From owner-chemistry@ccl.net Thu Apr 3 02:00:01 2008 From: "hxhgxy2 hxhgxy2~~163.com" To: CCL Subject: CCL: SYSMO package Message-Id: <-36627-080403012947-30390-hnR6G9kgjLoPyytDwVW8Og*|*server.ccl.net> X-Original-From: "hxhgxy2" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="gb2312" Date: Thu, 3 Apr 2008 12:46:57 +0800 Mime-Version: 1.0 Sent to CCL by: "hxhgxy2" [hxhgxy2{:}163.com] Dear All, I want computation the ring current of a system. Some reference indicate SYSMO package program can do it. How to get it? and is there any other program can computate the ring current? Thanks Ricky 2008-04-03 From owner-chemistry@ccl.net Thu Apr 3 03:54:01 2008 From: "Lukasz Cwiklik cwiklik{=}gmail.com" To: CCL Subject: CCL:G: Checkpoint files Message-Id: <-36628-080403035129-5845-x+qlvR4iHXLAHxW+hDs8HA**server.ccl.net> X-Original-From: "Lukasz Cwiklik" Content-Disposition: inline Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1 Date: Thu, 3 Apr 2008 09:49:43 +0300 MIME-Version: 1.0 Sent to CCL by: "Lukasz Cwiklik" [cwiklik]^[gmail.com] On Wed, Apr 2, 2008 at 11:23 PM, Soren Eustis soren~!~jhu.edu wrote: > I am having trouble reading in a checkpoint generated on a 64-bit linux > computer running G03 via webmo. When I download the checkpoint file > Gaussview and my other visualization programs are unable to open it. I have > tried formchk and unix2dos followed by formchk (as I am reading it on a > windows system). Dear Soren, You should use formchk and unix2dos in the opposite order, first - formchk to translate your checkpoint to a text file and only then format the text with unix2dos. So in my opinion this is, most likely, linux/dos issue. Best, Lukasz -- Lukasz Cwiklik http://cwiklik.wordpress.com From owner-chemistry@ccl.net Thu Apr 3 05:16:01 2008 From: "Pablo Vitoria pablo.vitoria()ehu.es" To: CCL Subject: CCL:G: Checkpoint files Message-Id: <-36629-080403043042-27159-T5kqwylpXFWd1vtNbbRIvg|server.ccl.net> X-Original-From: Pablo Vitoria Content-Type: multipart/mixed; boundary="------------020809020803050004040109" Date: Thu, 03 Apr 2008 09:58:36 +0200 MIME-Version: 1.0 Sent to CCL by: Pablo Vitoria [pablo.vitoria**ehu.es] This is a multi-part message in MIME format. --------------020809020803050004040109 Content-Type: text/plain; charset=windows-1252; format=flowed Content-Transfer-Encoding: 8bit Soren, You should use 'formchk -2' in the 64-bit linux computer to generate a formatted checkpoint file, and then either open this file with Gaussview in Windows; or use 'unfchk' in Windows to create a binary .chk file again. The '-2' option to formchk "should always be included when moving files between different types of computers", as stated in G03 manual. Regards Pablo Soren Eustis soren~!~jhu.edu escribió: > > I am having trouble reading in a checkpoint generated on a 64-bit > linux computer running G03 via webmo. When I download the checkpoint > file Gaussview and my other visualization programs are unable to open > it. I have tried formchk and unix2dos followed by formchk (as I am > reading it on a windows system). I have worked with checkpoint files > many times in the past. The difference here is I am working on a new > computer and the new elements are the 64-bit cpu and the Linux > operating system. > > Am I dealing with a unix to dos issue? If so, why doesn’t unix2dos > work? Is this somehow a 64-bit issue? > > Anyone encounter this before? > > Soren > > Soren N. Eustis > > Doctoral Candidate > > Department of Chemistry > > Johns Hopkins University > > Remsen Hall > > 3400 North Charles Street > > Baltimore, MD 21218 > > 410-516-4675 (office) > > 410-925-5167 (cell) > > 410-516-8420 (fax) > > soren{}jhu.edu > -- ******************************** Pablo Vitoria Garcia Servicios