From owner-chemistry@ccl.net Fri Sep 18 02:26:01 2009 From: "Shikha Varma-O Brien shikha:+:accelrys.com" To: CCL Subject: CCL: Accelrys announces the release of FREE DSVisualizer 2.5 Message-Id: <-40275-090918022447-384-mNYTzy0WLT3Vuacf3R6q4w!=!server.ccl.net> X-Original-From: "Shikha Varma-O Brien" Date: Fri, 18 Sep 2009 02:24:43 -0400 Sent to CCL by: "Shikha Varma-O Brien" [shikha+/-accelrys.com] Accelrys is pleased to announce the latest release of Discovery Studio Visualizer 2.5! This commercial-grade 3D visualization tool is absolutely FREE to everyone! DS Visualizer is not only a powerful tool for 3D visualization but also makes a great tool for sharing and communicating modeling data. Capabilities include: Advanced molecular visualization Manual pharmacophore generation Secondary Structure prediction Flexible display and graphical output Ability to build, import, and analyze structures Publication quality molecular images Customizable interface Etc. For a complete list of functionalities, please visit: http://accelrys.com/products/datasheets/ds-visualizer-0809.pdf Additionally, you also get the FREE DS ActiveX control, which allows you to easily embed live 3D structures in Microsoft PowerPoint, Word, and html documents enabling you to create and present powerful presentations and animations! To download your copy of the DSVisualizer and the ActiveX control, please visit: http://accelrys.com/products/discovery-studio/visualization/discovery-studio-visualizer-registration-25.php Already using a free visualizer? Read my blog and vote for your favorite 3D visualizer: http://blog.accelrys.com/ ************** Sincerely, Shikha Varma-O'Brien, Ph.D. Director, LS Modeling & Simulations Accelrys, Inc. 2009 Accelrys European User Group Meeting Barcelona Spain, 12-16 October http://accelrys.com/events/ugms/eugm-2009/ Learn new applications & techniques > from colleagues, experts and partners Blog: http://blog.accelrys.com Forum: http://accelrys.org Website: http://accelrys.com Support: http://accelrys.com/services/support.html From owner-chemistry@ccl.net Fri Sep 18 07:32:01 2009 From: "Eduardo Lemos de Sa edulsa],[quimica.ufpr.br" To: CCL Subject: CCL: Query regarding MOPAC THERMO calculations Message-Id: <-40276-090917155323-12497-A1V0LDS90VlU5goCAQdmbg]*[server.ccl.net> X-Original-From: "Eduardo Lemos de Sa" Content-Transfer-Encoding: 8bit Content-Type: text/plain;charset=iso-8859-1 Date: Thu, 17 Sep 2009 14:13:35 -0300 (BRT) MIME-Version: 1.0 Sent to CCL by: "Eduardo Lemos de Sa" [edulsa##quimica.ufpr.br] Hi Nilesh I suggest you first optimize the molecular geometry (grads gnorm=x.xx precise) and after this trying to get thermodynamics analysis. Yours Eduardo > > Sent to CCL by: "Nilesh Tawari" [tawari.nilesh()gmail.com] > Hi, > I am using "Thermo" keyword in MOPAC2009 for thermodynamic calculations, > but I getting an error > > GRADIENT NORM = 251.47110 > ** GRADIENT IS TOO LARGE TO ALLOW FORCE MATRIX TO BE CALCULATED, > (LIMIT=10) ** > EITHER ADD 'LET' OR REDUCE GRADIENT > USING 'TS' OR OTHER GEOMETRY OPTIMIZER > > So i used "LET" keyword, the job was completed but output shows following > warning.... > > > GRADIENT NORM = 250.61397 > > ** GRADIENT IS VERY LARGE, BUT SINCE "LET" IS USED, CALCULATION WILL > CONTINUE > > **** WARNING **** > > GRADIENT IS VERY LARGE FOR A THERMO CALCULATION > RESULTS ARE LIKELY TO BE INACCURATE IF THERE ARE > ANY LOW-LYING VIBRATIONS (LESS THAN ABOUT 400CM-1) > GRADIENT NORM SHOULD BE LESS THAN ABOUT 0.2 FOR THERMO > TO GIVE ACCURATE RESULTS > > And the calculated heat of formation is too high H.O.F. KCAL/MOL = > 241.996 > > Any comments suggestions on this?? > > Regards > -nilesh> > -- Eduardo Lemos de Sa edulsa[-]quimica.ufpr.br Professor Assoc. II - Departamento de Quimica Universidade Federal do Parana C. P. 19081 81531-990 Curitiba/PR - Brazil Fone (41) 3361 3300 From owner-chemistry@ccl.net Fri Sep 18 08:16:01 2009 From: "Dr P Ramasami ramchemi . intnet.mu" To: CCL Subject: CCL: Call for paper-5th CCA (Part of ICCS 2010) Message-Id: <-40277-090918074112-11499-wqbBvo1KvyyKDN6vxFYqyQ]~[server.ccl.net> X-Original-From: "Dr P Ramasami" Content-Type: multipart/alternative; boundary="----=_NextPart_000_00E2_01CA386E.6C3B63F0" Date: Fri, 18 Sep 2009 14:43:44 +0400 MIME-Version: 1.0 Sent to CCL by: "Dr P Ramasami" [ramchemi_+_intnet.mu] This is a multi-part message in MIME format. ------=_NextPart_000_00E2_01CA386E.6C3B63F0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable The 5th Workshop on Computational Chemistry and Its Applications (5th = CCA) will be held as part =20 The International Conference on Computational Science=20 31 May - 2 June, 2010,=20 Armsterdam,=20 The Netherlands=20 Conference website: http://www.iccs-meeting.org/=20 Workshop website: http://www.uom.ac.mu/Faculties/FOS/Chemistry/cca/ -------------------------------------------------------------------------= ------- Topics will include aspects of computational chemistry such as (but are = not limited to): (i) Methods: Semiempirical, force fields, ab initio, density functional = (ii) Applications: Kinetics, reaction mechanisms, catalysis, molecular = properties, conformational analysis, thermodynamics (iii) Research involving computational chemistry (iv) Computational chemistry in chemistry education (v) Interdisciplinary computational research involving chemistry is = specially invited =20 -------------------------------------------------------------------------= ------- The keynote address for this workshop will be delivered by, Prof. F. M. = Bickelhaupt, Department of Theoretical Chemistry, Amsterdam Center for = Multiscale Modeling, Scheikundig Laboratorium der Vrije.=20 http://www.few.vu.nl/~bickel The title of his talk will be "Stacked DNA-base Quartets: Structure, = Chemistry and Computational Intricacies". -------------------------------------------------------------------------= ------- Authors are invited to submit their papers, written in English, of up to = 10 pages, presenting the results of original research or innovative = practical applications relevant to the workshop topics.=20 Papers should be prepared according to the rules of Procedia Computer = Science.=20 Formatting information see for text/latex and for MSword.=20 Papers should be submitted in pdf or word file format.=20 Paper submissions should be done electronically, using submission system = on page:=20 http://www.iccs-meeting.org/iccs2010/papers/upload.php=20 At least one author of an accepted paper must register and present the = paper at the workshop.=20 -------------------------------------------------------------------------= ------- Full paper submission: 1st January , 2010=20 http://www.iccs-meeting.org/iccs2010/papers/upload.php=20 Notification of acceptance: 15th February, 2010=20 Camera-ready papers: 1st March, 2010=20 -------------------------------------------------------------------------= ------- ORGANISERS OF WORKSHOP Ponnadurai Ramasami and Henry Fritz Schaefer III Email: 5cca||uom.ac.mu=20 ------=_NextPart_000_00E2_01CA386E.6C3B63F0 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable
 
