did something related not so long ago. I gathered known oral drugs from a publication by Vieth et al (http://pubs.acs.org/servlet/linkout?suffix=ref15/cit15&dbid=20&doi=10.1021%2Fjm100574m&key=10.1021%2Fjm030267j) and crossed this information with PubCompound to find compounds that have a 3D structure. The remaining compounds with 3D structure (and protein) were crossed using http://www.drugbank.ca/ where you can get information about the actual target of a drug and it's status (approved and so on). More details on the procedure I used are available here (in Mat. & Meth.): http://pubs.acs.org/doi/full/10.1021/jm100574m But for what you need you can probably go with something more permissive. Probably you can also cross this data with the cambridge structural database, but on this people from the CCDC could guide you way better than me. Good luck. -- Peter Schmidtke PhD Student Dept. Physical Chemistry Faculty of Pharmacy University of Barcelona On 01/27/2011 05:47 AM, Anup Shah shahanup86#gmail.com wrote: > Sent to CCL by: "Anup Shah" [shahanup86%x%gmail.com] > Hello all, > > Can anybody suggest any source from which we can download 3D structures or > crystal structures of FDA approved drugs? > > Thanking you in anticipation > > > > Regards > > Anup Shah > IGIB, New Delhi, > India> > > From owner-chemistry@ccl.net Fri Jan 28 07:28:00 2011 From: "Gert Thijs gert.thijs(0)silicos.com" To: CCL Subject: CCL: How to get 3D structures of FDA approved drugs Message-Id: <-43786-110128064550-25041-XE9JAWaPxR/RScLgsZTP2g[*]server.ccl.net> X-Original-From: Gert Thijs Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes Date: Fri, 28 Jan 2011 12:46:37 +0100 Mime-Version: 1.0 (Apple Message framework v936) Sent to CCL by: Gert Thijs [gert.thijs(a)silicos.com] Anup, I guess this page at Binding DB will serve you well : http://www.bindingdb.org/bind/ByFDAdrugs.jsp Gert On Jan 27, 2011, at 5:47 AM, Anup Shah shahanup86#gmail.com wrote: > > Sent to CCL by: "Anup Shah" [shahanup86%x%gmail.com] > Hello all, > > Can anybody suggest any source from which we can download 3D > structures or > crystal structures of FDA approved drugs? > > Thanking you in anticipation > > > > Regards > > Anup Shah > IGIB, New Delhi, > India > > > > -= This is automatically added to each message by the mailing script > =- > To recover the email address of the author of the message, please > change> Conferences: http://server.ccl.net/chemistry/announcements/ > conferences/> > Gert Thijs Director Chemoinformatics Silicos NV. Wetenschapspark 7 B-3590 Diepenbeek Belgium Tel: +32 11 350703 Fax: +32 11 220525 http://www.silicos.com/ From owner-chemistry@ccl.net Fri Jan 28 08:15:00 2011 From: "Volker Engel voen^-^phys-chemie.uni-wuerzburg.de" To: CCL Subject: CCL: ELECTRONIC PROPERTIES OF PI-CONJUGATED MATERIALS II Message-Id: <-43787-110128044944-8547-DZy7fWpUYZqWZenO6Y27Kg(a)server.ccl.net> X-Original-From: "Volker Engel" Date: Fri, 28 Jan 2011 04:49:43 -0500 Sent to CCL by: "Volker Engel" [voen]=[phys-chemie.uni-wuerzburg.de] FIRST ANNOUNCEMENT ELECTRONIC PROPERTIES of PI-CONJUGATED MATERIALS II September 27-30, 2011 Wrzburg, Germany http://www.gk-1221.uni-wuerzburg.de/pi2011 In 2006, the German Science Foundation established the Graduate Research School Control of Electronic Properties of Aggregated pi-Conjugated Molecules at the Universitt of Wrzburg (http://www.gk-1221.uni-wuerzburg.de/startseite). The first international symposium of the Graduate Research School took place in 2008. We are pleased to announce the second international symposium ELECTRONIC PROPERTIES OF PI-CONJUGATED MATERIALS II which will take place from September 27th to September 30th 2011 in the Wrzburg in the Wrzburg Residenz, a site of UNESCOs world heritage (http://www.residenz-wuerzburg.de/englisch/residenz/index.htm). The focus of the conference is on the synthesis, spectroscopy and theory of pi-aggregates. The list of invited speakers includes J.