From owner-chemistry@ccl.net Tue Jun 11 07:16:01 2013 From: "Alex Allardyce aallardyce .. chemaxon.com" To: CCL Subject: CCL: ChemAxon launches version 6: All GUI's refreshed, major performance improvements and 5 new products Message-Id: <-48814-130611060445-18034-aBQdCsXLxfYbbUO7dtoXLQ*o*server.ccl.net> X-Original-From: Alex Allardyce Content-Type: multipart/alternative; boundary="----=_Part_21642_380430191.1370945069440" Date: Tue, 11 Jun 2013 12:04:29 +0200 (CEST) MIME-Version: 1.0 Sent to CCL by: Alex Allardyce [aallardyce*chemaxon.com] ------=_Part_21642_380430191.1370945069440 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: quoted-printable Excuse delay announcing this.=20 ChemAxon announces version 6: All GUI's refreshed and improved user experie= nce, new features, major performance improvements and 5 new products:=20 1. Marvin for JavaScript - at last a light, friendly editor/viewer with Che= mAxon's renown chemistry and web/enterprise deploy-ability=20 2. Metabolizer: Using our Reactor technology to predict all major and minor= metabolites=20 3. Instant JChem Web client layer - build forms in IJC to publish/share as = web pages=20 4. Web Services: Simpler to work with REST based Services join our existing= SOA Web Services=20 5. Plexus Project announced: chemicalise influenced, a simple handling and = discovery interface for medicinal and computational chemists=20 Full list of improvements for 6.0 available here: http://www.chemaxon.com/r= eleases/.=20 The version 6 features were discussed at our EUGM a week back and presentat= ions are already available in the archive covering all the developments and= new products in more depth, see links below=20 As usual all products are available for free download and evaluation and ar= e provided freely for academic research and teaching (Academic Package) and= for adding chemistry to non commercial web sites (FreeWeb).=20 Interested in your feedback.=20 Cheers / Alex=20 ChemAxon V6 product presentations from EUGM (May, 2013)=20 * Marvin: extending the scope of usability - www.chemaxon.com/library/2= 013-eugm/marvin-extending-the-scope-of-usability/=20 * Instant JChem - web vs desktop client - www.chemaxon.com/library/2013= -eugm/instant-jchem-web-vs-desktop-client/=20 * JChem for Excel: A better fit for my needs - www.chemaxon.com/library= /2013-eugm/jchem-for-excel-a-better-fit-for-my-needs/=20 * 3D visualization for medicinal chemists - www.chemaxon.com/library/20= 13-eugm/3d-visualization-for-medicinal-chemists/=20 * ChemAxon Plexus: A desktop application using web technology - www.che= maxon.com/library/2013-eugm/chemaxon-plexus-a-desktop-application-using-web= -technology/=20 * CRAIS Board - The virtual white board for scientific discussions - ww= w.chemaxon.com/library/2013-eugm/crais-board-a-virtual-white-board-for-chem= ical-discussions/=20 * ChemAxon=E2=80=99s Compound Registration - www.chemaxon.com/library/2= 013-eugm/chemaxons-compound-registration/=20 * Integrating Standardizer and Structure Checker into corporate environ= ment - www.chemaxon.com/library/2013-eugm/integrating-standardizer-and-stru= cture-checker-into-corporate-environment/=20 * JChem development: Why JChem breaks the sausage principle - www.chema= xon.com/library/2013-eugm/whats-new-in-jchem-base-and-cartridge/=20 * JChem Web Services: Reloaded - www.chemaxon.com/library/2013-eugm/jch= em-web-services-reloaded/=20 * Collaborate and search in SharePoint with ChemAxon - www.chemaxon.com= /library/2013-eugm/collaborate-and-search-in-sharepoint-with-chemaxon/=20 * Reaction Library Design - www.chemaxon.com/library/2013-eugm/reaction= -library-design/=20 * Discovery toolkit: Recent Successful Discovery Strategies: a Cheminfo= rmatist=E2=80=99s Perspective - www.chemaxon.com/library/2013-eugm/recent-s= uccessful-discovery-strategies-a-cheminformatists-perspective/=20 * Metabolizer: Prediction of Xenobiotic Metabolism - www.chemaxon.com/l= ibrary/2013-eugm/prediction-of-xenobiotic-metabolism/=20 * Name<>Structure, Document>Structure: What=E2=80=99s New with Naming -= www.chemaxon.com/library/2013-eugm/whats-new-with-naming/=20 * The Next Generation of Maximum Common Substructure Search at ChemAxon= - www.chemaxon.com/library/2013-eugm/the-next-generation-of-maximum-common= -substructure-search-at-chemaxon/=20 * Conformation search via cool dynamics - www.chemaxon.com/library/2013= -eugm/conformation-search-via-cool-dynamics/=20 See all presentations (ChemAxon and all clients), video up soon: http://www= .chemaxon.com/ugm-archive/2013-eu/=20 Alex Allardyce=20 Marketing Dir.=20 ChemAxon Ltd=20 Z=C3=A1hony u. 7. Building HX, Budapest, 1031 Hungary=20 http://www.chemaxon.com=20 Tel: + 361 453 0435=20 Fax: + 361 4532659=20 mailto:aa%chemaxon.com=20 ------=_Part_21642_380430191.1370945069440 Content-Type: text/html; charset=utf-8 Content-Transfer-Encoding: quoted-printable