Generales de Rayos X Universidad del País Vasco (UPV/EHU) Fac. Ciencia y Tecnología, Edificio CD3 c/ Barrio Sarriena s/n, 48940 Leioa (Bizkaia) Tfno. +34 946015334 Fax +34 946013500 ******************************** --------------020809020803050004040109 Content-Type: text/x-vcard; charset=utf-8; name="pablo_vitoria.vcf" Content-Transfer-Encoding: 7bit Content-Disposition: attachment; filename="pablo_vitoria.vcf" begin:vcard fn;quoted-printable:Pablo Vitoria Garc=C3=ADa n;quoted-printable:Vitoria Garc=C3=ADa;Pablo org;quoted-printable:Universidad del Pa=C3=ADs Vasco (UPV/EHU);Servicios Generales de Rayos X adr;quoted-printable;quoted-printable:Barrio Sarriena s/n;;Facultad de Ciencia y Tecnolog=C3=ADa, edificio CD3;Leioa;Bizkaia;E-48940;Espa=C3=B1a email;internet:pablo.vitoria##ehu.es title;quoted-printable:T=C3=A9cnico SGIKer tel;work:946015334 tel;fax:946013500 tel;cell:660959834 version:2.1 end:vcard --------------020809020803050004040109-- From owner-chemistry@ccl.net Thu Apr 3 05:35:01 2008 From: "Raji Raji raji]*[anal.chem.tohoku.ac.jp" To: CCL Subject: CCL:G: emission spectrum Message-Id: <-36630-080403051130-10744-g71OiSMlWdpgOWFkUtiIvA::server.ccl.net> X-Original-From: "Raji Raji" Date: Thu, 3 Apr 2008 05:11:26 -0400 Sent to CCL by: "Raji Raji" [raji^^^anal.chem.tohoku.ac.jp] Dear Guanna Li and Thanos, I am not sure whether GaussView can draw the absorption/emission spectrum from the TDDFT or CIS output. But, the programme "SWIZARD" can give you the wavelength (also wavenumber) and absorption/emission intensity from the TDDFT/CIS output. From this data you can draw the spectrum. Also this programme can help you to draw: 1) Absorption spectrum - From TDDFT and CIS output 2) Emission spectrum - CIS output 3) Please note that the energy of the Pi-Pi* states predicted by the CIS calculations are known to be too large. So one has to scale the energy by a constant factor of 0.72 (as recommended by Broo and Holmen, J. Phys. Chem. A, 1997, 101, 3589). After scalling the energies (editing your output file manually), you can use SWIZARD programme and it will give you the corrected spectrum. I have checked this and it works well for me. Besides, its a kind of utility programme and very easy to use. Also its a freeware. It will hardly take few seconds to get the spectrum. Just give a try. Hope it helps. With Kind Regards, Raji. --------------------------------------------------------------------------- Sent to CCL by: "Guanna Li" [gnli%a%dicp.ac.cn] Dear Raji, You talked about the step to calculate emission spectrum. If gaussianview can draw the spectrum directly? or should we need other program to deal with the data? Thank you! Best wishes Guanna Li Best wishes Guanna Li From owner-chemistry@ccl.net Thu Apr 3 06:41:01 2008 From: "Jens Thomas j.m.h.thomas..dl.ac.uk" To: CCL Subject: CCL: MOL2 program viewer Message-Id: <-36631-080403063941-32636-ba9XX8qOLg4KvgDYv6LqJw%a%server.ccl.net> X-Original-From: Jens Thomas Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Thu, 03 Apr 2008 11:34:43 +0100 MIME-Version: 1.0 Sent to CCL by: Jens Thomas [j.m.h.thomas]=[dl.ac.uk] Dear Meslamani, As this is a question that is often asked on the CCL, we've just started trying to put together a list of some of the more common/specialised programs for building/visualising molecules on the Blue Obelisk site: http://blueobelisk.sourceforge.net/wiki/Tools_and_data_formats_for_chemical_data_handling#Building_and_visualising_molecules Many of the codes already on that list should be able to do what you are interested in. The list is not intended to be comprehensive, but if anyone has any suggestions of codes or features that should be listed in the table, please let me know (off-list please - I don't