From owner-chemistry@ccl.net Wed May 30 00:20:00 2012 From: "Andreas Klamt klamt#,#cosmologic.de" To: CCL Subject: CCL: problem with COSMO model in ORCA-2.9 Message-Id: <-47008-120530000132-29687-I7FamLqNVrMKDXxvZSjveg:+:server.ccl.net> X-Original-From: Andreas Klamt Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Wed, 30 May 2012 06:01:25 +0200 MIME-Version: 1.0 Sent to CCL by: Andreas Klamt [klamt(~)cosmologic.de] Hi Puneet, that really has become a rare problem. 1) Are you able to send me the geometry of the molecule you tried to calculate? 2) As a workaround: change rsolv in very small delta increments, e.g. 1.30, 1.305 ... Most likely the problem will disappear soon. The small change of rsolv should not really influence the physics of the result. Andreas Am 29.05.2012 22:48, schrieb Puneet Gupta puneetg.iitk-.-gmail.com: > Dear All, > > I am using ORCA-2.9 to calculate single point energies of the > molecules. Normally I don't get any problem in running COSMO solvent > model in ORCA2.9 but for one of the molecules I am getting error. > Please see below- > > COSMO problem: a1mat not positive definite in consts.f > > Could someone please help me to resolve this problem. > > Thanks. > > regards, > Puneet -- Prof. Dr. Andreas Klamt CEO / Geschäftsführer COSMOlogic GmbH& Co. KG Burscheider Strasse 515 D-51381 Leverkusen, Germany phone +49-2171-731681 fax +49-2171-731689 e-mail klamt(!)cosmologic.de web www.cosmologic.de [University address: Inst. of Physical and Theoretical Chemistry, University of Regensburg] Join us at the 4th-COSMO-RS-Symposium April 2013 Details at www.cosmologic.de/symposium2013 HRA 20653 Amtsgericht Koeln, GF: Prof. Dr. Andreas Klamt Komplementaer: COSMOlogic Verwaltungs GmbH HRB 49501 Amtsgericht Koeln, GF: Prof. Dr. Andreas Klamt From owner-chemistry@ccl.net Wed May 30 03:26:01 2012 From: "Robert Perkins cclnanolab*gmail.com" To: CCL Subject: CCL: CASSCF on Cation Message-Id: <-47009-120530032500-24293-kukm6KBEKmjJfHwEeDEoig(_)server.ccl.net> X-Original-From: Robert Perkins Content-Type: multipart/alternative; boundary=f46d04016d8fc3961e04c13bd89f Date: Wed, 30 May 2012 11:54:50 +0430 MIME-Version: 1.0 Sent to CCL by: Robert Perkins [cclnanolab:gmail.com] --f46d04016d8fc3961e04c13bd89f Content-Type: text/plain; charset=ISO-8859-1 Hello I am going to perform CASSCF calculations on a monocation. For the choice of orbitals in the active space can I check the pi orbitals of the neutral molecule? If you know a good reference on recognizing and selecting appropriate orbitals, i.e if natural, localized or canonical etc. should be involved in the calculation and so on please mention. Thank you and best regards, RP --f46d04016d8fc3961e04c13bd89f Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Hello
I am going to perform CASSCF calculations on a monocation. For the= choice of orbitals in the active space can I check the pi orbitals of the = neutral molecule? If you know a good reference on recognizing and selecting= appropriate orbitals, i.e if natural, localized or canonical etc. should b= e involved in the calculation and so on please mention.
Thank you and best regards,
RP
--f46d04016d8fc3961e04c13bd89f-- From owner-chemistry@ccl.net Wed May 30 06:52:01 2012 From: "Michael F. Peintinger mpei[a]thch.uni-bonn.de" To: CCL Subject: CCL: CASSCF on Cation Message-Id: <-47010-120530065019-21048-Q0Wpw7P4QE1+MnLKkdJYvQ%%server.ccl.net> X-Original-From: "Michael F. Peintinger" Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Wed, 30 May 2012 12:49:33 +0200 MIME-Version: 1.0 Sent to CCL by: "Michael F. Peintinger" [mpei^^^thch.uni-bonn.de] Am 05/30/2012 09:24 AM, schrieb Robert Perkins cclnanolab*gmail.com: > Hello > I am going to perform CASSCF calculations on a monocation. For the > choice of orbitals