Excuse delay announcing this.

ChemAx= on announces version 6: All GUI's ref= reshed and improved user experience, new features, major performance improv= ements and 5 new products:

1. Marvin for JavaScript - at last = a light, friendly editor/viewer with ChemAxon's renown chemistry and web/en= terprise deploy-ability
2. Metabolizer: Using our Reactor technology to= predict all major and minor metabolites
3. Instant JChem Web client lay= er - build forms in IJC to publish/share as web pages
4. Web Services: S= impler to work with REST based Services join our existing SOA Web Services =
5. Plexus Project announced: chemicalise influenced, a simple handling = and discovery interface for medicinal and computational chemists

Full= list of improvements for 6.0 available here: http://www.chemaxon.com/relea= ses/.

The version 6 features were discussed at our EUGM a week back a= nd presentations are already available in the archive covering all the deve= lopments and new products in more depth, see links below

As usual all= products are available for free download and evaluation and are provided f= reely for academic research and teaching (Academic Package) and for ad= ding chemistry to non commercial web sites (FreeWeb).

Interested in y= our feedback.

Cheers / Alex

ChemAxon V6 product p= resentations from EUGM (May, 2013)

  • Marvin: extending the scope of usability - www= .chemaxon.com/library/2013-eugm/marvin-extending-the-scope-of-usability/
  • Instant JChem - web vs deskto= p client - www.chemaxon.com/library/2013-eugm/instant-jchem-web-vs-desktop-= client/
  • JChem for Excel: A = better fit for my needs - www.chemaxon.com/library/2013-eugm/jchem-for-exce= l-a-better-fit-for-my-needs/
  • ChemAxon Plexus: A desktop application using web technolo= gy - www.chemaxon.com/library/2013-eugm/chemaxon-plexus-a-desktop-applicati= on-using-web-technology/
  • CR= AIS Board - The virtual white board for scientific discussions - www.chemax= on.com/library/2013-eugm/crais-board-a-virtual-white-board-for-chemical-dis= cussions/
  • ChemAxon=E2=80=99= s Compound Registration - www.chemaxon.com/library/2013-eugm/chemaxons-comp= ound-registration/
  • Integrat= ing Standardizer and Structure Checker into corporate environment - www.che= maxon.com/library/2013-eugm/integrating-standardizer-and-structure-checker-= into-corporate-environment/
  • JChem development: Why JChem breaks the sausage principle - www.chemaxon.c= om/library/2013-eugm/whats-new-in-jchem-base-and-cartridge/
  • = JChem Web Services: Reloaded - www.chemaxo= n.com/library/2013-eugm/jchem-web-services-reloaded/
  • Collaborate and search in SharePoint with ChemAxo= n - www.chemaxon.com/library/2013-eugm/collaborate-and-search-in-sharepoint= -with-chemaxon/
  • Reaction Li= brary Design - www.chemaxon.com/library/2013-eugm/reaction-library-design/<= /span>
  • Discovery toolkit: Recent S= uccessful Discovery Strategies: a Cheminformatist=E2=80=99s Perspective - w= ww.chemaxon.com/library/2013-eugm/recent-successful-discovery-strategies-a-= cheminformatists-perspective/
  • Metabolizer: Prediction of Xenobiotic Metabolism - www.chemaxon.com/libr= ary/2013-eugm/prediction-of-xenobiotic-metabolism/
  • Name<>Structure, Document>Structure: What= =E2=80=99s New with Naming - www.chemaxon.com/library/2013-eugm/whats-new-w= ith-naming/
  • The Next Genera= tion of Maximum Common Substructure Search at ChemAxon - www.chemaxon.com/l= ibrary/2013-eugm/the-next-generation-of-maximum-common-substructure-search-= at-chemaxon/
  • Conformation s= earch via cool dynamics - www.chemaxon.com/library/2013-e= ugm/conformation-search-via-cool-dynamics/
See all presentations (ChemAxon and all clients),= video up soon: http://www.chemaxon.com/ugm-archive/2013-eu/