want to swamp the CCL with lots of "put my favourite code on there" emails :-) ). Best wishes, Jens jamel-eddine.meslamani*_*ulp.u-strasbg.fr wrote: > > Sent to CCL by: jamel-eddine.meslamani[A]ulp.u-strasbg.fr > Dear cclrs, > > Actually I'd like to know if there is an open source program that > could display molecules in mol2 format and to color all of them in a > one step. > I'm using linux as OS. > Thank you in advance for answers. > > Meslamani Jamelhttp://www.ccl.net/chemistry/sub_unsub.shtml> > Job: http://www.ccl.net/jobsConferences: > http://server.ccl.net/chemistry/announcements/conferences/> > > -- =================================================================== Jens Thomas, email: j.m.h.thomas=dl.ac.uk STFC Daresbury Lab, tel: +44-1925-603849 Warrington, fax: +44-1925-603634 WA4 4AD, UK. http: http://www.cse.scitech.ac.uk =================================================================== From owner-chemistry@ccl.net Thu Apr 3 07:54:01 2008 From: "Richard J Hart ric_hart(0)hotmail.com" To: CCL Subject: CCL: Formchk error Message-Id: <-36632-080403075227-32629-fYCuBQgr8t0aQrQonCNlTg%a%server.ccl.net> X-Original-From: "Richard J Hart" Date: Thu, 3 Apr 2008 07:52:24 -0400 Sent to CCL by: "Richard J Hart" [ric_hart|a|hotmail.com] Hi, Does anybody recognise this error when trying to formchk? "Atom out of range in LodBCor. Error termination via Lnk1e at......" "LodBCor" returns absolutely nothing when google searched, and I have no idea what it means. Thanks, Ric From owner-chemistry@ccl.net Thu Apr 3 13:15:01 2008 From: "Boyd, D. boyd[#]chem.iupui.edu" To: CCL Subject: CCL: Early Comp groups in industry Message-Id: <-36633-080403131152-12853-YSPuiWoNMQJZUH0wyZsl5Q%%server.ccl.net> X-Original-From: "Boyd, D." Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=us-ascii Date: Thu, 03 Apr 2008 13:11:48 -0500 MIME-Version: 1.0 Sent to CCL by: "Boyd, D." [boyd!A!chem.iupui.edu] Allen, That would be useful information that you are trying to collect about the early history. I would be interested in seeing a summary. For a discussion of the early history, I refer you to two book chapters: History of Computers in Pharmaceutical Research and Development: A Narrative. D. B. Boyd and M. M. Marsh, in Computer Applications in Pharmaceutical Research and Development, S. Ekins, Ed., Wiley, New York, 2006, pp. 1-50. How Computational Chemistry Became Important in the Pharmaceutical Industry. D. B. Boyd, in Reviews in Computational Chemistry, K. B. Lipkowitz and T. Cundari, Eds., Wiley-VCH, New York, 2007, Vol. 23, pp. 401- 451. These chapters cite your NetSci website, which is very useful. I would send you reprints, but I have none. Good luck. Don From owner-chemistry@ccl.net Thu Apr 3 16:08:01 2008 From: "gestionnaire licpro licpro.dechets^-^gmail.com" To: CCL Subject: CCL:G: Can HOMO have a positive energy? Message-Id: <-36634-080403141200-11360-8/uBRLEnlTCrS7r2KxhNfA{}server.ccl.net> X-Original-From: "gestionnaire licpro" Content-Type: multipart/alternative; boundary="----=_Part_2586_9587515.1207243022471" Date: Thu, 3 Apr 2008 19:17:02 +0200 MIME-Version: 1.0 Sent to CCL by: "gestionnaire licpro" [licpro.dechets]*[gmail.com] ------=_Part_2586_9587515.1207243022471 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline Dear cclers, I am Sorry in advence for this trivial question !!! Can HOMO have a positive energy? Because I performed recently a DFT 6-31g calculation on charged molecules with g03. After long hour of scf, my calculation converged well and I get positive HOMO energy. I thought that the eigenvalues must be negative !! Thank you for your help, Jeff ------=_Part_2586_9587515.1207243022471 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Content-Disposition: inline

