From owner-chemistry@ccl.net Wed Jul 26 02:15:00 2006 From: "nokophala]=[aim.com" To: CCL Subject: CCL: magnetic field Message-Id: <-32252-060725023459-1406-ADPZSnZBydNLOQx1ls+izg _ server.ccl.net> X-Original-From: nokophala---aim.com Content-Type: multipart/alternative; boundary="--------MailBlocks_8C87DCB912D8BB4_C5C_11D24_FWM-M08.sysops.aol.com" Date: Tue, 25 Jul 2006 02:34:51 -0400 MIME-Version: 1.0 Sent to CCL by: nokophala : aim.com ----------MailBlocks_8C87DCB912D8BB4_C5C_11D24_FWM-M08.sysops.aol.com Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: 7bit Hi All, I asked a question a while ago on whether there is software that one can use to calculate electronic structure/properties in the presence of an applied magnetic field. Thanks to Jeff Hammond who pointed out that there is some formalisms like GIAO and many other codes that can calculate magnetic properties. I will do a search on these. However, I am still uncertain as to whether the various codes calculate magnetic properties of the materials under study, or whether electronic properties are calculated 'in the presence of an applied external magnetic field'. It is the latter that I am interested in. Pointers to any recent publications will be appreciated. Kind regards, Noko ________________________________________________________________________ Check Out the new free AIM(R) Mail -- 2 GB of storage and industry-leading spam and email virus protection. ----------MailBlocks_8C87DCB912D8BB4_C5C_11D24_FWM-M08.sysops.aol.com Content-Type: text/html; charset="us-ascii" Content-Transfer-Encoding: 7bit

Hi All,

I asked a question a while ago on whether there is software that one can use to calculate electronic structure/properties in the presence of an applied magnetic field. Thanks to Jeff Hammond who pointed out that there is some formalisms like GIAO and many other codes that can calculate magnetic properties. I will do a search on these.

However, I am still uncertain as to whether the various codes calculate magnetic properties of the materials under study, or whether electronic properties are calculated 'in the presence of an applied external magnetic field'. It is the latter that I am interested in. Pointers to any recent publications will be appreciated.

Kind regards,

Noko

Check Out the new free AIM(R) Mail -- 2 GB of storage and industry-leading spam and email virus protection.

----------MailBlocks_8C87DCB912D8BB4_C5C_11D24_FWM-M08.sysops.aol.com-- From owner-chemistry@ccl.net Wed Jul 26 04:40:00 2006 From: "Sue Lam chsue2004=-=yahoo.com" To: CCL Subject: CCL:G: [CCL] PCM problem Message-Id: <-32253-060726043916-32594-pHDsReG8D4F4ySgQbhdLdQ ~ server.ccl.net> X-Original-From: Sue Lam Content-Transfer-Encoding: 8bit Content-Type: multipart/alternative; boundary="0-911563987-1153903150=:71082" Date: Wed, 26 Jul 2006 01:39:10 -0700 (PDT) MIME-Version: 1.0 Sent to CCL by: Sue Lam [chsue2004+/-yahoo.com] --0-911563987-1153903150=:71082 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit Did your calculated molecule have symmetry? I had the same problem before and I put nosym keyword. Evantually, it worked "ALBERT POATER TEIXIDOR albert.poater^-^udg.es" wrote: Sent to CCL by: "ALBERT POATER TEIXIDOR" [albert.poater:-:udg.es] Dear PCM users of Gaussian, I have made trials with all the mails I received and no solution is available for my system. I receive the following error message: ------------------------------------------------------------------------------ Polarizable Continuum Model (PCM) ================================= Model : PCM. Atomic radii : UA0 (Simple United Atom Topological Model). Polarization charges : Total charges. Charge compensation : None. Solution method : Matrix inversion. Cavity : GePol (RMin=0.200 OFac=0.890). Default sphere list used, NSphG= 39. Tesserae with average area of 0.200 Ang**2. Solvent : Water, Eps= 78.390000. ------------------------------------------------------------------------------ Using symmetry in molecular cavity generation. AdVTs1: ISph= 714 is engulfed by JSph= 716 but Ae( 714) is not yet zero! Error termination via Lnk1e in /estufa/soft/g03pedro/g03/l301.exe at Tue Jul 25 10:49:41 2006. Job cpu time: 0 days 0 hours 0 minutes 5.6 seconds. File lengths (MBytes): RWF= 11 Int= 0 D2E= 0 Chk= 1 Scr= 1 Anyone has any idea of what to do?http://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt__________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com --0-911563987-1153903150=:71082 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: 8bit Did your calculated molecule have symmetry? I had the same problem before and I put nosym keyword. Evantually, it worked