Alex Allardy= ce
Marketing = Dir.
ChemAxon LtdZ=C3=A1hony u. 7. Bui= lding HX, Budapest, 1031 Hungary
http://www.chemaxon.com
Tel: +361 453 0435
Fax: +361 4532659
mailto:aa%chemaxon.com<= /span>
------=_Part_21642_380430191.1370945069440-- From owner-chemistry@ccl.net Tue Jun 11 09:26:00 2013 From: "Roar A. Olsen Roar.A.Olsen_-_sintef.no" To: CCL Subject: CCL:G: NEB calculations with Gaussian using the ASE interface? Message-Id: <-48815-130611082406-24645-XpARDww3LCHSxvCrIscM0g-.-server.ccl.net> X-Original-From: "Roar A. Olsen" Date: Tue, 11 Jun 2013 08:24:05 -0400 Sent to CCL by: "Roar A. Olsen" [Roar.A.Olsen%x%sintef.no] Hello, I am wondering whether any CCLers have experience with running Nudged Elastic Band (NEB) calculations with the Gaussian electronic structure code using the Atomic Simulation Environment (ASE)? I would be very interested in "inheriting" a python script setting up such a calculation, but also to hear about experiences related to convergeing the NEB to a reaction path for a molecular reaction. Any special "tweaking" of Gaussian input parameters needed for successful NEB runs in ASE? Thanks for any help in this matter! Best regards, Roar A. Olsen (Roar.A.Olsen:at:sintef.no) From owner-chemistry@ccl.net Tue Jun 11 10:01:00 2013 From: "Eva Schlosser ecoitn[*]gmail.com" To: CCL Subject: CCL: Announcement of Conference in Environmental ChemOinformatics Message-Id: <-48816-130611091555-31195-GaODOT5iCc3+Do2+mpOF1Q!=!server.ccl.net> X-Original-From: "Eva Schlosser" Date: Tue, 11 Jun 2013 09:15:54 -0400 Sent to CCL by: "Eva Schlosser" [ecoitn++gmail.com] Conference in Environmental ChemOinformatics 2013 > From 15 to 18 September, 2013, the Final Conference of the Marie Curie ITN programme "Environmental ChemOinformatics" (ECO) will take place in Prien at Lake Chiemsee, Bavaria, Germany. All scientists and stakeholders interested in the newest developments in chemoinformatics - QSAR, REACH requirements and drug development included - will have the chance to join the conference program and to present own scientific results in posters and presentations. Besides exciting and inspiring plenary lectures by international accepted experts, the conference committee will award a price for the best poster as well as for the best presentation. All presentations will be published in a peer reviewed journal. Please find more information for registration and booking of accommodation on the conference webpage http://www.eco-itn.eu/node/136. From owner-chemistry@ccl.net Tue Jun 11 14:43:00 2013 From: "Zakieh Yousefi zakiehyousefi-,-yahoo.com" To: CCL Subject: CCL:G: Syntax error in Gaussian input file Message-Id: <-48817-130611144208-12049-K6Ck+Ip8C1w1w5xpszcjuw*|*server.ccl.net> X-Original-From: Zakieh Yousefi Content-Type: multipart/alternative; boundary="564823669-2024983879-1370976120=:67194" Date: Tue, 11 Jun 2013 19:42:00 +0100 (BST) MIME-Version: 1.0 Sent to CCL by: Zakieh Yousefi [zakiehyousefi.:.yahoo.com] --564823669-2024983879-1370976120=:67194 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable I think the name of chk is not common. sometimes, it causes a problem when = its name is difficault or complex. You can use a short and simple name. may= be it helps you=0Abest=0AYousefi=0A=0A=0A=0A=0A____________________________= ____=0A From: Herbert Fruchtl herbert.fruchtl:st-andrews.ac.uk =0ATo: "Yousefi, Zakieh " = =0ASent: Monday, 10 June 2013, 15:17:31=0ASubject: CCL:G: Syntax error in G= aussian input file=0A =0A=0A=0A=0ASent to CCL by: Herbert Fruchtl [herbert.