in the active space can I check the pi orbitals of > the neutral molecule? If you know a good reference on recognizing and > selecting appropriate orbitals, i.e if natural, localized or canonical > etc. should be involved in the calculation and so on please mention. > Thank you and best regards, > RP Dear Robert, CASSCF calculations require a lot of insight from the user. I recommend running a MP2 calculation to generate natural orbitals. Those are usually a good choice. But then you have to plot and LOOK at the orbitals to choose which ones you want to include into your active space. This needs chemical understanding. If you do not know how to do this CASSCF is not your method of choice! Best Regards Michael -- Dipl. Chem. Michael F. Peintinger Mulliken Center for Theoretical Chemistry University of Bonn, Germany Beringstraße 6 Room Number 2.003 D-53115 Bonn Phone: 0228/73-3834 E-Mail: mpei-*-thch.uni-bonn.de From owner-chemistry@ccl.net Wed May 30 07:36:00 2012 From: "Puneet Gupta puneetg.iitk|gmail.com" To: CCL Subject: CCL: problem with COSMO model in ORCA-2.9 Message-Id: <-47011-120530073515-648-uafE97op/TVUn4U1s3BiuA^server.ccl.net> X-Original-From: Puneet Gupta Content-Type: multipart/alternative; boundary=bcaec5523980aa2a7304c13f57fa Date: Wed, 30 May 2012 13:35:04 +0200 MIME-Version: 1.0 Sent to CCL by: Puneet Gupta [puneetg.iitk-$-gmail.com] --bcaec5523980aa2a7304c13f57fa Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Dear Prof. Klamt, Thank you very much for the help. The calculation has run successfully with a rsolv value of 1.285. Although I checked other values from 1.290-1.315 but those did not work. Regards, Puneet On Wed, May 30, 2012 at 6:01 AM, Andreas Klamt klamt#,#cosmologic.de < owner-chemistry..ccl.net> wrote: > > Sent to CCL by: Andreas Klamt [klamt(~)cosmologic.de] > Hi Puneet, > > that really has become a rare problem. > 1) Are you able to send me the geometry of the molecule you tried to > calculate? > 2) As a workaround: change rsolv in very small delta increments, e.g. > 1.30, 1.305 ... Most likely the problem will disappear soon. The small > change of rsolv should not really influence the physics of the result. > > Andreas > > Am 29.05.2012 22:48, schrieb Puneet Gupta puneetg.iitk-.-gmail.com: > > Dear All, >> >> I am using ORCA-2.9 to calculate single point energies of the molecules. >> Normally I don't get any problem in running COSMO solvent model in ORCA2= .9 >> but for one of the molecules I am getting error. Please see below- >> >> COSMO problem: a1mat not positive definite in consts.f >> >> Could someone please help me to resolve this problem. >> >> Thanks. >> >> regards, >> Puneet >> > > > -- > Prof. Dr. Andreas Klamt > CEO / Gesch=E4ftsf=FChrer > COSMOlogic GmbH& Co. KG > Burscheider Strasse 515 > D-51381 Leverkusen, Germany > > phone +49-2171-731681 > fax +49-2171-731689 > e-mail klamt-.-cosmologic.de > web www.cosmologic.de > > [University address: Inst. of Physical and > Theoretical Chemistry, University of Regensburg] > > Join us at the 4th-COSMO-RS-Symposium April 2013 > Details at www.cosmologic.de/**symposium2013 > > HRA 20653 Amtsgericht Koeln, GF: Prof. Dr. Andreas Klamt > Komplementaer: COSMOlogic Verwaltungs GmbH > HRB 49501 Amtsgericht Koeln, GF: Prof. Dr. Andreas Klamt > > > > -=3D This is automatically added to each message by the mailing script = =3D-> http://www.ccl.net/cgi-bin/**ccl/send_ccl_message http://www.ccl.net/cgi-bin/**ccl/send_ccl_message chemistry/announcements/**conferences/ > > Search Messages: http://www.ccl.net/chemistry/**searchccl/index.shtml http://www.ccl.net/spammers.**txt > > RTFI: http://www.ccl.net/chemistry/**aboutccl/instructions/ > > > --bcaec5523980aa2a7304c13f57fa Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Dear Prof. Klamt,

