From owner-chemistry@ccl.net Wed Aug 19 07:23:00 2009 From: "aa aa _ chemaxon.hu" To: CCL Subject: CCL: New speakers added: ChemAxon's 2009 US User Group Meeting: September 15-16, San Diego, CA Message-Id: <-40025-090819071950-1876-ALyIErVk+R1PnUcRnOFAgw^^^server.ccl.net> X-Original-From: aa Content-Type: multipart/alternative; boundary="------------010108060004030503050604" Date: Wed, 19 Aug 2009 13:19:36 +0200 MIME-Version: 1.0 Sent to CCL by: aa [aa*chemaxon.hu] This is a multi-part message in MIME format. --------------010108060004030503050604 Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit Excuse cross postings. We have added 2 new presentations to the Program for ChemAxon US UGM next month: * Yvonne Martin of Martin Consulting: "Tautomers: A Rant" * Patrick Walters of Vertex Pharmaceuticals: "ASAP - Emphasizing Multidimensional Drug Discovery" We also update on GlaxoSmithKline's presentation which will be "SOA at GSK - Working in a Mixed Technology Environment" To see the complete meeting program please visit this link . To see the developer and end user training day program (preceding the meeting) see this link . Meeting details and signup are below. I hope you can join us. Alex *Event details* US UGM: September 15-16. Developer and end user training: September 14. Location: Catamaran Resort Hotel & Spa, San Diego, CA * UGM page, links to registration: http://www.chemaxon.com/UGM/09/US/index.html * Archives of previous meetings, includes original presentations and meeting reports from Yvonne Martin and Wendy Warr: http://www.chemaxon.com/UGM/ugm_land.html *Confirmed guest speakers:* Isabella Haight - Abbott Laboratories Kirsten Blumeyer - Celgene Hongzhou Zhang - Eli Lilly and Co. Yingyao Zhou - Genomics Institute of the Novartis Research Foundation TBA - GlaxoSmithKline John McNeil - John McNeil & Co Tianhong Zhang - Pfizer Craig Martin - SkunkWerks Software Yvonne Martin - Martin Consulting Nicholas Goncharoff - SureChem Tobias Kind - UC Davis Genome Center - Metabolomics Craig Knox - University of Alberta Oleg Ursu - University of New Mexico Patrick Walters - Vertex Pharmaceuticals ChemAxon Partners participants (tbc) - see partner listing : *Alex Allardyce* Marketing Dir. *ChemAxon* *Ltd*. Maramaros koz 3/A, Budapest, 1037, Hungary Tel: +361 453 0435 skype: alex_allardyce --------------010108060004030503050604 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Excuse cross postings.

We have added 2 new presentations to the Program for ChemAxon US UGM next month:
  • Yvonne Martin of Martin Consulting: "Tautomers: A Rant"
  • Patrick Walters of Vertex Pharmaceuticals: "ASAP - Emphasizing Multidimensional Drug Discovery"
We also update on GlaxoSmithKline's presentation which will be "SOA at GSK - Working in a Mixed Technology Environment"

To see the complete meeting program please visit this link. To see the developer and end user training day program (preceding the meeting) see this link.

Meeting details and signup are below.

I hope you can join us.
Alex

Event details
US UGM: September 15-16. Developer and end user training: September 14. Location: Catamaran Resort Hotel & Spa, San Diego, CA
Confirmed guest speakers:
Isabella Haight  -  Abbott Laboratories
Kirsten Blumeyer  -  Celgene
Hongzhou Zhang  -  Eli Lilly and Co.
Yingyao Zhou  -  Genomics Institute of the Novartis Research Foundation
TBA  -  GlaxoSmithKline
John McNeil  -  John McNeil & Co
Tianhong Zhang  -  Pfizer
Craig Martin  -  SkunkWerks Software
Yvonne Martin  - Martin Consulting
Nicholas Goncharoff  -  SureChem
Tobias Kind  -  UC Davis Genome Center - Metabolomics
Craig Knox  -  University of Alberta
Oleg Ursu  -  University of New Mexico
Patrick Walters  - Vertex Pharmaceuticals
ChemAxon Partners participants (tbc) - see partner listing:

Alex Allardyce
Marketing Dir.
ChemAxon Ltd.
Maramaros koz 3/A, Budapest, 1037, Hungary
Tel: +361 453 0435
skype: alex_allardyce

