From owner-chemistry@ccl.net Wed Jan 23 09:04:00 2013 From: "David Rogers david.rogers*_*ed.ac.uk" To: CCL Subject: CCL: Distance Learning Certificate in Computational Chemistry Message-Id: <-48114-130123052014-13676-Rvzsb2Isti43yk1KUovmsA%a%server.ccl.net> X-Original-From: "David Rogers" Date: Wed, 23 Jan 2013 05:20:12 -0500 Sent to CCL by: "David Rogers" [david.rogers*ed.ac.uk] Dear CCL Subscribers The University of Edinburgh and its partner institutions are gauging interest for a distance-learning online course in computational chemistry, leading to the award of a Post-Graduate Certificate in Computational Chemistry. We should be grateful if you are interested - or you know of any other colleagues, especially experimentalists, who would be interested - to spend a few minutes completing an online questionnaire: http://www.ed.ac.uk/studying/postgraduate/online-distance-learning/programmes/future-programmes/future-overview Direct link to the questionnaire: https://www.surveymonkey.com/s/Z7RZKJQ Many thanks for your time. Best wishes, David Rogers -- Dr David M. Rogers Research Computing and Distance Education Development Officer School of Chemistry The University of Edinburgh Joseph Black Building The King's Buildings West Mains Road Edinburgh EH9 3JJ UK T. 0131 650 7748 F. 0131 650 6453 E. david.rogers : ed.ac.uk From owner-chemistry@ccl.net Wed Jan 23 09:40:00 2013 From: "Alexander Kos isciencesearch|akosgmbh.de" To: CCL Subject: CCL: iScienceSearch - web service - federated search over Internet sources Message-Id: <-48115-130123070402-19619-1b0gFmq+9LKAduNV6os+8g.@.server.ccl.net> X-Original-From: "Alexander Kos" Content-Language: de Content-Type: multipart/alternative; boundary="----=_NextPart_000_04F2_01CDF963.6BB0A670" Date: Wed, 23 Jan 2013 12:14:50 +0100 MIME-Version: 1.0 Sent to CCL by: "Alexander Kos" [isciencesearch*akosgmbh.de] This is a multipart message in MIME format. ------=_NextPart_000_04F2_01CDF963.6BB0A670 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Dear Dr.=20 =20 We have developed with iScienceSearch http://isciencesearch.com/iss/default.aspx, an Internet search engine = for chemists. In the background we extend your search query. For instance, = if you search by name, we extend automatically when possible the search by other synonyms, CAS Registry Number, and structure (InChIs, smiles, molfiles). This also enables us to find answers in databases that you = cannot search by structure, even if you start with drawing a chemical = structure. The result is a page with links like Google. These links can be sorted, filtered or grouped. =20 iScienceSearch also supports mobile devices and it works well to draw structures on something like an iPad. We use JSDraw from Scilligence ( www.scilligence.com) to draw chemical structures. This is a good application to find out for yourself if = mobile devices are useful for research.=20 =20 The application is plug-in free and opening the URL is all what the user needs to do. =20 As software developer you can use the iScienceSearch web service to = start a search from your application and bring back the hit list, or parse the answer pages to display selected data for the end user.=20 =20 Please try this version, = and let us know your comments. =20 More information is available at www.isciencesearch.com.=20 =20 With best regards, The iScienceSearch development team, Hans-J=FCrgen Himmler and = Alexander Kos =20 Please send an email to subscribe*akosgmbh.de if you want to receive future newsletter, or send = an email to unsubscribe*akosgmbh.de if = you want to be removed from the mailing list. AKos Consulting & Solutions Deutschland GmbH (AKos GmbH) Dr. Alexander Kos Austr. 26 D-79585 Steinen Germany Phone: +49 7627 970068 Fax: +49 7627 970067=20 Mobile +49 171 526 9392 Skype: akosgmbh E-mail: software*akosgmbh.de Homepage: www.akosgmbh.de Registered at Amtsgericht Freiburg HRB 700872, Ust-ID DE253131617, = General Manager: Greta Auf der Maur, Alexander Kos Authorized agent for several software companies. =20 Can you search Google by chemical structure? iScienceSearch can - The Internet Search Engine for Chemists! =96 ( http://isciencesearch.com/iss/default.aspx)=20 =20 =20 =20 =20 ------=_NextPart_000_04F2_01CDF963.6BB0A670 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable

Dear=A0 = Dr.

