From owner-chemistry@ccl.net Tue Jul 17 03:49:00 2012 From: "Hyunbok Lee mutebeat!^!gmail.com" To: CCL Subject: CCL: GaussView Error : CConnectionGFCHK::ParseGFCHK() Message-Id: <-47213-120717034825-12362-VnEjJzOG14A2t2oK8VzzHQ-$-server.ccl.net> X-Original-From: "Hyunbok Lee" Date: Tue, 17 Jul 2012 03:48:23 -0400 Sent to CCL by: "Hyunbok Lee" [mutebeat||gmail.com] Deal all, I opened chk file on GaussView, but it showed following error message: CConnectionGFCHK::Parse_GFCHK() Missing or bad data: Alpha Ortbial Energies Line Number 1737 I think the calculation is done without a problem. What is the problem? and what is the meaning of this error message? Any advise will be appreciated. Thanks in advance. Hyunbok Lee From owner-chemistry@ccl.net Tue Jul 17 05:26:00 2012 From: "Javier Cerezo jcb1-*-um.es" To: CCL Subject: CCL: GaussView Error : CConnectionGFCHK::ParseGFCHK() Message-Id: <-47214-120717052458-25226-KTChv6AzWioYzKZ4lOnbVg%x%server.ccl.net> X-Original-From: Javier Cerezo Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Tue, 17 Jul 2012 11:24:52 +0200 MIME-Version: 1.0 Sent to CCL by: Javier Cerezo [jcb1- -um.es] It seems to be a bug in your gv version (I also have the same problem). The workaround I'm using is: 1) Convert your chk in fchk: formchk yourfile.chk 2) Inspect the fchk file. Near the header you have info about number of basis set. The problem (at least in my case) arises when "Number of basis functions" is not the same as "Number of independent basis functions". To make it work you need to edit the file making Number of basis functions=Number of independent basis functions. The edited fchk file should be opened with no problems by gv. Javier El 17/07/12 09:48, Hyunbok Lee mutebeat!^!gmail.com escribió: > Sent to CCL by: "Hyunbok Lee" [mutebeat||gmail.com] > Deal all, > > I opened chk file on GaussView, but it showed following error message: > > CConnectionGFCHK::Parse_GFCHK() > Missing or bad data: Alpha Ortbial Energies > Line Number 1737 > > I think the calculation is done without a problem. > What is the problem? and what is the meaning of this error message? > Any advise will be appreciated. > > Thanks in advance. > > Hyunbok Lee> > -- Javier CEREZO BASTIDA PhD Student Physical Chemistry Universidad de Murcia Murcia (Spain) Tel: (+34)868887434 From owner-chemistry@ccl.net Tue Jul 17 06:00:00 2012 From: "Gerard Pujadas gerard.pujadas]*[gmail.com" To: CCL Subject: CCL: Any alternative to the TOPS server for drawing topological diagrams for PDB files? Message-Id: <-47215-120717055034-2527-bniWTpVFjQO1r4uIOKlL3g(_)server.ccl.net> X-Original-From: Gerard Pujadas Content-Type: multipart/alternative; boundary=e89a8ff25014f2c2ee04c50379e0 Date: Tue, 17 Jul 2012 11:50:28 +0200 MIME-Version: 1.0 Sent to CCL by: Gerard Pujadas [gerard.pujadas~!~gmail.com] --e89a8ff25014f2c2ee04c50379e0 Content-Type: text/plain; charset=ISO-8859-1 Dear CCL list members, first of all, sorry for cross-posting I would like to know if there is available any webserver (or software) that can draws topological diagrams for PDB files following the idea that was implemented some years ago at the TOPS webserver ( http://www.tops.leeds.ac.uk/). This server is not running since 2008 and it was quite useful in order to teach the protein architecture to my students. Currently PDBSum provides topological diagrams for PDB entries ( http://kpwu.wordpress.com/2006/02/14/pdbsum-announces-topology-diagrams-for-protein-domains/) but, in my opinion, those formerly provided by TOPS where more intuitive to correlate the diagram with the folding of the domain ... With many thanks in advances Yours sincerely -- Gerard Pujadas http://bioquimica.urv.cat/eng/fitxa.jsp?id=22 Nutrigenomics Research Group phone +34 977 55 (9565) Biochemistry and Biotechnology Department Office 106, Building N4, Campus Sescelades Universitat Rovira i Virgili Tarragona, Catalonia --e89a8ff25014f2c2ee04c50379e0 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Dear CCL list members,