--------------010108060004030503050604-- From owner-chemistry@ccl.net Wed Aug 19 09:29:01 2009 From: "Ulrike C Uhrig ulrike-.-tripos.com" To: CCL Subject: CCL: Announcing Tripos European Science Summit Message-Id: <-40026-090819062934-31456-YtojAK7F0qQud68CROfmnw..server.ccl.net> X-Original-From: "Ulrike C Uhrig" Date: Wed, 19 Aug 2009 06:29:30 -0400 Sent to CCL by: "Ulrike C Uhrig" [ulrike+/-tripos.com] Register to attend the Tripos European Science Summit September 28-29, 2009 in Munich. The meeting will cover a broad series of topics with the goal of bringing together scientists and users of Tripos software tools from all areas of computational and medicinal chemistry. Youll Interact with your peers, hear about or share innovative research strategies and discuss the complexities of today's drug discovery environment. Registration for the Tripos Science Summit is free. Get more information, view the meeting agenda, and register today at http://www.tripos.com/index.php?family=modules,SimplePage,,,&page=science_summit --- Dr. Ulrike Uhrig Application Scientist Manager & Discovery Software Trainer Tripos A Certara Company Martin-Kollar-Str. 17 D - 81829 Muenchen Phone: +49-89-451030-12 Email: ulrike++tripos.com From owner-chemistry@ccl.net Wed Aug 19 12:55:01 2009 From: "=?ISO-8859-1?Q?=22C=EDntia_C=2E_Vequi-Suplicy=22?= cintiadevequi===gmail.com" To: CCL Subject: CCL: Gromacs Error Message-Id: <-40027-090819122336-16136-j9wp6g3ERt9tQ3gK/bjDbw^-^server.ccl.net> X-Original-From: "=?ISO-8859-1?Q?=22C=EDntia_C=2E_Vequi-Suplicy=22?=" Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Wed, 19 Aug 2009 12:18:13 -0300 MIME-Version: 1.0 Sent to CCL by: "=?ISO-8859-1?Q?=22C=EDntia_C=2E_Vequi-Suplicy=22?=" [cintiadevequi===gmail.com] Hello, I am trying to simulate a lipid membrane with Gromacs. I am trying to generate the *.tpr file o run the simulation, but every time I use the command grompp I got the following error: checking input for internal consistency... ...ling /usr/bin/cpp : No such file or directory cpp exit code: 32512 dppc128.top > gromppzJXISa'cpp ' command is defined in the .mdp file ************************************************************* * Important: if you do not have a c-preprocessor installed, * * you MUST run grompp with the "-pp" command line option * * in place of the "-p" option. * ************************************************************* processing topology... processing coordinates... ------------------------------------------------------- Program grompp, VERSION 3.3.3 Source code file: ../../../../src/kernel/grompp.c, line: 469 Fatal error: number of coordinates in coordinate file (dppc128.gro, 17365) does not match topology (dppc128.top, 0) ------------------------------------------------------- "One Cross Each" (Monty Python) I don´t know if I have problems with the cpp or my input file for topology. In the topology file I have the following lines: ; ; File 'dppc128.top' was generated ; By user: onbekend (0) ; On host: onbekend ; At date: Tue Aug 18 10:02:52 2009 ; ; This is your topology file ; Pure DPPC bilayer with 128 lipids and 3655 water molecules ; ; The force field files to be include #include "ffoplsaa.itp" ; Include DPPC topology #include "dppc.itp" #include "lipid.itp" #include "spc.itp" [ molecules ] ; Compound #mol DPP 128 SOL 3655 If anyone can help It will be very nice, Thank you very much so far, Cíntia C. Vequi-Suplicy Biophysics Group Physics Institute São Paulo University From owner-chemistry@ccl.net Wed Aug 19 13:30:01 2009 From: "Roy Jensen JensenRH-.-MacEwan.ca" To: CCL Subject: CCL: And now something completely different! Message-Id: <-40028-090819030224-13370-XUQEXHVlfzNF6nv+aLCCkQ{=}server.ccl.net> X-Original-From: Roy Jensen Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=ISO-8859-1 Date: Wed, 19 Aug 2009 00:28:16 -0600 MIME-Version: 1.0 Sent to CCL by: Roy Jensen [JensenRH .. MacEwan.ca] I am shocked that this is used at the university level to teach students about electromagnetic interactions with matter!? There are serious problems with the incoming knowledge level of your students and/or your departments expectation of them. Sorry, way too simplistic for my students.