 

We have = developed with iScienceSearch http://isciencesearch.com/iss/defaul= t.aspx, an Internet search engine for = chemists. In the background we extend your search query. For instance, = if you search by name, we extend automatically when possible the search = by other synonyms, CAS Registry Number, and structure (InChIs, smiles, = molfiles). This also enables us to find answers in databases that you = cannot search by structure, even if you start with drawing a chemical = structure. The result is a page with links like Google. These links can = be sorted, filtered or grouped.

 

iScienceSearch also supports mobile = devices and it works well to draw structures on something like an iPad. = We use JSDraw from Scilligence (www.scilligence.com) to draw chemical structures.=A0 This is a good application to find = out for yourself if mobile devices are useful for research. =

 

The = application is plug-in free and opening the URL is all what the user = needs to do.

 

As software = developer you can use the iScienceSearch web service to start a search = > from your application and bring back the hit list, or parse the answer = pages to display selected data for the end user. =

 

Please try this version, and let us know your = comments.

 

More = information is available at www.isciencesearch.com.

 

With best = regards,

The iScienceSearch=A0 development team, Hans-J=FCrgen = Himmler and Alexander Kos

 

Please send an email to subscribe*akosgmbh.de if you want to receive future newsletter, or = send an email to unsubscribe*akosgmbh.de if you want to be removed from the mailing = list.

AKos Consulting & Solutions Deutschland = GmbH

(AKos GmbH)
Dr. Alexander Kos
Austr. = 26
D-79585 Steinen
Germany

Phone: +49 7627 = 970068

Fax: +49 7627 970067 =

Mobile +49 171 526 = 9392

Skype: akosgmbh

E-mail: software*akosgmbh.de
Homepage: www.akosgmbh.de

Registered at Amtsgericht Freiburg HRB 700872, = Ust-ID DE253131617, General Manager: Greta Auf der Maur, Alexander = Kos

Authorized agent for several software = companies.

 

Can you search Google by chemical structure?  iScienceSearch can - = The Internet Search Engine for Chemists! – = (http://iscien= cesearch.com/iss/default.aspx)

 

 

 

 

------=_NextPart_000_04F2_01CDF963.6BB0A670-- From owner-chemistry@ccl.net Wed Jan 23 10:14:00 2013 From: "Neese, Frank frank.neese^^^cec.mpg.de" To: CCL Subject: CCL: parallel ORCA Message-Id: <-48116-130123085413-24462-HRxY9pjg/TgAAVR7I/5mHg{=}server.ccl.net> X-Original-From: "Neese, Frank" Content-Language: en-US Content-Type: multipart/alternative; boundary="_000_C2DF06F53DDC834AB9E845E1183B773D3D0E3866UMEXCDAGA01umgw_" Date: Wed, 23 Jan 2013 13:54:04 +0000 MIME-Version: 1.0 Sent to CCL by: "Neese, Frank" [frank.neese/a\cec.mpg.de] --_000_C2DF06F53DDC834AB9E845E1183B773D3D0E3866UMEXCDAGA01umgw_ Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Dear CCLers, I just wanted to mention that there is a new forum site for ORCA discussion= s where you will find many questions and answers related to the software. http://cec.mpg.de/forum/portal.php We are presently working hard on the upcoming release which will be ORCA 3.= 0 and will have a number of new and exciting features. With my best regards, Frank Neese Am 22.01.2013 um 13:41 schrieb Patrick Pang skpang(-)ctimail.com >: Sent to CCL by: "Patrick Pang" [skpang%x%ctimail.com] Dear all, Do you know how to run a job in parallel using ORCA and DeinoMPIWin? Are t= here any tutorial materials for teaching us this issue step by setp? Regards, Patrick -=3D This is automatically added to each message by the mailing script =3D-E-mail to subscribers: CHEMISTRY^^^ccl.net or use:E-mail to administrators: CHEMISTRY-REQUEST^^^ccl.net or usehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt------------------------------------------------------------------------- Prof. Dr. Frank Neese - Director - Max-Planck Institut for Chemical Energy Conversion Stiftstr. 34-36 D-45470 M=FClheim an der Ruhr Germany E-Mail: Frank.Neese^^^cec.mpg.de ------------------------------------------------------------------------- --_000_C2DF06F53DDC834AB9E845E1183B773D3D0E3866UMEXCDAGA01umgw_ Content-Type: text/html; charset="iso-8859-1" Content-ID: <974A575BA8DEB044A3E761C251A8119C^^^um.gwdg.de> Content-Transfer-Encoding: quoted-printable Dear CCLers,

I just wanted to mention that there is a new forum site for ORCA discu= ssions where you will find many questions and answers related to the softwa= re. 


