From owner-chemistry@ccl.net Wed May 21 02:05:01 2014 From: "Raphael Berger berger===chem.helsinki.fi" To: CCL Subject: CCL: Fermi Energies of different Modifications of Molecular Solid Message-Id: <-50103-140521020336-24978-USMS+DicAa0E5Kj6fYoaUg%a%server.ccl.net> X-Original-From: "Raphael Berger" Date: Wed, 21 May 2014 02:03:35 -0400 Sent to CCL by: "Raphael Berger" [berger . chem.helsinki.fi] Hello CCL readers, doing some furst steps with solid state computations, I found the following case. I have two slightly different modifications of a organometallic molecular compound, essentially differing in the packing of the molecules. I did some DFT calculations of both modifications resulting according to expectations in very similar band gaps (1.771 and 1.778 eV). However the Fermi Energies are quite different (-3.940 and -4.995 eV). Out of lack of experience I wonder if this is unusual or not. I am happy about any comments! kind regards R.B. From owner-chemistry@ccl.net Wed May 21 04:15:00 2014 From: "Georg Lefkidis lefkidis!A!physik.uni-kl.de" To: CCL Subject: CCL: AW: increasing MAXIT in GAMESS Message-Id: <-50104-140521041152-29988-9v+5YtMolmYuGpjNeV044w|a|server.ccl.net> X-Original-From: "Georg Lefkidis" Content-Language: de Content-Type: multipart/alternative; boundary="----=_NextPart_000_001E_01CF74DC.E86B3180" Date: Wed, 21 May 2014 10:10:35 +0200 MIME-Version: 1.0 Sent to CCL by: "Georg Lefkidis" [lefkidis!A!physik.uni-kl.de] This is a multipart message in MIME format. ------=_NextPart_000_001E_01CF74DC.E86B3180 Content-Type: text/plain; charset="UTF-8" Content-Transfer-Encoding: quoted-printable Dear all, =20 thank you for your replies. I changed the upper MAXIT value in = inputa.src and recompiled. Now everything works beautifully, with a = typical (almost monotonous) energy convergence within about 400 cycles. = The reason it takes so long is because I use a large damping to avoid = oscillations caused by the many degenerate orbitals, and the results for = all geometries look reasonable. Of course, post-HF calculations will = follow. =20 Best regards George =20 =20 =20 Von: owner-chemistry+lefkidis=3D=3Dphysik.uni-kl.de#,#ccl.net = [mailto:owner-chemistry+lefkidis=3D=3Dphysik.uni-kl.de#,#ccl.net] Im = Auftrag von wai-to chan wai-to.chan*|*alumni.uoguelph.ca Gesendet: Mittwoch, 21. Mai 2014 00:37 An: Lefkidis, Georg Betreff: CCL: increasing MAXIT in GAMESS =20 You may have to change this line from comp.src (line 1578 2013 version) = MAXIT =3D 200 =20 to the umber of iteration you want as well as the line from inputa.src as suggested by the other poster.=20 Wai-To Chan=20 ------=_NextPart_000_001E_01CF74DC.E86B3180 Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable

Dear all,

 

thank you for your replies. I changed the upper MAXIT value in = inputa.src and recompiled. Now everything works beautifully, with a = typical (almost monotonous) energy convergence within about 400 cycles. = The reason it takes so long is because I use a large damping to avoid = oscillations caused by the many degenerate orbitals, and the results for = all geometries look reasonable. Of course, post-HF calculations will = follow.

 

Best regards

George

 

 

 

Von:<= /b> = owner-chemistry+lefkidis=3D=3Dphysik.uni-kl.de#,#ccl.net = [mailto:owner-chemistry+lefkidis=3D=3Dphysik.uni-kl.de#,#ccl= .net] Im Auftrag von wai-to chan = wai-to.chan*|*alumni.uoguelph.ca
Gesendet: Mittwoch, 21. Mai = 2014 00:37
An: Lefkidis, Georg
Betreff: = CCL: increasing MAXIT in GAMESS

 