=20 And if I can offer a recommendation: make instructional material that can be built upon in future years. Your video introduces incorrect perceptions regarding atomic structure and EM interactions that must be unlearned in future p.chem courses -- very poor pedagogically. Dr. Roy Jensen (=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D)-----------------------------------------= =A4 Chemistry, Grant MacEwan College VP Professional Affairs, MacEwan Faculty Association Room 5-172J, 10700-104 Avenue Edmonton, AB T5J 4S2 780.633.3915 On Tue, 18 Aug 2009 22:15:45 +0200, you wrote: > >Sent to CCL by: kadir [kadir..visual1.chem.pitt.edu] >Dear Friends and Colleagues, > >Please check out our short (4 min 16 sec) educational film explaining = the interaction of molecules with light using non-traditional = visualization tools. > >"Shine a light": >http://www.youtube.com/watch?v=3DceoO18RTiZI > >Like it? Please vote on it on Digg: >http://digg.com/general_sciences/Shine_A_Light_4 > >And don't miss the trailer: >http://www.youtube.com/watch?v=3DxYjoEvRpVbI&feature=3Dvideo_response > >When your friends or relatives ask why pchem research is so much fun, = just show them the film! > >Enjoy and share! >kadir > > >Kadir Diri, PhD >Research Scientist >Department of Chemistry and iOpenShell Center >SSC #426 >University of Southern California >Los Angeles, CA 90089-0482 >-------------------------- >Relativistic correction to Murphy's law: >Whether things can go wrong or not, depends on your frame of reference. > > > >-=3D This is automatically added to each message by the mailing script = =3D-> >Subscribe/Unsubscribe:=20> >Job: http://www.ccl.net/jobs=20> From owner-chemistry@ccl.net Wed Aug 19 15:01:01 2009 From: "chen modigger~!~gmail.com" To: CCL Subject: CCL: MD package suitable for transition-metal complexes. Message-Id: <-40029-090818111735-16650-KTWeCEcyTYKQHmSNpsfPnA.:.server.ccl.net> X-Original-From: chen Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Tue, 18 Aug 2009 11:17:17 -0400 MIME-Version: 1.0 Sent to CCL by: chen [modigger=-=gmail.com] Dear all, I am new to the molecular dynamic simulation. Would you suggest some MD simulation packages (free packages are preferred) that are good for simulation on systems involving transition-metal atoms? Thank a lot. ryan From owner-chemistry@ccl.net Wed Aug 19 17:41:00 2009 From: "Sanjay Kumar computationalchemist/./gmail.com" To: CCL Subject: CCL: Cu-Ni Alloy Message-Id: <-40030-090819173910-21166-T79+31KDHsUPoTN12efp0w[*]server.ccl.net> X-Original-From: "Sanjay Kumar" Date: Wed, 19 Aug 2009 17:39:06 -0400 Sent to CCL by: "Sanjay Kumar" [computationalchemist-$-gmail.com] Dear Folks, Sorry if i am demanding too much. I am very new beginner to model alloys and i am looking for the '.CIF' files of Copper Nickel Alloys, which could help me for the GSAS refinement and for further modelling. It would be greateful, if you could help me with the structure. best regards, Dr. Sanjay kumar From owner-chemistry@ccl.net Wed Aug 19 19:16:01 2009 From: "Brian Salter-Duke brian.james.duke===gmail.com" To: CCL Subject: CCL: ZINDO Documentation Message-Id: <-40031-090819084215-1911-jlxpyt9Y/CgpJL3xeq66Pw-#-server.ccl.net> X-Original-From: Brian Salter-Duke Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Wed, 19 Aug 2009 21:09:57 +1000 MIME-Version: 1.0 Sent to CCL by: Brian Salter-Duke [brian.james.duke(_)gmail.com] Are you saying that I can not report results obtained from a copy of ZINDO I obtained from Mike Zerner himself early in the 1990s? I have not actually used it for years, which is why I did not respond to your message, but if I can help, let me know. I think I compiled it last about 12 yeras ago, but I do still have it around. Brian. John McKelvey jmmckel||gmail.com wrote: > Hello, > > I fear that no one can. Current people who have a copy of the source > can not even report that they used the code by name without buying a > license. As I understand