= fruchtl,+,st-andrews.ac.uk]=0A=0AThere's a typo in the basis set. It should= be 6-31+g(d), not=0A=0A6-31g+(d).=0A=0A=0AHTH,=0A=0A=0A=A0 Herbert=0A=0A= =0AOn 10/06/13 19:29, Silas Silva silas.silva]~[ufabc.edu.br wrote:=0A=0A>= =0A=0A> Sent to CCL by: Silas Silva [silas.silva#%#ufabc.edu.br]=0A=0A> Hel= lo all!=0A=0A>=0A=0A> I'm administrator of a supercomputing system.=A0 Much= of our users run=0A=0A> chemistry software.=0A=0A>=0A=0A> Recently, a user= came up with a syntax error in her input file.=A0 This=0A=0A> syntax error= happens both in Gaussian 03 and Gaussian 09.=0A=0A> Unfortunatelly, I coul= dn't help her, but I decided to come to this=0A=0A> forum and ask experts.= =A0 Below, I transcribe the error message and the=0A=0A> whole input file.= =0A=0A>=0A=0A> Can you please help me?=0A=0A>=0A=0A> Thanks!=0A=0A>=0A=0A> = ---=0A=0A>=0A=0A> The error:=0A=0A>=0A=0A>=A0 QPErr --- A syntax error was= detected in the input line.=0A=0A>=0A=0A>=A0 inglets,nstates=3D55) olyp/6= -31g+(d)=0A=0A>=0A=0A> ---=0A=0A>=0A=0A> Part of the file:=0A=0A>=0A=0A> %c= hk=3DF_n2acc_1_td_va_BL=0A=0A> %mem=3D46GB=0A=0A> %nprocshared=3D8=0A=0A> #= p td=3D(singlets,nstates=3D55) olyp/6-31g+(d)=0A=0A>=0A=0A> F_n2acc_1_td_va= _BL=0A=0A>=0A=0A> -1 1=0A=0A>=A0 C=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 -3.2382= 2700=A0 =A0 6.57445500=A0 =A0 0.17417400=0A=0A>=A0 C=A0 =A0 =A0 =A0 =A0 = =A0 =A0 =A0 -1.83011200=A0 =A0 6.66437000=A0 =A0 0.03801300=0A=0A>=0A=0A>= =A0 ...=0A=0A>=0A=0A=0A-- =0A=0AHerbert Fruchtl=0A=0ASenior Scientific Com= puting Officer=0A=0ASchool of Chemistry, School of Mathematics and Statisti= cs=0A=0AUniversity of St Andrews=0A=0A--=0A=0AThe University of St Andrews = is a charity registered in Scotland:=0A=0ANo SC013532=0A=0A=0A=0A=0A-=3D Th= is is automatically added to each message by the mailing script =3D-=0A=0AT= o recover the email address of the author of the message, please change=0A= =0A=0A=0A==0A=0A=0AE-mail to sub= scribers: CHEMISTRY]_[ccl.net or use:=0A=0A=A0 =A0 =A0 http://www.ccl.net/cgi= -bin/ccl/send_ccl_message=0A=0A=0AE-mail to administrators: CHEMISTRY-REQUE= ST]_[ccl.net or use=0A=0A=A0 =A0 =A0 http://www.ccl.net/cgi-bin/ccl/send_ccl_= message=0A=0A=0A=0A=0A=A0 =A0 =A0 http://www.ccl.net= /chemistry/sub_unsub.shtml=0A=0A=0ABefore posting, check wait time at: http= ://www.ccl.net=0A=0A=0A=0A=0AConferences: http= ://server.ccl.net/chemistry/announcements/conferences/=0A=0A=0ASearch Messa= ges: http://www.ccl.net/chemistry/searchccl/index.shtml=0A=0A=0AIf your mai= l bounces from CCL with 5.7.1 error, check:=0A=0A=A0 =A0 =A0 http://www.ccl= .net/spammers.txt=0A=0A=0ARTFI: http://www.ccl.net/chemistry/aboutccl/instr= uctions/ --564823669-2024983879-1370976120=:67194 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable
I think the name of c= hk is not common. sometimes, it causes a problem when its name is difficaul= t or complex. You can use a short and simple name. maybe it helps you
be= st
Yousefi