 You may have to = change this line from comp.src (line 1578 2013 version) =


      MAXIT   =3D = 200 

to the umber = of iteration you want as well as the line from = inputa.src

as suggested by the other poster. =

Wai-To Chan =

------=_NextPart_000_001E_01CF74DC.E86B3180-- From owner-chemistry@ccl.net Wed May 21 08:14:00 2014 From: "fernando jardim fernandojardim12::gmail.com" To: CCL Subject: CCL:G: question SCRF gaussian example Message-Id: <-50105-140521011422-8150-tU9BbZddykll2QSR4nqwyQ|-|server.ccl.net> X-Original-From: "fernando jardim" Date: Wed, 21 May 2014 01:14:21 -0400 Sent to CCL by: "fernando jardim" [fernandojardim12^^^gmail.com] The gaussian closes and asks to debug and the message l301.exe stopped working can someone help me? I'm trying to do the example with the SCRF fluorescence G09 manual ( http://www.gaussian.com/g_tech/g_ur/k_scrf.htm ) From owner-chemistry@ccl.net Wed May 21 08:49:00 2014 From: "Philipp Marquetand philipp.marquetand%univie.ac.at" To: CCL Subject: CCL: 50th Symposium on Theoretical Chemistry - Deadline is approaching Message-Id: <-50106-140521023256-4042-iteWKhnQ3qjk9Zx+xUtycw,+,server.ccl.net> X-Original-From: "Philipp Marquetand" Date: Wed, 21 May 2014 02:32:04 -0400 Sent to CCL by: "Philipp Marquetand" [philipp.marquetand%%univie.ac.at] Dear Colleague, Please note that the registration deadline is less than 2 weeks from now (May 30) for the 50th Symposium on Theoretical Chemistry, which will take place in Vienna, Austria from September 14-18, 2014. Important dates: Registration is still open and closes on the 30th of May. Abstract deadline for oral contributions: 15th June. Abstract deadline for posters: 15th July. The registration fee (250 EUR, reduced to 200 EUR for PhD students) includes the book of abstracts, a welcome reception, lunches, coffee breaks, evening food, free drinks during the two poster sessions, and the closing conference dinner in a typical Viennese wine tavern. A number of excursions can also be booked through the registration home page. The number of participants is limited, so we cordially invite you to register as soon as possible. A contingent of affordable rooms have been reserved to facilitate housing in Vienna. September is conference high season and cheap accommodation runs out fast. It is therefore recommended to book early. If you fly with Austrian airlines, a discount of 15% is applied for STC participants. For further details, check our conference website http://stc2014.univie.ac.at For correspondence, please use the email address: stc2014(!)univie.ac.at We are looking forward to seeing you in Vienna! Greetings, Leticia Gonzalez PS. Apologies for cross-posting! -- Univ.-Prof. Dr. Leticia Gonzlez University of Vienna Institute of Theoretical Chemistry, Whringer Str. 17, A-1090 Vienna leticia.gonzalez(!)univie.ac.at www.theochem.univie.ac.at Tel: +43-1-4277-52750 Fax: +43-1-4277-9527 From owner-chemistry@ccl.net Wed May 21 12:45:00 2014 From: "wai-to chan wai-to.chan!A!alumni.uoguelph.ca" To: CCL Subject: CCL: Critical energy Message-Id: <-50107-140521124337-12386-wwlhmYQsWxauwntyging6Q-#-server.ccl.net> X-Original-From: wai-to chan Content-Type: multipart/alternative; boundary=001a11c3494034973004f9ebb29d Date: Wed, 21 May 2014 11:43:29 -0500 MIME-Version: 1.0 Sent to CCL by: wai-to chan [wai-to.chan],[alumni.uoguelph.ca] --001a11c3494034973004f9ebb29d Content-Type: text/plain; charset=UTF-8 <<<<<<<<<<<<<>>>>>>>>>>>>> Activation energy generally refers to Arrhenius activation energy. The starting point of kinetic calculations aimed to complement kinetic measurement of reaction rates and Arrhenius factor is usually the conventional transition state theory method based on the harmonic-oscillator-rigid-rotor approximation rather than RRKM theory. Use RRKM theory if you intend to estimate overall reaction rate of a complicated reaction mechanism, intermediate reactions in a combustion system for instance, or if you want to elucidate the pressure-dependence of the reaction studied. Wai-To Chan --001a11c3494034973004f9ebb29d Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable
<<<<<<<<<<<<<<I&= #39;m using on RRKM theory to calculate the critical energy (E0). In the gi= ven expression for such calculation we have Ecl (E0=3DEcl+sum...). My quest= ion is: Is this Ecl just Ea (activation energy)? or is it calculated diffre= ntly?>>>>>>>>>>>>>>