Dear cclers,

 

I am Sorry in adve= nce for this trivial question !!!

 

Can HOMO have a po= sitive energy?  Because I per= formed recently a DFT 6-31g calculation on charged molecules with g03. Afte= r long hour of scf, my calculation converged well and I get positive HOMO e= nergy. I thought  that the= eigenvalues must be negative !!

 

Thank you for your help,

Jeff

------=_Part_2586_9587515.1207243022471-- From owner-chemistry@ccl.net Thu Apr 3 16:52:01 2008 From: "Alcides Simao alsimao-*-gmail.com" To: CCL Subject: CCL:G: Formchk error Message-Id: <-36635-080403164833-10441-sR7aJxqWE69zAeRO9RrZnw _ server.ccl.net> X-Original-From: "Alcides Simao" Content-Disposition: inline Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1 Date: Thu, 3 Apr 2008 21:48:21 +0100 MIME-Version: 1.0 Sent to CCL by: "Alcides Simao" [alsimao]|[gmail.com] Dear Ric, If you are using GAUSSIAN, your error appears due to the fact that the GAUSSIAN version of your computed checkpoint file is older than the version you're using to translate. Please, try to use the same program version that you used to make the calculation. Best, Al From owner-chemistry@ccl.net Thu Apr 3 17:34:01 2008 From: "John McKelvey jmmckel===gmail.com" To: CCL Subject: CCL:G: Can HOMO have a positive energy? Message-Id: <-36636-080403162146-27018-EWczmJ5prg3hlF3oD9C7tg]^[server.ccl.net> X-Original-From: "John McKelvey" Content-Type: multipart/alternative; boundary="----=_Part_5351_33383527.1207254094554" Date: Thu, 3 Apr 2008 16:21:34 -0400 MIME-Version: 1.0 Sent to CCL by: "John McKelvey" [jmmckel[a]gmail.com] ------=_Part_5351_33383527.1207254094554 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline Is the molecule negatively charged? Positive HOMOS can ofter happen under such circumstances. Cheers, John McKelvey On Thu, Apr 3, 2008 at 1:17 PM, gestionnaire licpro licpro.dechets^-^ gmail.com wrote: > Dear cclers, > > > > I am Sorry in advence for this trivial question !!! > > > > Can HOMO have a positive energy? Because I performed recently a DFT 6-31g > calculation on charged molecules with g03. After long hour of scf, my > calculation converged well and I get positive HOMO energy. I thought that > the eigenvalues must be negative !! > > > > Thank you for your help, > > Jeff > ------=_Part_5351_33383527.1207254094554 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline Is the molecule negatively charged?  Positive HOMOS can ofter happen under such circumstances.

Cheers,

John McKelvey

On Thu, Apr 3, 2008 at 1:17 PM, gestionnaire licpro licpro.dechets^-^gmail.com <owner-chemistry() ccl.net> wrote:

Dear cclers,

 

I am Sorry in advence for this trivial question !!!

 

Can HOMO have a positive energy?  Because I performed recently a DFT 6-31g calculation on charged molecules with g03. After long hour of scf, my calculation converged well and I get positive HOMO energy. I thought  that the eigenvalues must be negative !!