The 5th Workshop on = Computational=20 Chemistry and Its Applications (5th CCA) will be held as=20 part 
31 May =96 2=20 June, 2010,
Armsterdam,=20
The=20 Netherlands
Conference=20 website: http://www.iccs-meeting.org/ =
Workshop=20 website: http://www.uom.ac.mu/Faculties/FOS/Chemistry/cca/
Topics will include aspects of computational chemistry such as (but = are not=20 limited to):
(i) Methods:  Semiempirical, force fields, = ab=20 initio, density functional
(ii) Applications: Kinetics, = reaction=20 mechanisms, catalysis, molecular properties, conformational analysis,=20 thermodynamics
(iii) Research involving computational = chemistry
(iv)=20 Computational chemistry in chemistry education
(v) Interdisciplinary=20 computational research involving chemistry is specially invited  =20
The keynote address for this workshop will be delivered by, Prof. = F. M.=20 Bickelhaupt, Department of Theoretical Chemistry, Amsterdam Center for=20 Multiscale Modeling, Scheikundig Laboratorium der Vrije.
http://www.few.vu.nl/~bickel
The title of his talk will be =93Stacked DNA-base Quartets: = Structure, Chemistry and Computational Intricacies=94.
Authors are invited to submit their = papers, written in English, of up to 10 pages, presenting the results of original research = or=20 innovative practical applications relevant to the workshop=20 topics.

Papers should be=20 prepared according to the rules of Procedia Computer=20 Science.=20

Formatting information see for = text/latex and for MSword. =

Papers should be submitted in = pdf or word file format. =

Paper submissions should be done electronically,=20 using=20 submission system on page:

http://www.iccs-meeting.org/iccs2010/papers/upload.php= =20

At least one author of an accepted paper must = register and=20 present the paper at the workshop. =