=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 Activation= energy generally refers to Arrhenius activation energy.
The starting po= int of kinetic calculations aimed to complement kinetic
=C2=A0measuremen= t of reaction rates and Arrhenius factor is
usually the conventional tra= nsition state theory method based on the
harmonic-oscillator-rigid-rotor approximation rather than RRKM
theory.= =C2=A0 Use RRKM theory if you intend to estimate overall reaction
rate o= f a complicated reaction mechanism, intermediate reactions in a
combusti= on system for instance, or if you want to elucidate the
pressure-dependence of the reaction studied.


Wai-To Chan

=
--001a11c3494034973004f9ebb29d-- From owner-chemistry@ccl.net Wed May 21 15:57:00 2014 From: "sara sarfaraz awaanee**gmail.com" To: CCL Subject: CCL: Structure minimization Message-Id: <-50108-140521145244-31358-yIgmlsPbdLkoOFI1nheGcg|a|server.ccl.net> X-Original-From: "sara sarfaraz" Date: Wed, 21 May 2014 14:52:43 -0400 Sent to CCL by: "sara sarfaraz" [awaanee{:}gmail.com] Dear team I have a question regarding minimizing a protein structure. I modelled the structure via Modeller and now I want to minimize it. The structure has also got GDP in it. I did the minimization via Chimera but I am not sure for how many steps of steepest descent and conjugate gradient am I supposed to minimize it? How would I know if the structure has converged? what is the parameter for checking the convergence? Besides Chimera, is there any other freely available tool which I can use for minimization? Looking forward to your valuable suggestions. Thanking you in advance. Regards Sara email id: awaanee(-)gmail.com From owner-chemistry@ccl.net Wed May 21 17:39:00 2014 From: "Elaine Meng meng[-]cgl.ucsf.edu" To: CCL Subject: CCL: Structure minimization Message-Id: <-50109-140521171202-5300-VhzIa+Rz8qiqeP+45kwYDQ|-|server.ccl.net> X-Original-From: "Elaine Meng" Date: Wed, 21 May 2014 17:12:00 -0400 Sent to CCL by: "Elaine Meng" [meng::cgl.ucsf.edu] Dear Sara, In my opinion this is one of those "scientific judgement" issues for which there is no single answer that fits all situations. It would depend on the specific structure and whether you see problem areas in that model structure. However, I believe that Modeller itself performs optimization, so it is not necessary to minimize the Modeller results using some other program. Sometimes minimization can make the structure worse. If you see loops or other parts that seem to be poorly modeled because they weren't in the template structure, you can run another Modeller calculation for loop re-modeling. In Chimera, there are interfaces to Modeller for both templated ("comparative" or "homology") modeling and untemplated building and remodeling. Here's the documentation for that: http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/modeller.html I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco From owner-chemistry@ccl.net Wed May 21 23:02:00 2014 From: "Sharang Phatak sharang.phatak ~~ dotmatics.com" To: CCL Subject: CCL: Dotmatics UGM Announcement Message-Id: <-50110-140521225118-23921-lDqpfB1l/++7wGaTUvfpsg ~ server.ccl.net> X-Original-From: Sharang Phatak Content-Type: multipart/alternative; boundary=089e016354d4f8015604f9f42ec9 Date: Wed, 21 May 2014 19:51:02 -0700 MIME-Version: 1.0 Sent to CCL by: Sharang Phatak [sharang.phatak%x%dotmatics.com] --089e016354d4f8015604f9f42ec9 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: quoted-printable Hi Jan, Please find our announcement for Dotmatics Days. ________________________________________ Gilead Sciences Hosts Dotmatics Day: Save your space in Boston and San Francisco! Whether you're an academic lab, start-up biotech or a large pharma, interested in learning about data management, ELN and visualization tools, please note the two event below. Attendance is FREE where you will have the opportunity to network with industry leaders and learn about the way modern informatics tools are making research more efficient. ________________________________________ Hear from companies like Vertex, Celgene, AstraZeneca, Genentech, Gilead, NIH and many more on their use of the Dotmatics Platform Data management, ELN for real-time collaboration, visualization and analysis, and more. Thursday 5th June 2014: Join us at the Museum of Science, Boston Full agenda and free registration: http://www.dotmatics.com/dotmatics-day-east-coast-2014/ Thursday 12th June 2014: The Structural Chemistry department at Gilead Sciences is delighted to host the West Coast Dotmatics Day held at the Embassy Suites, South San Francisco Full agenda and free registration: http://www.dotmatics.com/dotmatics-day-west-coast-2014/ Thank you, Sharang ---------------------------------------------------------------- Sharang Phatak, PhD Application Scientist Dotmatics Inc. 11300 Sorrento Valley Road Suite 115 San Diego, CA, 92121 Office 858.552.8906 Cell 713.447.4566 www.dotmatics.com Secure your place at our Annual Dotmatics Days=E2=80=A6 June 5, 2014 - Dotmatics Day - Boston, USA June 12, 2014 - Dotmatics Day - San Francisco, USA Website =E2=94=82Events=E2=94=82 News --=20 This electronic mail and its attachments are intended solely for the=20 person(s) to whom they are addressed and contain information which is =20 confidential or otherwise protected from disclosure, except for the purpose= =20 for which they are intended. Dissemination, distribution, or reproduction= =20 by anyone other than the intended recipients is prohibited and may be=20 illegal. If you are not an intended recipient, please immediately inform=20 the sender and return the electronic mail and its attachments and destroy= =20 any copies which may be in your possession. Dotmatics Limited screens=20 electronic mails for viruses but does not warrant that this electronic mail= =20 is free of any viruses. Dotmatics Limited accepts no liability for any=20 damage caused by any virus transmitted by this electronic mail. Dotmatics= =20 Limited is registered in England & Wales No. 5614524 with offices at The= =20 Old Monastery, Windhill, Bishops Stortford, Herts, CM23 2ND, UK. --089e016354d4f8015604f9f42ec9 Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable

Hi Jan,

Please find our announcement for Dotmatics Days.

=C2=A0

______________________= __________________

Gilead Sciences Hosts Dotmatics Day: Save your space in Boston and S= an Francisco!

Whether you're an = academic lab, start-up biotech or a large pharma, interested in learning ab= out data management, ELN and visualization tools, please note the two event= below. Attendance is FREE where you will have the opportunity to network w= ith industry leaders and learn about the way modern informatics tools are m= aking research more efficient.

______________________= __________________

=C2=A0

Hear from companies like Vertex, Celgene, AstraZeneca, Genentech, Gilead,= NIH and many more on their use of the Dotmatics Platform

Data management, ELN f= or real-time collaboration, visualization and analysis, and more.

Thursday 5th June 201= 4: Join us at the Museum of Science, Boston

Full agenda and free r= egistration: http://www.dotmatics.com/dotmatics-day-east-coast-2014/

Thursday 12th June 201= 4: The Structural Chemistry department at Gilead Sciences is delighted to h= ost the West Coast Dotmatics Day held at the Embassy Suites, South San Fran= cisco

Full agenda and free r= egistration: http://www.dotmatics.com/dotmatics-day-west-coast-2014/

=C2=A0

=C2=A0

Thank you,

Sharang

=C2=A0

----------------------------------------------------------------

Shara= ng Phatak, PhD

Application Scientist
Dotmatics Inc.

11300 Sorrento Valley Road
Suite 115
San Diego, CA, 92121
Office 858.552.8906<= /span>

Cell = 713.447.4566
www.dotmatics.com=

=C2=A0

Secure your place at our Annual = Dotmatics Days=E2=80=A6
June 5, 2014 - Dotmatics Day - Boston, USA
June 12, 2014 - Dotmatics Day= - San Francisco, USA