 

Thank you for your help,

Jeff


------=_Part_5351_33383527.1207254094554-- From owner-chemistry@ccl.net Thu Apr 3 18:24:01 2008 From: "Nicholas Labello label030-*-umn.edu" To: CCL Subject: CCL:G: Can HOMO have a positive energy? Message-Id: <-36637-080403182248-22422-wqbBvo1KvyyKDN6vxFYqyQ^-^server.ccl.net> X-Original-From: Nicholas Labello Content-Type: multipart/alternative; boundary="------------080004090202080006090100" Date: Thu, 03 Apr 2008 17:22:20 -0500 MIME-Version: 1.0 Sent to CCL by: Nicholas Labello [label030|,|umn.edu] This is a multi-part message in MIME format. --------------080004090202080006090100 Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit Hi Jeff, A positive HOMO eigenvalue could be a sign that the theoretical treatment you are using is inappropriate for the system, or that the system itself is not stable. If the charge is negative (as the HOMO is positive, it almost certainly is) the basis set 6-31G is not adequate. For an anion diffuse functions are a necessity. Additional functions allow the density to relax and polarize significantly lowering the total energy with the largest effect realized on the valence orbitals. The first step here is to rerun with 6-31+G* or larger. Nick gestionnaire licpro licpro.dechets^-^gmail.com wrote: > > Dear cclers, > > > > I am Sorry in advence for this trivial question !!! > > > > Can HOMO have a positive energy? Because I performed recently a DFT > 6-31g calculation on charged molecules with g03. After long hour of > scf, my calculation converged well and I get positive HOMO energy. I > thought that the eigenvalues must be negative !! > > > > Thank you for your help, > > Jeff > -- *Nicholas Labello Postdoctoral Associate* /Center for Drug Design The University of Minnesota 308 Harvard Street Minneapolis, MN 55455 (612) 626-4429/ --------------080004090202080006090100 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Hi Jeff,

A positive HOMO eigenvalue could be a sign that the theoretical treatment you are using is inappropriate for the system, or that the system itself is not stable.  If the charge is negative (as the HOMO is positive, it almost certainly is) the basis set 6-31G is not adequate. For an anion diffuse functions are a necessity.  Additional  functions allow the density to relax and polarize significantly lowering the total energy with the largest effect realized on the valence orbitals.  The first step here is to rerun with 6-31+G* or larger. 

Nick

gestionnaire licpro licpro.dechets^-^gmail.com wrote:

Dear cclers,

 

I am Sorry in advence for this trivial question !!!

 

Can HOMO have a positive energy?  Because I performed recently a DFT 6-31g calculation on charged molecules with g03. After long hour of scf, my calculation converged well and I get positive HOMO energy. I thought  that the eigenvalues must be negative !!

 

Thank you for your help,

Jeff


--
Nicholas Labello
Postdoctoral Associate
Center for Drug Design
The University of Minnesota
308 Harvard Street
Minneapolis, MN 55455
(612) 626-4429