first of all, sorry for cross-posting

= I would like to know if there is available any webserver (or software)=20 that can draws topological diagrams for PDB files following the idea=20 that was implemented some years ago at the TOPS webserver (http://www.tops.leeds.ac.uk/= ). This server is not running since 2008 and it was quite useful in order to= =20 teach the protein architecture to my students. Currently PDBSum provides topological diagrams for PDB entries (http://kpwu.wordpress.com/2006/02/14/pdbsum-announces-topology-= diagrams-for-protein-domains/) but, in my opinion, those formerly provided by TOPS where more=20 intuitive to correlate the diagram with the folding of the domain ...

With many thanks in advances

Yours sincerely
--
Gerard Pujadas
http= ://bioquimica.urv.cat/eng/fitxa.jsp?id=3D22
Nutrigenomics Research Group
phone +34 977 55 (9565)
Biochemistry and Biotechnology Department
Office 106, Building N4, Campu= s Sescelades
Universitat Rovira i Virgili
Tarragona, Catalonia=

--e89a8ff25014f2c2ee04c50379e0-- From owner-chemistry@ccl.net Tue Jul 17 11:55:00 2012 From: "uekstrom+/-gmail.com uekstrom+/-gmail.com" To: CCL Subject: CCL: Latest issue of Foundations of Chemistry Message-Id: <-47216-120717030521-10441-7+eGSb5nZGMLSTxgrPCiXA:+:server.ccl.net> X-Original-From: "uekstrom=gmail.com" Content-Type: text/plain; charset=ISO-8859-1 Date: Tue, 17 Jul 2012 09:05:15 +0200 MIME-Version: 1.0 Sent to CCL by: "uekstrom]|[gmail.com" [uekstrom]|[gmail.com] >On Tue, Jul 17, 2012 at 12:40 AM, Eric Scerri scerri:+:chem.ucla.edu wrote: > > >Foundations of Chemistry, Volume 14, Number 2 / July 2012 > >http://www.springerlink.com/content/1386-4238/14/2/ [..] Seriously? Can you at least make your posts mildly relevant to the CCL list? Aren't you past the point of desperate self promotion by spamming? Cheers, Ulf Ekstrom, University of Oslo From owner-chemistry@ccl.net Tue Jul 17 18:55:00 2012 From: "David A Mannock dmannock###ualberta.ca" To: CCL Subject: CCL: Any alternative to the TOPS server for drawing topological diagrams for PDB files? Message-Id: <-47217-120717150616-4571-eqbexNY9/giggKLUfHlBDg(-)server.ccl.net> X-Original-From: David A Mannock Content-Type: multipart/alternative; boundary=f46d04071785d183e104c50b3cac Date: Tue, 17 Jul 2012 13:06:02 -0600 MIME-Version: 1.0 Sent to CCL by: David A Mannock [dmannock{}ualberta.ca] --f46d04071785d183e104c50b3cac Content-Type: text/plain; charset=ISO-8859-1 A quick Google search using "Tops protein server" found the following sites. The first is a new link to the new TOPS server at Glasgow. Hope this helps you. Not all links on the home page are active. David http://www.brc.dcs.gla.ac.uk/projects/tops/ http://balabio.dcs.gla.ac.uk/drg/compare.html http://www.bioinf.org.uk/topscan/ http://fatcat.burnham.org/TOPS/ http://bioinformatics.burnham.org/pages/servers/ http://www.biochem.ucl.ac.uk/~roman/links/index.html On Tue, Jul 17, 2012 at 3:50 AM, Gerard Pujadas gerard.pujadas]*[gmail.com < owner-chemistry!^!ccl.net> wrote: > Dear CCL list members, > > first of all, sorry for cross-posting > > I would like to know if there is available any webserver (or software) > that can draws topological diagrams for PDB files following the idea that > was implemented some years ago at the TOPS webserver ( > http://www.tops.leeds.ac.uk/). This server is not running since 2008 and > it was quite useful in order to teach the protein architecture to my > students. Currently PDBSum provides topological diagrams for PDB entries ( > http://kpwu.wordpress.com/2006/02/14/pdbsum-announces-topology-diagrams-for-protein-domains/) > but, in my opinion, those formerly provided by TOPS where more intuitive to > correlate the diagram with the folding of the domain ... > > With many thanks in advances > > Yours sincerely > > -- > Gerard Pujadas > http://bioquimica.urv.cat/eng/fitxa.jsp?id=22 > Nutrigenomics Research Group > phone +34 977 55 (9565) > Biochemistry and Biotechnology Department > Office 106, Building N4, Campus Sescelades > Universitat Rovira i Virgili > Tarragona, Catalonia > > --f46d04071785d183e104c50b3cac Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable A quick Google search using "Tops protein server" found the follo= wing sites. The first is a new link to the new TOPS server at Glasgow. Hope= this helps you. Not all links on the home page are active. David