Thank you very much for the help. The calculation = has run successfully with a rsolv value of 1.285. Although I checked other = values from 1.290-1.315 but those did not work.

Regards,
Puneet<= br>
On Wed, May 30, 2012 at 6:01 AM, Andreas Kla= mt klamt#,#cosmologic.de <owner= -chemistry..ccl.net> wrote:

Sent to CCL by: Andreas Klamt [klamt(~)cosmologic.de]
Hi Puneet,

that really has become a rare problem.
1) Are you able to send me the geometry of the molecule you tried to calcul= ate?
2) As a workaround: change rsolv in very small delta increments, e.g. 1.30,= 1.305 ... Most likely the problem will disappear soon. The small change of= rsolv should not really influence the physics of the result.

Andreas

Am 29.05.2012 22:48, schrieb Puneet Gupta puneetg.iitk-.-gmail.com:

Dear All,

I am using ORCA-2.9 to calculate single point energies of the molecules. No= rmally I don't get any problem in running COSMO solvent model in ORCA2.= 9 but for one of the molecules I am getting error. Please see below-

COSMO problem: a1mat not positive definite in consts.f

Could someone please help me to resolve this problem.

Thanks.

regards,
Puneet


--
Prof. Dr. Andreas Klamt
CEO / Gesch=E4ftsf=FChrer
COSMOlogic GmbH& =A0Co. KG
Burscheider Strasse 515
D-51381 Leverkusen, Germany

phone =A0 +49-2171-731681
fax =A0 =A0 +49-2171-731689
e-mail =A0klamt-.-cosmol= ogic.de
web =A0 =A0 www.cosm= ologic.de

[University address: =A0 =A0 =A0Inst. of Physical and
Theoretical Chemistry, University of Regensburg]

Join us at the 4th-COSMO-RS-Symposium April 2013
Details at www.cosmologic.de/symposium2013

HRA 20653 Amtsgericht Koeln, GF: Prof. Dr. Andreas Klamt
Komplementaer: COSMOlogic Verwaltungs GmbH
HRB 49501 Amtsgericht Koeln, GF: Prof. Dr. Andreas Klamt