<= div style=3D"font-family: times new roman, new york, times, serif; font-siz= e: 12pt;">
From: Herbert Fruchtl h= erbert.fruchtl:st-andrews.ac.uk <owner-chemistry]_[ccl.net>
To: "Yousefi, Zakieh " &l= t;zakiehyousefi]_[yahoo.com>
Se= nt: Monday, 10 June 2013, 15:17:31
Subject: CCL:G: Syntax error in Gaussian input file
=


Sent to CCL by: Herbert Fruchtl [herbert.fruchtl,+,st-an= drews.ac.uk]
There's a typo in the basis set. It = should be 6-31+g(d), not
6-31g+(d).

HTH,

=
  Herbert

=
On 10/06/13 19:29, Silas Silva silas.silva]~[ufabc.edu.br = wrote:
>
> Sent t= o CCL by: Silas Silva [silas.silva#%#ufabc.edu.br]
> Hello all!
>
= > I'm administrator of a supercomputing system.  Much of our users = run
> chemistry software.
>
> Recently, a user came up with a syntax error in her input= file.  This
> syntax error happens both = in Gaussian 03 and Gaussian 09.
> Unfortunatel= ly, I couldn't help her, but I decided to come to this
> forum and ask experts.  Below, I transcribe the error messa= ge and the
> whole input file.
>
> Can you please help me?
<= /div>
>
> Thanks!
=
>
> ---
>
> The error:
>
>  QPErr --- A syntax erro= r was detected in the input line.
>
<= div dir=3D"ltr">>  inglets,nstates=3D55) olyp/6-31g+(d)
<= div dir=3D"ltr">>
> ---
>
> Part of the file:
>
> %chk=3DF_n2acc_1_td_va_BL
> %mem= =3D46GB
> %nprocshared=3D8
> #p td=3D(singlets,nstates=3D55) olyp/6-31g+(d)
>
> F_n2acc_1_td_va_BL
>
> -1 1
>  C              &nb= sp; -3.23822700    6.57445500    0.17417400
<= div dir=3D"ltr">>  C            &nbs= p;   -1.83011200    6.66437000    0.03801300
<= /div>
>
>  ...
>

--
Herbert Fruchtl
Senior Scientific Computing Officer
<= /div>
School of Chemistry, School of Mathematics and Statis= tics
University of St Andrews
--
The University of St Andrews is a cha= rity registered in Scotland:
No SC013532


-=3D This is automatically added to each message by= the mailing script =3D-
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--564823669-2024983879-1370976120=:67194--