Thanks

Chris

On 26 Aug = 2009, at 15:14, John McKelvey jmmckel_._gmail.com wrote:

Folks,

Many thnaks to all those who responded = offering suggestions.. Significant cudos to Kevin Gilert at Serena = Software for his help in finally getting it running.

We now have = ZINDO running fine on 32bit hardware, or on 64bit X86 hardware in 32bit = mode. Getting it runniing in 64bit mode on any hardware was = far beyond our willingness... We did not spend much time trying to = getting it running on any non-linux, non-x86 hardware, Runs = fine on a recent MAC.

Best = regards,

John
--
John McKelvey
10819 Middleford = Pl
Ft Wayne, IN 46818
260-489-2160
jmmckel=3D-=3Dgmail.com

= --Boundary_(ID_k6DAVm0cCB+cBXj9MVuEHw)-- From owner-chemistry@ccl.net Wed Aug 26 14:09:00 2009 From: "Timothy Pyrkov pyrkov###nmr.ru" To: CCL Subject: CCL: the atomic logP of the natural amino acids Message-Id: <-40083-090826121537-16373-udWxfgeDGRMi+fPSFdCxUA/./server.ccl.net> X-Original-From: Timothy Pyrkov Content-Type: multipart/alternative; boundary=001485f6db20e364bc04720cc82b Date: Wed, 26 Aug 2009 19:05:42 +0400 MIME-Version: 1.0 Sent to CCL by: Timothy Pyrkov [pyrkov()nmr.ru] --001485f6db20e364bc04720cc82b Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Dear Xu Zhijian, You can use all-atom parameterization from the paper Ghose AK, Viswanadhan VN, Wendoloski JJ. Prediction of hydrophobic (lipophilic) properties of small organic molecules using fragmental methods: An analysis of ALOGP and CLOGP methods. J Phys Chem A 102, 3762-3772, 1998. It is not a list of amino-acid atoms, rather general atom-types. However you can construct a peptide chain of all 20 aminoacids and submit to http://model.nmr.ru/platinum - there you can download the table of atoms that you need. If otherwise you need these values for only-heavy-atom representation - you will have to perform some additional work, namely sum logP constants of each heavy atom with its hydrogens'. Best regards, Ph.D. Tim Pyrkov junior research associate at Laboratory of Biomolecular Modeling, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia --001485f6db20e364bc04720cc82b Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Dear Xu Zhijian,

You can use all-atom parameterization from the pape= r Ghose AK, Viswanadhan VN, Wendoloski JJ. Prediction of hydrophobic (lipop= hilic) properties of small organic molecules using fragmental methods: An a= nalysis of ALOGP and CLOGP methods. J Phys Chem A 102, 3762-3772, 1998.
It is not a list of amino-acid atoms, rather general atom-types. Howeve= r you can construct a peptide chain of all 20 aminoacids and submit to http://model.nmr.ru/platinum - the= re you can download the table of atoms that you need.

If otherwise you need these values for only-heavy-atom representation -= you will have to perform some additional work, namely sum logP constants o= f each heavy atom with its hydrogens'.

Best regards,

Ph.D. Tim Pyrkov
junior research associate at Laboratory of Biomolecular= Modeling,
Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry,
R= ussian Academy of Sciences, Moscow, Russia

--001485f6db20e364bc04720cc82b-- From owner-chemistry@ccl.net Wed Aug 26 18:07:00 2009 From: "Richard Compton rcompton**accelrys.com" To: CCL Subject: CCL: Accelrys European UGM 2009 Message-Id: <-40084-090826180454-22844-bQVNL7jnqiiDfdA/hUKhvg|server.ccl.net> X-Original-From: "Richard Compton" Date: Wed, 26 Aug 2009 18:04:50 -0400 Sent to CCL by: "Richard Compton" [rcompton^^^accelrys.com] Dear Colleagues, We are pleased to announce that registration is open for the 2009 Accelrys European User Group Meeting. The EUGM will be held in Barcelona at La Mola Hotel & Conference Centre. Sessions run from October 14th-16th, Wednesday afternoon to Friday afternoon. Places are filling up extremely quickly this year so please register as early as possible to ensure your attendance and take advantage of the discounted rate. Please visit our website for the preliminary agenda and to register: http://accelrys.com/events/ugms/eugm-2009/ Many thanks to confirmed speakers who include: Adel Kassim, AstraZeneca Blair Johnston, University of Strathclyde Brian Bartel, Notiora Colin Groom, CCDC Dieter Hofmann, Maria Entrialgo & Andreas Lendlein, GKSS Research Center Frank Oellien, Intervet Guosheng Shao, University of Bolton Horacio Prez-Snchez, Karlsruhe Institut Jrmy Besnard, University of Dundee Karen Abraham, Unilever Nick Brown, Astra-Zeneca Obduliah Rabal, CNIO Ole Hlck, Fraunhofer IZM Ole Swang, SINTEF Pierre Ducrot, Discngine Rebecca Wells, AstraZeneca Rob Smith, Pfizer Sirimon O-Charoen, Torrey Path Finally thank you to Brad Sherborne of Schering Plough who will be chairing the Pet Peeves session this year. Optional training courses will be held on 12th, 13th & 14th October. Please see the website for further details. I look forward to seeing lots of you in Barcelona. If you have any further questions, please contact European support on +44 1223 228822 or support-eu..accelrys.com Kind regards, Richard. _______________________ Mr Richard Compton Vice President, EMEA Accelrys Ltd. 334 Cambridge Science Park Cambridge, CB4 0WN UK From owner-chemistry@ccl.net Wed Aug 26 21:10:00 2009 From: "zjxu zjxu]=[mail.shcnc.ac.cn" To: CCL Subject: CCL: reply: the atomic logP of the natural amino acids Message-Id: <-40085-090826205916-8406-iOp7WLDunAWG1bU8y4Dvig:+:server.ccl.net> X-Original-From: "zjxu" Content-Type: multipart/alternative; boundary="----=_NextPart_000_004A_01CA26F5.F4FC5120" Date: Thu, 27 Aug 2009 09:08:35 +0800 MIME-Version: 1.0 Sent to CCL by: "zjxu" [zjxu[A]mail.shcnc.ac.cn] This is a multi-part message in MIME format. ------=_NextPart_000_004A_01CA26F5.F4FC5120 Content-Type: text/plain; charset="gb2312" Content-Transfer-Encoding: quoted-printable Dear Tim Pyrkov Thanks very much for your kindly reply. I will try it and thanks again. =20 Best wishes, =20 Xu Zhijian =20 _____ =20 =B7=A2=BC=FE=C8=CB: owner-chemistry+zjxu=3D=3Dmail.shcnc.ac.cn:+:ccl.net [mailto:owner-chemistry+zjxu=3D=3Dmail.shcnc.ac.cn:+:ccl.net] =B4=FA=B1=ED = Timothy Pyrkov pyrkov###nmr.ru =B7=A2=CB=CD=CA=B1=BC=E4: 2009=C4=EA8=D4=C226=C8=D5 =D0=C7=C6=DA=C8=FD = 23:06 =CA=D5=BC=FE=C8=CB: Xu, Z J =D6=F7=CC=E2: CCL: the atomic logP of the natural amino acids =20 Dear Xu Zhijian, You can use all-atom parameterization from the paper Ghose AK, = Viswanadhan VN, Wendoloski JJ. Prediction of hydrophobic (lipophilic) properties of small organic molecules using fragmental methods: An analysis of ALOGP = and CLOGP methods. J Phys Chem A 102, 3762-3772, 1998.=20 It is not a list of amino-acid atoms, rather general atom-types. However = you can construct a peptide chain of all 20 aminoacids and submit to http://model.nmr.ru/platinum - there you can download the table of atoms that you need. If otherwise you need these values for only-heavy-atom representation - = you will have to perform some additional work, namely sum logP constants of = each heavy atom with its hydrogens'. Best regards, Ph.D. Tim Pyrkov junior research associate at Laboratory of Biomolecular Modeling, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia ------=_NextPart_000_004A_01CA26F5.F4FC5120 Content-Type: text/html; charset="gb2312" Content-Transfer-Encoding: quoted-printable

Dear Tim = Pyrkov

Thanks very much for = your kindly reply. I will try it and thanks = again.

Best = wishes,

Xu = Zhijian

<= /span>

=B7=A2=BC=FE= =C8=CB: owner-chemistry+zjxu=3D=3Dmail.shcnc.ac.cn:+:ccl.net [mailto:owner-chemistry+zjxu=3D=3Dmail.shcnc.ac.cn:+:ccl.net] = =B4=FA=B1=ED Timothy = Pyrkov pyrkov###nmr.ru
=B7=A2=CB=CD=CA=B1=BC=E4: 2009=C4=EA8=D4=C226=C8=D5 =D0=C7=C6=DA=C8=FD 23:06
=CA=D5=BC=FE=C8=CB: Xu, Z J
=D6=F7=CC=E2: CCL: the atomic logP of the natural amino = acids

Dear Xu Zhijian,

You can use all-atom parameterization from the paper Ghose AK, Viswanadhan VN, Wendoloski JJ. Prediction of hydrophobic (lipophilic) properties of small organic molecules using fragmental methods: An = analysis of ALOGP and CLOGP methods. J Phys Chem A 102, 3762-3772, 1998.

It is not a list of amino-acid atoms, rather general atom-types. However = you can construct a peptide chain of all 20 aminoacids and submit to http://model.nmr.ru/platinum - = there you can download the table of atoms that you need.

If otherwise you need these values for only-heavy-atom representation - = you will have to perform some additional work, namely sum logP constants of = each heavy atom with its hydrogens'.

Best regards,

Ph.D. Tim Pyrkov
junior research associate at Laboratory of Biomolecular Modeling,
Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry,
Russian Academy of = Sciences, Moscow, Russia

------=_NextPart_000_004A_01CA26F5.F4FC5120-- From owner-chemistry@ccl.net Wed Aug 26 21:45:01 2009 From: "Yves Wang yves.wang-$-duke.edu" To: CCL Subject: CCL: Two GAMESS questions Message-Id: <-40086-090826212707-2357-zUfUj5h9O5ZahE99Nz7NbA]-[server.ccl.net> X-Original-From: "Yves Wang" Date: Wed, 26 Aug 2009 21:27:03 -0400 Sent to CCL by: "Yves Wang" [yves.wang_+_duke.edu] Hi folks, I'm starting to learn GAMESS and have two questions: 1. How do I include BSSE correction in a geometry optimization? I searched "BSSE" and "Counterpoise" in the Input doc, but found nothing related to geometry optimization. 2. The manual says if I want to make geometry optimization with CCSD method, I have to use non-gradient method $TRUDGE and use the HINT internal coordinate. Is there any software that is able generate structure in that weird format? Thank you for reading this message and giving answers Yves From owner-chemistry@ccl.net Wed Aug 26 22:19:01 2009 From: "Kadir Diri kadir%%visual1.chem.pitt.edu" To: CCL Subject: CCL: And now something completely different! Message-Id: <-40087-090826212917-3441-f8yH8uBjqutyLPJAUkMwsA**server.ccl.net> X-Original-From: Kadir Diri Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Wed, 26 Aug 2009 17:26:45 -0700 MIME-Version: 1.0 Sent to CCL by: Kadir Diri [kadir(_)visual1.chem.pitt.edu] Dear Dr. Jensen and everyone who commented on our video "Shine a light", First, thank you for the comments! I guess we did not clearly communicate the goal of the film, which is to excite interest for science and encourage young people (e.g., high-school students) to learn more. Moreover, we want to break the existing attitude that science is boring and unattractive. Science is fun and doing science is cool - this is the most important message of the film. The video by no means intends to replace rigorous university-level presentations, however, an instructor can use it as a teaser, to initiate an in-depth discussion of the concepts that the film introduces (molecular orbitals, excited states, etc). Of course, it takes much longer than 5 minutes to teach about all subtle aspects of interaction of molecules with light at a university level. From a pedagogical point of view, as with any educational material, one must be very careful with the content of such films and must avoid introducing misconceptions, despite the necessary simplifications. This is where, I think, constructive criticism by the professional community is most valuable, and I welcome any specific feedback, which will be very useful in guiding our future attempts to bring science to the "masses". Best regards, 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. Roy Jensen JensenRH-.-MacEwan.ca wrote: > 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. > > 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 > (==========)-----------------------------------------� > 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=ceoO18RTiZI >> >> 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=xYjoEvRpVbI&feature=video_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.> >> > > > > -> > RTFI: http://www.ccl.net/chemistry/aboutccl/instructions