We are presently working hard on the upcoming release which will be OR= CA 3.0 and will have a number of new and exciting features.

With my best regards,
Frank Neese 


Am 22.01.2013 um 13:41 schrieb Patrick Pang skpang(-)ctimail.com <owner-chemistry^^^ccl.net>:


Sent to CCL by: "Patrick  Pang" [skpang%x%ctimail.com]
Dear all,

Do you know how to run a job in parallel using ORCA and DeinoMPIWin?  = Are there any tutorial materials for teaching us this issue step by setp?
Regards,

Patrick



-=3D This is automatically added to each message by the mailing script =3D-=
E-mail to subscribers: CHEMISTRY^^^ccl.n= et or use:
     http://www.ccl.net/cgi-bin/ccl/send_ccl_message

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     http://www.ccl.net/chemistry/sub_unsub.shtml

Before posting, check wait time at: http://w= ww.ccl.net

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     h= ttp://www.ccl.net/spammers.txt

RTFI: http:= //www.ccl.net/chemistry/aboutccl/instructions/





--------------= -----------------------------------------------------------
Prof. Dr. Frank Neese
- Director -
Max-Planck Ins= titut for Chemical Energy Conversion
Stiftstr. 34-36
D-45470 M=FClheim an der Ruhr
Germany
E-Mail: <= a href=3D"mailto:Frank.Neese^^^cec.mpg.de">Frank.Neese^^^cec.mpg.de
-------------------------------------------------------------------------