"ALBERT POATER TEIXIDOR albert.poater^-^udg.es" <owner-chemistry(!)ccl.net> wrote:

Sent to CCL by: "ALBERT POATER TEIXIDOR" [albert.poater:-:udg.es]
Dear PCM users of Gaussian,
I have made trials with all the mails I received and no solution is
available for my system. I receive the following error message:
------------------------------------------------------------------------------
Polarizable Continuum Model (PCM)
=================================
Model : PCM.
Atomic radii : UA0 (Simple United Atom Topological Model).
Polarization charges : Total charges.
Charge compensation : None.
Solution method : Matrix inversion.
Cavity : GePol (RMin=0.200 OFac=0.890).
Default sphere list used, NSphG= 39.
Tesserae with average area of 0.200 Ang**2.
Solvent : Water, Eps= 78.390000.
------------------------------------------------------------------------------
Using symmetry in molecular cavity generation.
AdVTs1: ISph= 714 is engulfed by JSph= 716 but Ae( 714) is not yet zero!
Error termination via Lnk1e in /estufa/soft/g03pedro/g03/l301.exe at Tue
Jul 25 10:49:41 2006.
Job cpu time: 0 days 0 hours 0 minutes 5.6 seconds.
File lengths (MBytes): RWF= 11 Int= 0 D2E= 0 Chk= 1
Scr= 1

Anyone has any idea of what to do?