--------------080004090202080006090100-- From owner-chemistry@ccl.net Thu Apr 3 18:59:00 2008 From: "Eduard Matito ematito%%gmail.com" To: CCL Subject: CCL: similarity of different molecules Message-Id: <-36638-080403182250-22459-GHa3AL4khZxupve5hNN5Dw###server.ccl.net> X-Original-From: Eduard Matito Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Thu, 03 Apr 2008 22:37:17 +0200 MIME-Version: 1.0 Sent to CCL by: Eduard Matito [ematito..gmail.com] Some papers: - R.Carbó,L.Leyda,M.Arnau. "How similar is a molecule to another? An electron density measure of similarity between two molecular structures", Int.J.Quantum Chemistry, 17 (1980) 1185 - MESSEM: A Quantum molecular similarity system of programs, *E. Besalú, R. Carbó, M. Duran, J. Mestres, M. Solà*, Methods and techniques in computational chemistry (METECC-95), E. Clementi and G. Corongiu (Eds.), STEF, Cagliari, 1995, 491-508 Software: MEssEM program. It's a bit old, but it can do the work and it's freeware. You can download it from here: http://iqc.udg.edu/~miquel/mike.html Hope it helps, Eduard > Sent to CCL by: "Diego Moreno" [dvmorenor~~unal.edu.co] > Sent to CCL by: "JunJun Liu" [ljjlp03\a/gmail.com] > Hello everybody, > > I want to know how similar two different molecules are. Does anybody know how to do this? Any suggestions regarding algorithms or softwares are highly appreciated! > > Thanks in advance! > > Junjun > -- Eduard Matito Postdoctoral Researcher Lundbeck Foundation, Center for Theoretical Chemistry Univer sity of Aarhus, Aarhus (Denmark) http://lctc.dcmedia.dk/index.php?id=77 From owner-chemistry@ccl.net Thu Apr 3 19:34:00 2008 From: "Aleksey Kuznetsov AlexKuznetsov2007||yandex.ru" To: CCL Subject: CCL:G: Can HOMO have a positive energy? Message-Id: <-36639-080403180224-31181-6Rw5uW0NhbZK4J0M7JDS4g..server.ccl.net> X-Original-From: Aleksey Kuznetsov Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=KOI8-R Date: Fri, 04 Apr 2008 01:16:46 +0400 MIME-Version: 1.0 Sent to CCL by: Aleksey Kuznetsov [AlexKuznetsov2007=-=yandex.ru] Dear Jeff, sure, for negatively chargedšspeciesšthe HOMO energy can be positive. I deal a lot withšmultiply charged anions and they have positive energies of HOMOs.š With best regards, Aleksey. 03.04.08, 21:17, "gestionnaire licpro licpro.dechets^-^gmail.com" : >Dear cclers, > >š > > >I am Sorry in advence for this trivial questionš!!! > > >Can HOMO have a positive energy? šBecause I performed recently a DFT 6-31g calculation on charged molecules with g03. After long hour of scf, my calculation converged well and I get positive HOMO energy.Ithought šthat the eigenvalues must be negative !! > > >Thank you for your help, > > >Jeff ------------------------------------------- Dr. Aleksey Kuznetsov Cherry L. Emerson Center for Scientific Computation Emory University 1515 Dickey Drive Atlanta, GA 30322 USA Phone: (404)727-2381 Email: akuznets-$-euch4e.chem.emory.edu ------------------------------------------- From owner-chemistry@ccl.net Thu Apr 3 22:27:00 2008 From: "Mikael Johansson mpjohans]=[chem.au.dk" To: CCL Subject: CCL:G: Can HOMO have a positive energy? Message-Id: <-36640-080403175135-21815-f41WYhYubFOFcbe0tZsNbw,,server.ccl.net> X-Original-From: Mikael Johansson Content-Disposition: inline Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=UTF-8; DelSp="Yes"; format="flowed" Date: Thu, 03 Apr 2008 22:57:24 +0200 MIME-Version: 1.0 Sent to CCL by: Mikael Johansson [mpjohans_-_chem.au.dk] Hello Jeff! On Thu, 03 Apr 2008 "gestionnaire licpro licpro.dechets^-^gmail.com" =20 wrote: > Can HOMO have a positive energy? Because I performed recently a DFT 6-31g > calculation on charged molecules with g03. After long hour of scf, my > calculation converged well and I get positive HOMO energy. I thought that > the eigenvalues must be negative !! Yes, due to the electron self interaction error present in most =20 functionals, anions easily get positive energies assigned to their =20 highest occupied orbitals. If the energy of the anion is higher than =20 that of the corresponding neutral (or less negatively charged) =20 species, this means that DFT cannot describe the system properly; =20 increasing the basis set would show that the electron(s) is unbound =20 and would leave the system. A brief discussion on this can be found in: D.J. Tozer, F. De Proft, "Computation of the Hardness and the Problem =20 of Negative Electron Affinities in Density Functional Theory", J. =20 Phys. Chem. A 109 (2005) 8923-8929. I'm sure there are more complete reviews on the topic available, too. Have a nice day, Mikael J. http://www.iki.fi/~mpjohans ---------------------------------------------------------------- This message was sent using IMP, the Internet Messaging Program.