Website<= /a> =E2=94=82Events =E2=94= =82News

=C2=A0


This electronic mail and its attachments are intended sole= ly for the person(s) to whom they are addressed and contain information whi= ch is=C2=A0 confidential or otherwise protected from disclosure, except for= the purpose for which they are intended. Dissemination, distribution, or r= eproduction by anyone other than the intended recipients is prohibited and = may be illegal. If you are not an intended recipient, please immediately in= form the sender and return the electronic mail and its attachments and dest= roy any copies which may be in your possession. Dotmatics Limited screens e= lectronic mails for viruses but does not warrant that this electronic mail = is free of any viruses. Dotmatics Limited accepts no liability for any dama= ge caused by any virus transmitted by this electronic mail. Dotmatics Limit= ed is=C2=A0 registered in England & Wales No. 5614524 with offices at T= he Old Monastery,=C2=A0 Windhill, Bishops Stortford, Herts, CM23 2ND, UK. --089e016354d4f8015604f9f42ec9-- From owner-chemistry@ccl.net Wed May 21 23:37:00 2014 From: "Sharang Phatak sharang.phatak^dotmatics.com" To: CCL Subject: CCL: Elemental From Dotmatics is now available as a free App Message-Id: <-50111-140521225354-24117-KUl+2FlAUOCwXBlyGSh45Q__server.ccl.net> X-Original-From: Sharang Phatak Content-Type: multipart/alternative; boundary=089e01537be2e2447004f9f43839 Date: Wed, 21 May 2014 19:53:48 -0700 MIME-Version: 1.0 Sent to CCL by: Sharang Phatak [sharang.phatak{=}dotmatics.com] --089e01537be2e2447004f9f43839 Content-Type: text/plain; charset=UTF-8 Elemental from Dotmatics a FREE chemistry sketcher app. In addition to the regularly used sketcher functionalities (built in functional groups, rotate, zoom in/out, undo/redo) one can save structures as images or even email structure files. The Elemental app serves as a front-end search the CheMBL database of ~1 million compounds using the free ElementalDB app. Both apps are now available as a Universal Apps that support iPad, iPhone and iPod Touch. For more information please contact: Alyssa Castanares alyssa.castanares:dotmatics.com Office 858.314.3869 -- This electronic mail and its attachments are intended solely for the person(s) to whom they are addressed and contain information which is confidential or otherwise protected from disclosure, except for the purpose for which they are intended. Dissemination, distribution, or reproduction by anyone other than the intended recipients is prohibited and may be illegal. If you are not an intended recipient, please immediately inform the sender and return the electronic mail and its attachments and destroy any copies which may be in your possession. Dotmatics Limited screens electronic mails for viruses but does not warrant that this electronic mail is free of any viruses. Dotmatics Limited accepts no liability for any damage caused by any virus transmitted by this electronic mail. Dotmatics Limited is registered in England & Wales No. 5614524 with offices at The Old Monastery, Windhill, Bishops Stortford, Herts, CM23 2ND, UK. --089e01537be2e2447004f9f43839 Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable

Elemental from Dotmatics a FREE chemistry sketcher app. In addition to the regularly used sketcher function= alities (built in functional groups, rotate, zoom in/out, undo/redo) one ca= n save structures as images or even email structure files. The Elemental ap= p serves as a front-end search the CheMBL database of ~1 million compounds = using the free ElementalDB app. Both apps are now available as a Universal Apps that support iPad, iPhone and iPod T= ouch.

=C2=A0

For m= ore information please contact:

Alyssa Castanares

alyssa.castanares:dotmatics.com=

Office 858.314.3869



=C2=A0


This electronic mail and its attachments are intended sole= ly for the person(s) to whom they are addressed and contain information whi= ch is=C2=A0 confidential or otherwise protected from disclosure, except for= the purpose for which they are intended. Dissemination, distribution, or r= eproduction by anyone other than the intended recipients is prohibited and = may be illegal. If you are not an intended recipient, please immediately in= form the sender and return the electronic mail and its attachments and dest= roy any copies which may be in your possession. Dotmatics Limited screens e= lectronic mails for viruses but does not warrant that this electronic mail = is free of any viruses. Dotmatics Limited accepts no liability for any dama= ge caused by any virus transmitted by this electronic mail. Dotmatics Limit= ed is=C2=A0 registered in England & Wales No. 5614524 with offices at T= he Old Monastery,=C2=A0 Windhill, Bishops Stortford, Herts, CM23 2ND, UK. --089e01537be2e2447004f9f43839--