it instead they have to cite the papers upon > which the methodologies in ZINDO were developed and tested. > > John McKelvey > > > On Tue, Aug 18, 2009 at 7:39 PM, lyzhao lyzhao###zjnu.cn > > wrote: > > > Sent to CCL by: "lyzhao" [lyzhao{}zjnu.cn ] > Dear All, > Thank Tamm and Jan for sharing the ZINDO Docs, but who can > share the "Original" ZINDO Source Code. > > Best regards!! > Youzhao Lan > ======================================================== > > > From:Toomas Tamm toomas^_^yki.ttu.ee > Date:2009-08-18 22:35:26 > To:Lan, Youzhao > Cc: > Subject:CCL: ZINDO Documentation > > > Sent to CCL by: Toomas Tamm [toomas]~[yki.ttu.ee ] > Hello all! > > As one of the last people who worked on the Zindo code between > 1994 and > 1996, I also have a set of manuals (including documentation of some of > the internals of the code). I sent them to Jan for posting to the > document archive. > > -- > Toomas Tamm e-mail: tt-ccl2 (at) > kky . ttu . ee > Chair of Inorganic Chemistry voice: INT+372-620-2810 > Tallinn University of Technology fax: INT+372-620-2828 > Ehitajate tee 5, EE-19086 Tallinn, Estonia > http://www.kk.ttu.ee/toomas/ > > > > > On Sun, 2009-08-02 at 18:09 -0400, Jan Labanowski > janla/speakeasy.net > wrote: > > Sent to CCL by: Jan Labanowski [janl++speakeasy.net > ] > > Serge Gorelsky wrote: > > > Hi, I happen to have the ZINDO manual from Mike Zerner (dated > before > > > 1999). See the attached text file. S.G. > > > > Serge, > > > > Since CCL scripts did not like the attachment (yes, they are > paranoid) I placed > > the copy of the ZINDO manual that was in your attachment on the > CCL Web site in > > Document Archive page, namely: > > > > > > http://www.ccl.net/cca/documents/ZINDO_manual_1996.txt > > > > > Janhttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt > > > > -= This is automatically added to each message by the mailing > script =- > > > > E-mail to subscribers: CHEMISTRY|-|ccl.net > or use:> > E-mail to administrators: CHEMISTRY-REQUEST|-|ccl.net > or use> Conferences: > http://server.ccl.net/chemistry/announcements/conferences/> > > > > > -- > John McKelvey > 10819 Middleford Pl > Ft Wayne, IN 46818 > 260-489-2160 > jmmckel|-|gmail.com From owner-chemistry@ccl.net Wed Aug 19 20:02:00 2009 From: "clara song clarasong83-$-gmail.com" To: CCL Subject: CCL: problem of defining spin multiplicity in NWchem Message-Id: <-40032-090819195847-11421-jESpMT0ZB3KDTh5oF+Kefw__server.ccl.net> X-Original-From: "clara song" Date: Wed, 19 Aug 2009 19:58:44 -0400 Sent to CCL by: "clara song" [clarasong83() gmail.com] Hi, I am a new user to Nwchem. When I tried to calculated excited states by suing tddft for Nb_9 (doublet state), I experienced problem when defining the spin multi, the following is my input file, and I do not know where I should put the word "doublet", if I insert it after MP2, it gave me error, and if I do not specify, there is the default value: multi=1 in my output, which conflicts with number of electron. I know if I use DFT i.e. b3lyp, I can define by MULT=2, I just wonder how can I do that within MP2(UMP2)? Please give your advice. Thank you very much. start nb9lowest_mp2_tddft title "nb9lowest_mp2_tddft" geometry Nb -1.448794 -0.453923 -1.535258 Nb 1.115437 -0.937601 1.610466 Nb 0.176599 1.493887 -1.555186 Nb -0.486721 -2.387848 -0.135716 Nb 0.374053 1.612074 1.405017 Nb -1.458063 -0.679815 1.443668 Nb -1.858453 1.516153 0.182833 Nb 2.251542 0.921053 -0.095359 Nb 1.333402 -1.084980 -1.323466 end basis Nb library lanl2dz_ecp end ecp Nb library lanl2dz_ecp end UMP2 freeze core end TDDFT NROOTS 3 TARGET 1 END TASK TDDFT OPTIMIZE From owner-chemistry@ccl.net Wed Aug 19 21:56:01 2009 From: "neeraj misra neerajmisra^_^hotmail.com" To: CCL Subject: CCL:G: DOPING Message-Id: <-40033-090819215439-22915-ii+tHa2knB4WMSV54aO/WA{:}server.ccl.net> X-Original-From: "neeraj misra" Date: Wed, 19 Aug 2009 21:54:35 -0400 Sent to CCL by: "neeraj misra" [neerajmisra(-)hotmail.com] DEAR ALL, COULD ANYONE SUGGEST ME HOW TO DOPE AN ANTIMONIDE WITH A 3D TRANSITION ELEMENT(THEORETICALLY) USING GAUSSIAN... NM