http://www.brc.dcs.= gla.ac.uk/projects/tops/

http://balabio.dcs.gla.ac.uk/drg/compare.html
http://www.bioinf.org.uk/tops= can/

http://fatcat.b= urnham.org/TOPS/

http://bioinformatics.burnham.org/pages/servers/

http:/= /www.biochem.ucl.ac.uk/~roman/links/index.html

On Tue, Jul 17, 2012 at 3:50 AM, Gerard Pujadas gerard.pujadas]*[= gmail.com <owner-chemistry!^!ccl.net<= /a>> wrote:
Dear CCL list members,

first of all, = sorry for cross-posting

I would like to know if there is available any webserver (or software)=20 that can draws topological diagrams for PDB files following the idea=20 that was implemented some years ago at the TOPS webserver (http://www.tops.leeds.ac.uk/= ). This server is not running since 2008 and it was quite useful in order to= =20 teach the protein architecture to my students. Currently PDBSum provides topological diagrams for PDB entries (http://kpwu.wordpress.com/2006/02/14/pdbsum-announces-topology-= diagrams-for-protein-domains/) but, in my opinion, those formerly provided by TOPS where more=20 intuitive to correlate the diagram with the folding of the domain ...

With many thanks in advances

Yours sincerely

--
G= erard Pujadas
http://bioquimica.urv.cat/eng/fitxa.jsp?id=3D22
Nutrigenomics Research Group
phone +34 977 55 (9565)
Biochemistry and Biotechnology Department
Office 106, Building N4, Campu= s Sescelades
Universitat Rovira i Virgili
Tarragona, Catalonia=


--f46d04071785d183e104c50b3cac-- From owner-chemistry@ccl.net Tue Jul 17 19:31:00 2012 From: "Tom Albright talbright%x%uh.edu" To: CCL Subject: CCL: Latest issue of Foundations of Chemistry Message-Id: <-47218-120717182025-19247-iO8cLnG6ux/9JuowSpJXoQ%%server.ccl.net> X-Original-From: Tom Albright Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=us-ascii Date: Tue, 17 Jul 2012 17:20:04 -0500 Mime-Version: 1.0 (Apple Message framework v1084) Sent to CCL by: Tom Albright [talbright!=!uh.edu] Seriously Ulf I rather enjoy seeing the contents of Frontiers of Chemistry. Yes, some of that material IS relevant to CCL. As for self promotion - one shouldn't live in a glass house... Cheers, On Jul 17, 2012, at 2:05 AM, uekstrom+/-gmail.com uekstrom+/-gmail.com wrote: > > Sent to CCL by: "uekstrom]|[gmail.com" [uekstrom]|[gmail.com] >> On Tue, Jul 17, 2012 at 12:40 AM, Eric Scerri scerri:+:chem.ucla.edu wrote: >> >> >> Foundations of Chemistry, Volume 14, Number 2 / July 2012 >> >> http://www.springerlink.com/content/1386-4238/14/2/ > > [..] > > Seriously? Can you at least make your posts mildly relevant to the CCL > list? Aren't you past the point of desperate self promotion by > spamming? > > Cheers, > Ulf Ekstrom, University of Oslo> >