Full=20 paper submission:         =20 1st January , 2010

http://www.iccs-meeting.org/iccs2010/papers/upload.php=

Notification of acceptance:    15th = February,=20 2010

Camera-ready papers:          =20 1st March, 2010

ORGANISERS OF WORKSHOP

Ponnadurai Ramasami and Henry Fritz Schaefer = III

Email: = 5cca||uom.ac.mu=20

------=_NextPart_000_00E2_01CA386E.6C3B63F0-- From owner-chemistry@ccl.net Fri Sep 18 08:51:00 2009 From: "Yukiko Okada alchjhy,,hotmail.com" To: CCL Subject: CCL: To determine atom type from electron density map Message-Id: <-40278-090918032938-31722-RfXnB0r2drVyhZfpbeaQWA%server.ccl.net> X-Original-From: "Yukiko Okada" Date: Fri, 18 Sep 2009 03:29:34 -0400 Sent to CCL by: "Yukiko Okada" [alchjhy_+_hotmail.com] What i doubt is when we determine atom type from electron density map, could we distinguish magneium ion(+2) and oxygen ion from water? What is the diffrent point between Mg2+ electron density map and Oxygen electron density map from water? name : Yukiko Okada email : alchjhy{=}hotmail.com From owner-chemistry@ccl.net Fri Sep 18 09:25:01 2009 From: "Santhanamoorthi N santhanamoorthi[a]rediffmail.com" To: CCL Subject: CCL:G: Constrained Optimization Regarding Message-Id: <-40279-090918052559-28251-tLh/TGyJpkjaKi5S+6Attw[A]server.ccl.net> X-Original-From: "Santhanamoorthi N" Date: Fri, 18 Sep 2009 05:25:51 -0400 Sent to CCL by: "Santhanamoorthi N" [santhanamoorthi~~rediffmail.com] I want to perform constrained optimization. I want to fix two unbonded atoms in particular distance. Is it possible this in Gaussian? Thanks in advance. From owner-chemistry@ccl.net Fri Sep 18 14:19:00 2009 From: "Egon Willighagen egon.willighagen(~)gmail.com" To: CCL Subject: CCL: Free and open source retrosynthesis software project Message-Id: <-40280-090918084920-10466-jkhM/P79VAYS13fnbA61fA**server.ccl.net> X-Original-From: Egon Willighagen Content-Type: text/plain; charset=ISO-8859-1 Date: Fri, 18 Sep 2009 14:17:31 +0200 MIME-Version: 1.0 Sent to CCL by: Egon Willighagen [egon.willighagen{=}gmail.com] Hi Bryan, On Fri, Sep 11, 2009 at 5:28 PM, Bryan Bishop kanzure],[gmail.com wrote: > Right now the main hold up in > development is getting access to a chemical reaction database in some > common, standard format. Typing in this information by hand for the > hundreds of thousands of reaction mechanisms is inappropriate. This is likely the only reason why there did not already exist an OpenSource tool for retrosynthesis. I am afraid that manually entering this data is your best option at this moment. This is indeed a lot of work, and OpenData will be crucial here to get critical mass... Maybe we can take this to the BlueObelisk mailing list and discuss more technical details there? For example, what format to use... I'd suggest CMLReact, but perhaps RDF is the way to go... Egon -- Post-doc !=! Uppsala University Blog: http://chem-bla-ics.blogspot.com/ PubList: http://www.citeulike.org/user/egonw/tag/papers From owner-chemistry@ccl.net Fri Sep 18 15:27:01 2009 From: "Victor M. Rosas-Garcia rosas.victor:+:gmail.com" To: CCL Subject: CCL: Computational Materials Chemistry Message-Id: <-40281-090918093339-8668-IGv/jyO1Umf6iAyun5RAnQ]~[server.ccl.net> X-Original-From: "Victor M. Rosas-Garcia" Date: Fri, 18 Sep 2009 09:33:35 -0400 Sent to CCL by: "Victor M. Rosas-Garcia" [rosas.victor * gmail.com] Hello everybody, I hope this is not a dumb question. Is there such a thing as Computational Materials Chemistry? I am aware of the proposed definition by IUPAC "Materials chemistry comprises the application of chemistry to the design, synthesis, characterization, processing, understanding and utilisation of materials, particularly those with useful, or potentially useful, physical properties." Pure Appl. Chem., 2009, Vol. 81, No. 9, pp. 1707-1717 doi:10.1351/PAC-REP-09-03-02 So I guess the part of "understanding" could be construed to include research by computational means. I am trying to convince some people that Materials Chemistry is not only about getting some solid and measuring its properties, but so far I have not been successful. Any ideas or arguments you would like to share? Have a nice day! Victor From owner-chemistry@ccl.net Fri Sep 18 16:02:00 2009 From: "John Travers jtravers70###yahoo.com" To: CCL Subject: CCL:G: parallel Gaussian on ibm under aix Message-Id: <-40282-090917231936-30914-CHX/7O48sygNDgN7PGo5Bg%server.ccl.net> X-Original-From: "John Travers" Date: Thu, 17 Sep 2009 23:19:32 -0400 Sent to CCL by: "John Travers" [jtravers70%%yahoo.com] Hello, i was trying to run gaussian 03 on an ibm power 5 under aix (8 processe/core), but I can not set the number of processors more than 1. The program will stop and give the error message like Inconsistency in NProc: NTCur= 8 but real number of threads=1 N= 10 NumPrc= 8 MaxCur= 8 NP= 8. if I set %NprocShared=8 in the input file. Any insight? John