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http://mail.yahoo.com --0-911563987-1153903150=:71082-- From owner-chemistry@ccl.net Wed Jul 26 05:51:01 2006 From: "Raji Raji raji+*+anal.chem.tohoku.ac.jp" To: CCL Subject: CCL:G: CCL PCM problem Message-Id: <-32254-060726054953-27482-JOz924HG+FT3IRQNX5aRoA(~)server.ccl.net> X-Original-From: "Raji Raji" Date: Wed, 26 Jul 2006 05:49:53 -0400 Sent to CCL by: "Raji Raji" [raji _ anal.chem.tohoku.ac.jp] Dear Dr.ALBERT POATER TEIXIDOR, 1) Some times back the same question was posted in CCL and Dr. Hess gave the following explanation and I personally tried this, it is working for me. "This is a problem that sometimes occurs when Gaussian is using a very large number of added spheres to built the cavity. In most cases, specifying "scrf=read" and supplying the PCM options "OFAC=0.8 RMIN=0.5" will resolve the issue. These options decrease the number of added spheres." 2)Dr.Luis Simon gave the following explanation : I had the same problem. Try the following: scfr (solvent=-the solvent that you want to use-, read, pcm -or cpcm-)and after the molecule coordinates, leave one blank line and write the following: RADII=UAKS or RADII=UFF. The problem is related with the way that it is used to generate the cavity. Probably one H atom is located far from any of the heavy atoms, and UA0 does not generate a cavity for H atoms (I think so, but surely someone will give you a more detailed information in ccl) but enclosed H atoms in the cavity of heavy atoms. Both UAKS (recommended for cpcm) and UFF requires more calculation time than UA0, but they will hopefully allow you to obtain the results. If you came from G98, you had never find this problem. I think that defaults of PCM and CPCM have changed between G98 and G03. I hope it helps. Best Regards, Raji. From owner-chemistry@ccl.net Wed Jul 26 12:28:00 2006 From: "Kurt De Grave kurt.degrave^_^pharmadm.com" To: CCL Subject: CCL: new hypothesis formulation software Message-Id: <-32255-060726110142-19754-kC3jADUAzy4UQ8MwUVg/HA^server.ccl.net> X-Original-From: "Kurt De Grave" Date: Wed, 26 Jul 2006 11:01:42 -0400 Sent to CCL by: "Kurt De Grave" [kurt.degrave ~~ pharmadm.com] Hi, I'd like to announce our recently released DMax Chemistry Assistant (TM) software. It constructs descriptive rules (hypotheses) that discriminate molecules with a high or low value for a given target property. You can then apply the rules to new cases for property prediction or ranking, or use them as a guideline to design new molecules. This software is build on relational data mining (ILP) technology licensed from the universities of Leuven, Oxford and Aberystwyth. URL: http://www.pharmadm.com/DMaxChemistryAssistant.asp The software is available for selected versions of Windows and Linux. kurt. From owner-chemistry@ccl.net Wed Jul 26 13:02:01 2006 From: "JunJun Liu ljjlp03]![gmail.com" To: CCL Subject: CCL: seeking free chemical geometry builder software in Linux Message-Id: <-32256-060726123427-1894-VnuubneqKp0u71cLiWQJbA|*|server.ccl.net> X-Original-From: "JunJun Liu" Content-Transfer-Encoding: 8bit Content-Type: text/plain; format=flowed; delsp=yes; charset=utf-8 Date: Wed, 26 Jul 2006 12:35:57 -0300 MIME-Version: 1.0 Sent to CCL by: "JunJun Liu" [ljjlp03||gmail.com] Hi all, I'm wondering if there's a free chemical geometry builder software under Linux. I hope this builder can handle two seperate molecules respectively in one window. For example, with molecule A being fixed, molecule B can be rotated/translated to close to molecule A in a desired orientation. Any recommendations are welcome and appreciated! Regards! Liu -- JunJun Liu College of Chemistry Central China Normal University WuHan 430079 P.R. China From owner-chemistry@ccl.net Wed Jul 26 13:37:00 2006 From: "huanglei huanglei],[mail.utexas.edu" To: CCL Subject: CCL: seeking free chemical geometry builder software in Linux Message-Id: <-32257-060726133400-10225-Iwn/6U+fkBBCqp75C0BFnw*server.ccl.net> X-Original-From: "huanglei" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="gb2312" Date: Wed, 26 Jul 2006 12:40:52 -0600 Mime-Version: 1.0 Sent to CCL by: "huanglei" [huanglei a mail.utexas.edu] Dear JunJun Liu ljjlp03]![gmail.com, VMD can work perfectly. Good luck! lei ======= 2006-07-26 11:06:07 ======= >Sent to CCL by: "JunJun Liu" [ljjlp03||gmail.com] >Hi all, > >I'm wondering if there's a free chemical geometry builder software under >Linux. I hope this builder can handle two seperate molecules respectively >in one window. For example, with molecule A being fixed, molecule B can be >rotated/translated to close to molecule A in a desired orientation. Any >recommendations are welcome and appreciated! > >Regards! > >Liu > >-- >JunJun Liu > >College of Chemistry >Central China Normal University >WuHan 430079 >P.R. China> > From owner-chemistry@ccl.net Wed Jul 26 14:23:00 2006 From: "JunJun Liu ljjlp03..gmail.com" To: CCL Subject: CCL: seeking free chemical geometry builder software in Linux Message-Id: <-32258-060726142223-30635-EPXKvjkYqodAZjOcnUdncQ .. server.ccl.net> X-Original-From: "JunJun Liu" Content-Transfer-Encoding: 8bit Content-Type: text/plain; format=flowed; delsp=yes; charset=utf-8 Date: Wed, 26 Jul 2006 14:23:53 -0300 