--_000_C2DF06F53DDC834AB9E845E1183B773D3D0E3866UMEXCDAGA01umgw_-- From owner-chemistry@ccl.net Wed Jan 23 10:49:00 2013 From: "Mannan K malie_03(0)yahoo.co.in" To: CCL Subject: CCL: Why Chlorine atom is more hydrophobic than Hydrogen Message-Id: <-48117-130123093628-7028-3zryq7rk0oc3Cgf8+qRnqA]_[server.ccl.net> X-Original-From: "Mannan K" Date: Wed, 23 Jan 2013 09:36:26 -0500 Sent to CCL by: "Mannan K" [malie_03|*|yahoo.co.in] Hi CCLers, Chlorine/Fluorine atoms are commonly used to influence the hydrophobic contact in small molecule design. But how the hydrophobicity is being measured for halogen atoms with reference to Hydrogen atom? How Molar refractivity and steric paramemters are connected to hydrophobicity of an atom? Thanks in Advance, Mannan From owner-chemistry@ccl.net Wed Jan 23 11:24:01 2013 From: "bonoit bonoit bonoit_10],[yahoo.fr" To: CCL Subject: CCL:G: Transition state using ROCBS-QB3 Message-Id: <-48118-130123093728-7436-rhXaKTe4N1/tpXOmN6VPyQ|,|server.ccl.net> X-Original-From: "bonoit bonoit" Date: Wed, 23 Jan 2013 09:37:26 -0500 Sent to CCL by: "bonoit bonoit" [bonoit_10(~)yahoo.fr] Dear CClers, Ive some troubles using the method ROCBS-QB3 in Gaussian 09. When I launch the transition state calculation, after just a while I get this message: ****************************************** Gaussian 09: IA32W-G09RevA.02 11-Jun-2009 14-Jan-2013 ****************************************** ----------------------------------------------------- # opt=(calcfc,ts,noeigentest, maxcycle=500) rocbs-qb3 ----------------------------------------------------- No analytic 2nd derivatives for this method. Error termination via Lnk1e in C:\G09W\l1.exe at Mon Jan 14 17:16:18 2013. Job cpu time: 0 days 0 hours 0 minutes 1.0 seconds. File lengths (MBytes): RWF= 1 Int= 0 D2E= 0 Chk= 1 Scr= 1 For information, I tried CBS-QB3 and it works very well. Could someone what is it related to? Thank you in advance Benoit From owner-chemistry@ccl.net Wed Jan 23 11:59:00 2013 From: "Sergio Manzetti sergio.manzetti**gmx.com" To: CCL Subject: CCL: On PhD degrees and long distance learning Message-Id: <-48119-130123111140-18739-Yxw+TbICoolYACzTpYLSPQ,,server.ccl.net> X-Original-From: "Sergio Manzetti" Content-Type: multipart/alternative; boundary="========GMXBoundary259501358957484280646" Date: Wed, 23 Jan 2013 17:11:24 +0100 MIME-Version: 1.0 Sent to CCL by: "Sergio Manzetti" [sergio.manzetti%x%gmx.com] --========GMXBoundary259501358957484280646 Content-Type: text/plain; charset="utf-8" Content-Transfer-Encoding: 8bit Dear CCLrs, does anyone know where one can find a University where they accept voluntary PhD students that carry out the PhD on a distance, on a free-basis? Thus, the costs of a PhD program are absent, and so are the salaries for the candidate. Best wishes Sergio --========GMXBoundary259501358957484280646 Content-Type: text/html; charset="utf-8" Content-Transfer-Encoding: quoted-printable Dear CCL= rs, does anyone know where one can find a University where they accept volu= ntary PhD students that carry out the PhD on a distance, on  a free-ba= sis? Thus, the costs of a PhD program are absent, and so are the salaries f= or the candidate.
=20
=20 Best wishes
=20
=20 Sergio --========GMXBoundary259501358957484280646-- From owner-chemistry@ccl.net Wed Jan 23 16:16:00 2013 From: "Billy McCann bwm0005/./tigermail.auburn.edu" To: CCL Subject: CCL:G: Transition state using ROCBS-QB3 Message-Id: <-48120-130123154908-23340-XEGze+UI5r58Ul8PhtoYgA(a)server.ccl.net> X-Original-From: Billy McCann Content-Language: en-US Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="us-ascii" Date: Wed, 23 Jan 2013 20:48:52 +0000 MIME-Version: 1.0 Sent to CCL by: Billy McCann [bwm0005- -tigermail.auburn.edu] Hi Benoit, Gaussian is telling you that there are no analytical 2nd derivatives for ROCSB-QB3. I suppose a pertinent question would be, "why are analytical 2nd derivatives necessary for locating transition structures?". Reading the Gaussian webpage[1] on optimization may guide you in the right direction. [1] http://www.gaussian.com/g_tech/g_ur/k_opt.htm Regards, Billy ****************************** Billy Wayne McCann Ph.D. Candidate Orlando Acevedo Research Auburn University, Alabama, USA Office # = 1-334-844-6948 bwayne on irc.freenode.net ****************************** -----Original Message----- > From: owner-chemistry+bwm0005==auburn.edu^^ccl.net [mailto:owner-chemistry+bwm0005==auburn.edu^^ccl.net] On Behalf Of bonoit bonoit bonoit_10],[yahoo.fr Sent: Wednesday, January 23, 2013 8:37 AM To: Billy McCann Subject: CCL:G: Transition state using ROCBS-QB3 Sent to CCL by: "bonoit bonoit" [bonoit_10(~)yahoo.fr] Dear CClers, Ive some troubles using the method ROCBS-QB3 in Gaussian 09. When I launch the transition state calculation, after just a while I get this message: ****************************************** Gaussian 09: IA32W-G09RevA.02 11-Jun-2009 14-Jan-2013 ****************************************** ----------------------------------------------------- # opt=(calcfc,ts,noeigentest, maxcycle=500) rocbs-qb3 ----------------------------------------------------- No analytic 2nd derivatives for this method. Error termination via Lnk1e in C:\G09W\l1.exe at Mon Jan 14 17:16:18 2013. Job cpu time: 0 days 0 hours 0 minutes 1.0 seconds. File lengths (MBytes): RWF= 1 Int= 0 D2E= 0 Chk= 1 Scr= 1 For information, I tried CBS-QB3 and it works very well. Could someone what is it related to? Thank you in advance Benoithttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt