From owner-chemistry@ccl.net Wed Mar 12 05:21:00 2008 From: "Stan van Gisbergen vangisbergen|*|scm.com" To: CCL Subject: CCL: Help :problems in excited states calculation of Ag4 using ADF Message-Id: <-36486-080312051649-27693-ixkCTrP3PoL0qHNzRisrCw.@.server.ccl.net> X-Original-From: Stan van Gisbergen Content-Type: multipart/alternative; boundary=Apple-Mail-51--630086244 Date: Wed, 12 Mar 2008 09:26:20 +0100 Mime-Version: 1.0 (Apple Message framework v753) Sent to CCL by: Stan van Gisbergen [vangisbergen---scm.com] --Apple-Mail-51--630086244 Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed Dear Xiao Hong Zhao, ADF support requests are best sent to support###scm.com or posted on the forum on our website http://www.scm.com/forums/ The OCCUPATIONS keyword may help in this case: http://www.scm.com/Doc/Doc2007.01/ADF/ADFUsersGuide/ page140.html#keyscheme%20OCCUPATIONS or search for occupations on our documented examples page: http:// www.scm.com/Doc/Doc2007.01/ADF/Examples/page1.html Best regards, Stan van Gisbergen On Mar 11, 2008, at 7:46 AM, xiao hong zhao zhaoxiaohong1237{} sina.com wrote: > > Sent to CCL by: "xiao hong zhao" [zhaoxiaohong1237/a\sina.com] > Dear: > An error Error in scfrho: fractional occupation numbers have not > yet been implemented ! occurred when I calculated excitation states > of an Ag4 molecule of Td geometry, while the other modules are > normal. I have read the user-guider carefully and tried some ways, > but I can't designate occupation number. Would you tell me what may > induce this error in ADF? How could I solve this problem > Thank you so much. > > Best wishes, > > > > -= This is automatically added to each message by the mailing > script =- > To recover the email address of the author of the message, please > change> Conferences: http://server.ccl.net/chemistry/announcements/ > conferences/ > > Search Messages: http://www.ccl.net/htdig (login: ccl, Password: > search)> > Dr. S.J.A. van Gisbergen Scientific Computing & Modelling NV Theoretical Chemistry, Vrije Universiteit De Boelelaan 1083 1081 HV Amsterdam The Netherlands vangisbergen###scm.com http://www.scm.com T: +31-20-5987626 F: +31-20-5987629 --Apple-Mail-51--630086244 Content-Transfer-Encoding: quoted-printable Content-Type: text/html; charset=ISO-8859-1 Dear Xiao Hong Zhao,=A0

ADF support requests are = best sent to support###scm.com or = posted on the forum on our website=A0http://www.scm.com/forums/

The OCCUPATIONS = keyword may help in this case:=A0
http://www.scm.com/Doc/Doc2007.01/ADF/ADFUsersGuid= e/page140.html#keyscheme%20OCCUPATIONS
or search for = occupations on our documented examples page:=A0http://= www.scm.com/Doc/Doc2007.01/ADF/Examples/page1.html

Best = regards,
Stan van Gisbergen=A0

On Mar = 11, 2008, at 7:46 AM, xiao hong zhao zhaoxiaohong1237{}sina.com = wrote:


Sent to CCL by: "xiao hong zhao" = [zhaoxiaohong1237/a\sina.com]
=A0=A0 An error Error in scfrho: = fractional occupation numbers have not yet been implemented ! occurred = when I calculated excitation states of an Ag4 molecule of Td geometry, = while the other modules are normal. I have read the user-guider = carefully and tried some ways, but I can't designate occupation number. = Would you tell me what may induce this error in ADF? How could I solve = this problem
Thank you so much.=A0

Best = wishes,



-=3D This is = automatically added to each message by the mailing script =3D-
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If your mail bounces from CCL with 5.7.1 error, = check:






Dr. S.J.A. van Gisbergen
Scientific Computing & Modelling NV
Theoretical Chemistry, Vrije Universiteit
De Boelelaan 1083
1081 HV = Amsterdam
The Netherlands=A0=A0 =A0 =A0 =A0 = =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0

 =

= --Apple-Mail-51--630086244-- From owner-chemistry@ccl.net Wed Mar 12 06:44:00 2008 From: "Jennifer Clare Brookes ucapjcb . ucl.ac.uk" To: CCL Subject: CCL: Dreiding model Message-Id: <-36487-080312063910-10917-MKqyVDvBb2Ze/bMvKgkMDw**server.ccl.net> X-Original-From: "Jennifer Clare Brookes" Date: Wed, 12 Mar 2008 06:39:06 -0400 Sent to CCL by: "Jennifer Clare Brookes" [ucapjcb]*[ucl.ac.uk] Hi all, Does anybody know where (UK) I can buy a traditional Dreiding model kit, that I can use to build molecules that show all conformations? Thanks Jenny From owner-chemistry@ccl.net Wed Mar 12 07:19:01 2008 From: "Cyril Bauvais cyril.bauvais-x-u-psud.fr" To: CCL Subject: CCL: 3D data visualisation software Message-Id: <-36488-080312065724-17634-W/7UtOzAn43SQzrG96a+0Q ~~ server.ccl.net> X-Original-From: Cyril Bauvais Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Wed, 12 Mar 2008 10:59:30 +0100 MIME-Version: 1.0 Sent to CCL by: Cyril Bauvais [cyril.bauvais##u-psud.fr] also LabPlot, easy to use and free Cyril Bauvais -- Laboratoire "Molécules Fluorées et Chimie Médicinale" BioCIS UMR 8076 Faculté de Pharmacie Université Paris-sud 5, rue J.B. Clément 92296 Chatenay-Malabry Cedex tel: 0146835743 & 0687477897 email: cyril.bauvais::u-psud.fr -- Alcides Simao alsimao(a)gmail.com a écrit : > OpenOffice? > Gnuplot? > KOffice? > GOffice? > SciGraphica? > Google worksheets? From owner-chemistry@ccl.net Wed Mar 12 09:30:00 2008 From: "Jeff Lowrie lowrie-x-schrodinger.com" To: CCL Subject: CCL: Dreiding model Message-Id: <-36489-080312082518-21576-tQhlV0G4U8YjCAzABbsooA%a%server.ccl.net> X-Original-From: Jeff Lowrie Content-Transfer-Encoding: 7bit Content-Type: text/plain Date: Wed, 12 Mar 2008 07:53:59 -0400 Mime-Version: 1.0 Sent to CCL by: Jeff Lowrie [lowrie#%#schrodinger.com] Have a look here: http://www.darlingmodels.com/ http://www.indigo.com/models/molecular-models.html On Wed, 2008-03-12 at 06:39 -0400, Jennifer Clare Brookes ucapjcb . ucl.ac.uk wrote: > Sent to CCL by: "Jennifer Clare Brookes" [ucapjcb]*[ucl.ac.uk] > > Hi all, > > Does anybody know where (UK) I can buy a traditional Dreiding model kit, that I can use to build molecules that show all conformations? > > Thanks > Jenny> From owner-chemistry@ccl.net Wed Mar 12 10:10:00 2008 From: "Tiejun Cheng tjcheng^-^mail.sioc.ac.cn" To: CCL Subject: CCL: Characterization of binding pocket (hydrophobic or hydrophilic) ? Message-Id: <-36490-080312094547-6543-+2qddkiM/kaSHNq/67bhLQ-.-server.ccl.net> X-Original-From: "Tiejun Cheng" Date: Wed, 12 Mar 2008 09:45:43 -0400 Sent to CCL by: "Tiejun Cheng" [tjcheng::mail.sioc.ac.cn] Dear CCLers, Is there any methods or softwares that can determine whether a binding pocket is hydrophobic or hydrophilic? Thanks in advance. Best regards, Jay From owner-chemistry@ccl.net Wed Mar 12 14:24:00 2008 From: "David Hose Anthrax_brothers]-[hotmail.com" To: CCL Subject: CCL: Dreiding model Message-Id: <-36491-080312142210-2690-08zHajW8EAWB20JC7S1kBg .. server.ccl.net> X-Original-From: "David Hose" Date: Wed, 12 Mar 2008 14:22:07 -0400 Sent to CCL by: "David Hose" [Anthrax_brothers[*]hotmail.com] Hi Jenny, Sigma-Aldrich in the UK sell these types of models. http://www.sigmaaldrich.com/ A search for 'Molecular Models' will bring up the list of products they sell. Personally I had some Cochranes models since I was an undergrad, and the still get use today even with of the fancy molecular modelling programs I have. Regards, Dave. ===== Hi all, Does anybody know where (UK) I can buy a traditional Dreiding model kit, that I can use to build molecules that show all conformations? Thanks Jenny From owner-chemistry@ccl.net Wed Mar 12 15:32:01 2008 From: "maxim totrov max!