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--bcaec5523980aa2a7304c13f57fa-- From owner-chemistry@ccl.net Wed May 30 08:14:00 2012 From: "Oluwakemi Whenu oluwakemi.whenu . gmail.com" To: CCL Subject: CCL: Save image in GaussView Message-Id: <-47012-120530025251-15500-GFR7IfsmgSo561jOhS5xdg : server.ccl.net> X-Original-From: Oluwakemi Whenu Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=us-ascii Date: Wed, 30 May 2012 07:52:35 +0100 Mime-Version: 1.0 (1.0) Sent to CCL by: Oluwakemi Whenu [oluwakemi.whenu%a%gmail.com] Hi Plot from results-surfaces/contours Plot on the same window of the chk file that you opened using the camera icon which can also be obtained from the edit menu as image capture. You cannot get this from the MO window that you obtain by clicking on MOs from the edit menu as this only allows you to edit the arrangement of the orbitals Good luck Sent from my iPhone On May 29, 2012, at 4:10 PM, "Nguyen Minh Ly nguyenminhly2209*|*yahoo.com" wrote: > > Sent to CCL by: "Nguyen Minh Ly" [nguyenminhly2209()yahoo.com] > Hi all, I have saved .chk file to show MOs of moleculas When I openned my .chk > file, I updated one MO. But I don't know how to save the image if this MO. > (I wanted to save this image so that I can copy it to Office Word 2007 > Please help me ! > Thanks> > From owner-chemistry@ccl.net Wed May 30 08:49:00 2012 From: "Robert Kiss rkiss.:.mcule.com" To: CCL Subject: CCL: new features at mcule.com Message-Id: <-47013-120530065931-4561-Ag0v1c3Y2KCcWcE8G2LIyw---server.ccl.net> X-Original-From: "Robert Kiss" Date: Wed, 30 May 2012 06:59:29 -0400 Sent to CCL by: "Robert Kiss" [rkiss!^!mcule.com] Dear All, We are pleased to announce a major release of mcule. It includes live- docking, property filtering, sampler filter, and a new table view. Docking calculations are carried out by AutoDock Vina. Target can be selected > from ~10,000 prepared protein structures (integrated from sc-PDB). Live- docking functionality allows to browse the results as they are generated. Molecules can be filtered by properties, such as molar mass, logP, PSA, molar refractivity, number of atoms, heavy atoms, hydrogens, heteroatoms, stereocentres, cis-trans double bonds, rings, rotatable bonds, H-bond donors, H-bond acceptors, RO3 and RO5 violations. Sampler filter can be used to cut the database at a certain threshold and retain only the top x molecules. It can also sample an input collection randomly. Table view was designed to make the browsing of results even more efficient. Properties (incl. screening results) can be easily added/removed from the view. Our technology allows blindingly fast sorting: millions of molecules can be done in a few seconds. For a more detailed description of the mcule release, click here: http://blog.mcule.com To get access to mcule, enter your e-mail address at: http://mcule.com Robert Kiss CSO mcule.com -- About mcule.com Mcule.com is an online drug discovery platform providing a carefully curated, up-to-date database of purchasable compounds integrated with searching and screening tools and a fast molecule procurement service. From owner-chemistry@ccl.net Wed May 30 09:23:00 2012 From: "Andreas Bender, PhD Andreas.Bender%cantab.net" To: CCL Subject: CCL: "New Horizons in Toxicity Prediction", Cambridge/UK, 5-6 September 2012 Message-Id: <-47014-120530082943-16270-KTChv6AzWioYzKZ4lOnbVg|server.ccl.net> X-Original-From: "Andreas Bender, PhD" Content-Type: text/plain; charset=ISO-8859-1 Date: Wed, 30 May 2012 13:29:29 +0100 MIME-Version: 1.0 Sent to CCL by: "Andreas Bender, PhD" [Andreas.Bender~!~cantab.net] Dear All, It is my great pleasure to invite you to our conference "New Horizons in Toxicity Prediction" http://www.lhasasymposium.com/ which will take place in Cambridge/UK on 5-6 September 2012. The Symposium will feature presentations from high profile speakers working in the area of toxicity prediction, representing commerce, academia and associated industry bodies, such as: Dr David J. Dix - The US Environmental Protection Agency Professor Patrik Rydberg - University of Copenhagen Professor Ivan Rusyn - University of North Carolina Professor Hans Westerhoff - Manchester Centre for Integrative Systems Biology (MCISB) Dr Kyle Kolaja - Hoffmann-La Roche Professor Roland Wolf - University of Dundee Professor Hugo Kubinyi - University of Heidelberg Professor Steve Oliver - University of Cambridge Dr Harvey Clewell - The Hamner Institutes for Health Sciences, US Professor Yuichi Sugiyama - University of Tokyo Professor Geoff Tucker - University of Sheffield Dr Teri Klein - Stanford University Dr Richard Brennan - Thomson Reuters, US For more information about the event and on how to register please visit the conference website at http://www.lhasasymposium.com/. Best wishes, Andreas -- Andreas Bender, PhD Lecturer for Molecular Informatics Unilever Centre, Cambridge University http://www-ucc.ch.cam.ac.uk Personal: http://www.andreasbender.de From owner-chemistry@ccl.net Wed May 30 13:01:00 2012 From: "Dan Maftei dan.maftei]_[uaic.ro" To: CCL Subject: CCL:G: How to compute Tozer's Lambda diagnostic in Gaussian? Message-Id: <-47015-120530125625-20890-fCXFnLaGUOcxVY3OwlqzjQ- -server.ccl.net> X-Original-From: Dan Maftei Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=UTF-8 Date: Wed, 30 May 2012 19:56:03 +0300 MIME-Version: 1.0 Sent to CCL by: Dan Maftei [dan.maftei**uaic.ro] Dear CCLers, In computing excitation energies for charge-transfer (CT) states within TD-DFT, usual hybrid functionals are known to fail in many cases. I intend to use the Tozer's Lambda diagnostic [1] to assess the degree of overlap between the occupied and virtual orbitals involved in excitations. My question is how to compute <|Psi_i|||Psi_j|> for each MO pair involved in a specific transition in Gaussian (09). My early trial-and-error efforts include extraction of MO coefficients from the formatted checkpoint followed by a quick check of dot product values. As expected, this doesn't work, as MOs are not expanded in an orthogonal basis. Should I try to extract the AOs overlap matrix for further multiplication or is there a simple way to do this? I see that GAMESS-US (and probably other codes) implemented this since 2009. Thank you in advance, Dan Maftei. [1] Peach, M. J. G.; Benfield, P.; Helgaker, T.; Tozer, D. J. The Journal of Chemical Physics 2008, 128, 044118.