-L. Bredas (Georgia Tech) S. Grimme (Mnster) K. Leo (Dresden) E. Nakamura (Tokyo) J.P. Oglivie (Michigan) F. Spano (Temple) N. Ueno (Chiba) E. Vauthey (Geneva) S. Wang (Queen's) M.R. Wasielewski (Northwestern) Arrival is scheduled on Tuesday, September 27, 2011. The registration is accompanied by a reception in the afternoon/evening. The program starts on Wednesday and ends on Friday, lunchtime. It includes invited lectures, lectures given by students from the Graduate school and a poster session. Further information will soon be provided at our web site and in the Second announcement. On behalf of the Graduate Research School 1221, Volker Engel Institute for Physical and Theoretical Chemistry University of Wrzburg E-mail: voen-#-phys-chem.uni-wuerzburg.de From owner-chemistry@ccl.net Fri Jan 28 11:20:00 2011 From: "vincent zoete vincent.zoete{:}gmail.com" To: CCL Subject: CCL: How to get 3D structures of FDA approved drugs Message-Id: <-43788-110128091932-22976-nXymrcMd2arbYfUROlizRg__server.ccl.net> X-Original-From: vincent zoete Content-Type: text/plain; charset=ISO-8859-1 Date: Fri, 28 Jan 2011 15:19:14 +0100 MIME-Version: 1.0 Sent to CCL by: vincent zoete [vincent.zoete]|[gmail.com] Dear Anup, They are several databases that provides 3D structures of FDA approved drugs, like those already mentioned in this thread (DrugBank..), but also the Zinc database from which you can get a collection of mol2 files (http://zinc.docking.org/vendor0/ look for "FDA-approved drugs (via DSSTOX)" You may find others here: http://www.click2drug.org/ (See databases sections). Have a nice day! From owner-chemistry@ccl.net Fri Jan 28 15:36:00 2011 From: "Jim Kress ccl_nospam/./kressworks.com" To: CCL Subject: CCL: ELECTRONIC PROPERTIES OF PI-CONJUGATED MATERIALS II Message-Id: <-43789-110128114847-21489-Kr20jGp+aWmT3wIi3h8WRQ::server.ccl.net> X-Original-From: "Jim Kress" Content-Language: en-us Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="us-ascii" Date: Fri, 28 Jan 2011 11:48:16 -0500 MIME-Version: 1.0 Sent to CCL by: "Jim Kress" [ccl_nospam|*|kressworks.com] I've noticed an increasing volume of symposia being presented to the CCL, the attached just being one example. Is there any particular reason that none, or an insignificant minority, of these symposia are not being presented via webcast, webinars or podcasts? It would seem that those methods would make the symposia available to a much larger audience, providing for a much wider dissemination of information, while allowing for the acquisition of additional revenue for the symposia organizers and perhaps even lowering symposia costs. Is there any reason Corporations, Foundations, Universities, and Government Agencies are not adopting this 20th century technology for use in the 21st? Jim > -----Original Message----- > From: owner-chemistry+ccl_nospam==kressworks.com..ccl.net [mailto:owner- > chemistry+ccl_nospam==kressworks.com..ccl.net] On Behalf Of Volker Engel > voen^-^phys-chemie.uni-wuerzburg.de > Sent: Friday, January 28, 2011 4:50 AM > To: Kress, Jim > Subject: CCL: ELECTRONIC PROPERTIES OF PI-CONJUGATED MATERIALS II > > > Sent to CCL by: "Volker Engel" [voen]=[phys-chemie.uni-wuerzburg.de] > FIRST ANNOUNCEMENT > > ELECTRONIC PROPERTIES of PI-CONJUGATED MATERIALS II > > September 27-30, 2011 > > Wrzburg, Germany > > http://www.gk-1221.uni-wuerzburg.de/pi2011 > > In 2006, the German Science Foundation established the Graduate > Research School > Control of Electronic Properties of Aggregated pi-Conjugated Molecules > at the Universitt of Wrzburg (http://www.gk-1221.uni- > wuerzburg.de/startseite). > The first international symposium of the Graduate Research School took > place in 2008. > > We are pleased to announce the second international symposium > > ELECTRONIC PROPERTIES OF PI-CONJUGATED MATERIALS II > > which will take place from September 27th to September 30th 2011 in the > Wrzburg > in the Wrzburg Residenz, a site of UNESCOs world heritage > (http://www.residenz-wuerzburg.de/englisch/residenz/index.htm). > > The focus of the conference is on the synthesis, spectroscopy and > theory of > pi-aggregates. The list of invited speakers includes > > J.-L. Bredas (Georgia Tech) > S. Grimme (Mnster) > K. Leo (Dresden) > E. Nakamura (Tokyo) > J.P. Oglivie (Michigan) > F. Spano (Temple) > N. Ueno (Chiba) > E. Vauthey (Geneva) > S. Wang (Queen's) > M.R. Wasielewski (Northwestern) > > Arrival is scheduled on Tuesday, September 27, 2011. The registration > is > accompanied by a reception in the afternoon/evening. > > The program starts on Wednesday and ends on Friday, lunchtime. It > includes > invited lectures, lectures given by students from the Graduate school > and a > poster session. > > Further information will soon be provided at our web site and in the > Second announcement. > > On behalf of the Graduate Research School 1221, > > Volker Engel > Institute for Physical and Theoretical Chemistry > University of Wrzburg > E-mail: voen * phys-chem.uni-wuerzburg.de> To recover the email address of the author of the message, please > change>