=!molsoft.com" To: CCL Subject: CCL: calculating and displaying surface residues Message-Id: <-36492-080312152526-32557-ej/BuVQa6K54IBtIFaa5CQ*|*server.ccl.net> X-Original-From: maxim totrov Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes Date: Wed, 12 Mar 2008 11:25:12 -0700 Mime-Version: 1.0 (Apple Message framework v919.2) Sent to CCL by: maxim totrov [max!^!molsoft.com] Hi Kalpana, free Molsoft Browser can display and calculate accessible surface areas for arbitrary subsets of atoms, such as hydrophobic atoms. You can download from www.molsoft.com Regards, Max Totrov > > Hi > We would like to calculate and display exposed hydrophobic surfaces > on a protein. We would also like to list the residues on the > surface. Are there freeware/ scripts/plugins to pymol/rasmol that > would do this? > Thanks > -- > Kalpana Krishnaswami From owner-chemistry@ccl.net Wed Mar 12 16:31:00 2008 From: "Felix Koziol koziol() fas.harvard.edu" To: CCL Subject: CCL: 3D data visualisation software Message-Id: <-36493-080312130338-25464-nHCzSi2HiWVWoDdFG5ufgA]-[server.ccl.net> X-Original-From: Felix Koziol Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=US-ASCII; format=flowed Date: Wed, 12 Mar 2008 12:07:05 -0400 Mime-Version: 1.0 (Apple Message framework v753) Sent to CCL by: Felix Koziol [koziol^_^fas.harvard.edu] Hi, Another suggestion would be OpenDX. Felix On Mar 11, 2008, at 4:22 PM, Alcides Simao alsimao(a)gmail.com wrote: > OpenOffice? > Gnuplot? > KOffice? > GOffice? > SciGraphica? > Google worksheets? From owner-chemistry@ccl.net Wed Mar 12 17:06:00 2008 From: "Dr David N Haney haney^-^edusoft-lc.com" To: CCL Subject: CCL: Characterization of binding pocket (hydrophobic or hydrophilic) ? Message-Id: <-36494-080312160940-23317-hG58VXazQpuDwbExVCaUvw=-=server.ccl.net> X-Original-From: Dr David N Haney Content-Disposition: inline Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=utf-8 Date: Wed, 12 Mar 2008 11:56:22 -0700 Mime-Version: 1.0 Sent to CCL by: Dr David N Haney [haney-$-edusoft-lc.com] Dear Jay, I just sent a post about hydrophobicity under the subject "calculating and displaying surface residues". Binding pockets are surface residues, and HINT is one of the best tools for displaying the hydropathic (hydrophobic/hydrophilic) nature as well as calculating the components of the hydropathic "energies". For a ligand bound to the binding pocket, you can determine the relative contributions of the hydrophobic and hydrophilic parts. #### > Although HINT is not freeware, it is one of the best tools to display > hydrophobic energy surfaces as well as hydrophobic-hydrophobic surface interactions. > HINT scoring has been shown to provide a good correlation with binding energy. > It is currently available as a TOOLKIT and the libraries can be used with > external programs like PyMol. > > Please see www.edusoft-lc.com/hint ++ > J. Med. Chem. 1991, 34, 758-767. > J. Computer Aided Mol. Design 1991, 5, 545-552. > J. Med. Chem. 2003, 46, 4487-4500. > J. Med. Chem. 2004, 47, 4507-4516. > J. Mol. Biol. 2006, 358, 289–309 #### On Wed, Mar 12, 2008 at 09:45:43AM -0400, Tiejun Cheng tjcheng^-^mail.sioc.ac.cn wrote: > > Sent to CCL by: "Tiejun Cheng" [tjcheng::mail.sioc.ac.cn] > Dear CCLers, > > Is there any methods or softwares that can determine whether a binding pocket is hydrophobic or hydrophilic? Thanks in advance. > > Best regards, > > Jay> -- ######### David N. Haney, Ph.D. ######### # EduSoft, LC Phone - 858-483-1197 # # 5455 Westknoll Dr. FAX - 858-483-1046 # # La Jolla, CA 92037 Email - haney^^edusoft-lc.com # ################# #####################