MIME-Version: 1.0 Sent to CCL by: "JunJun Liu" [ljjlp03() gmail.com] Hi Lei, I only know VMD has a plugin molefacture which can do a few operation on a small molecule. I don't know it can rotate/translate one molecule to another molecule. Can you tell me a bit more details about this? Thanks! By the way, I'm not saying a displayer but a builder, which can build/construct molecular geometry just like InsightII. Thanks! On Wed, 26 Jul 2006 14:38:47 -0300, huanglei huanglei],[mail.utexas.edu wrote: > Sent to CCL by: "huanglei" [huanglei a mail.utexas.edu] > Dear JunJun Liu ljjlp03]![gmail.com, > > VMD can work perfectly. Good luck! > > lei > > > ======= 2006-07-26 11:06:07 ======= > >> Sent to CCL by: "JunJun Liu" [ljjlp03||gmail.com] >> Hi all, >> >> I'm wondering if there's a free chemical geometry builder software under >> Linux. I hope this builder can handle two seperate molecules >> respectively >> in one window. For example, with molecule A being fixed, molecule B can >> be >> rotated/translated to close to molecule A in a desired orientation. Any >> recommendations are welcome and appreciated! >> >> Regards! >> >> Liu >> >> -- >> JunJun Liu >> >> College of Chemistry >> Central China Normal University >> WuHan 430079 >> P.R. China> From owner-chemistry@ccl.net Wed Jul 26 14:58:00 2006 From: "Rafal A. Bachorz rafal.bachorz_._chemie.uni-karlsruhe.de" To: CCL Subject: CCL: seeking free chemical geometry builder software in Linux Message-Id: <-32259-060726142216-30614-orcwBrgwMfvjAZaUS2yZiQ**server.ccl.net> X-Original-From: "Rafal A. Bachorz" Content-Disposition: inline Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="utf-8" Date: Wed, 26 Jul 2006 19:38:28 +0200 MIME-Version: 1.0 Sent to CCL by: "Rafal A. Bachorz" [rafal.bachorz],[chemie.uni-karlsruhe.de] > I'm wondering if there's a free chemical geometry builder software under > Linux. I hope this builder can handle two seperate molecules respectively > in one window. For example, with molecule A being fixed, molecule B can be > rotated/translated to close to molecule A in a desired orientation. Any > recommendations are welcome and appreciated! Hi Liu, You might check ECCE (graphical interface to NWChem). The molecular builder of ECCE has the feature you have mentioned. It is possible to operate on one molecule (rotation, translation) when other parts of you system are fixed. This software works under Linux and is free of charge. Here you have a link http://ecce.emsl.pnl.gov/ Have fun! Best regards, -- Rafal Bachorz University of Karlsruhe From owner-chemistry@ccl.net Wed Jul 26 19:51:01 2006 From: "Petrina Kamya kpetrina2(a)yahoo.com" To: CCL Subject: CCL:G: Graphic visualization software compatible with G03 Message-Id: <-32260-060726165639-22220-7dTr0ypoI29Ksm/XxS3uXg.:.server.ccl.net> X-Original-From: "Petrina Kamya" Date: Wed, 26 Jul 2006 16:56:39 -0400 Sent to CCL by: "Petrina Kamya" [kpetrina2|-|yahoo.com] Hi, I am wondering if anyone knows of a graphic visualization software program that has similar capabilities to Molekel that is compatible with Gaussian 03? Thankyou. Petrina From owner-chemistry@ccl.net Wed Jul 26 21:39:00 2006 From: "Agalya G agalya81 ~ gmail.com" To: CCL Subject: CCL: Radical cation Message-Id: <-32261-060726042117-31799-5dy6Gz/VurkND9XyadKnkQ]~[server.ccl.net> X-Original-From: "Agalya G" Date: Wed, 26 Jul 2006 04:21:16 -0400 Sent to CCL by: "Agalya G" [agalya81#%#gmail.com] How to model compounds with radical cation or anion? Is it ok, if i do unrestricted calculation with doblet multiplicity and charge +1 for radical cation? From owner-chemistry@ccl.net Wed Jul 26 22:15:00 2006 From: "Masahiko Suenaga alohascc() mbox.nc.kyushu-u.ac.jp" To: CCL Subject: CCL:G: Graphic visualization software compatible with G03 Message-Id: <-32262-060726221113-436-ed08AOL+UMvUd2a7tvtIdQ_-_server.ccl.net> X-Original-From: Masahiko Suenaga Content-Type: text/plain; charset=us-ascii Date: Thu, 27 Jul 2006 11:10:55 +0900 Mime-Version: 1.0 Sent to CCL by: Masahiko Suenaga [alohascc(!)mbox.nc.kyushu-u.ac.jp] Try Facio. http://www1.bbiq.jp/zzzfelis/Facio.html It's a freeware. Although Facio is a native application of Windows environment, it also works on Linux (FedoraCore4 and Scientific Linux) with a help of WINE and Mesa. Facio is introduced at Gaussian's official web site (Links to Related Sites). http://www.gaussian.com/links_top_level.htm Facio's selected features related to Gaussian 03 are as follows. (1) Visualization of molecular orbitals, electron density (2) Visualization of normal mode of vibration as animated model. (3) Mapping electrostatic potential on solvent excluded surface (4) Visualization of IRC and trajectory structure sequence (5) Simulation of IR, Raman and VCD spectrum (6) Assigning atoms to ONIOM layers (7) SSH/SFTP client for remote Gaussian job Another feature of this software is advanced capabilities for molecular modelling. For example, with molecule A being fixed, molecule B can be rotated/translated to close to molecule A in a desired orientation. It's an easy job for Facio. Best regards, Masahiko Suenaga, Ph.D. Department of Chemistry, Faculty of Sciences, Kyushu University, Japan > Sent to CCL by: "Petrina Kamya" [kpetrina2|-|yahoo.com] > Hi, > I am wondering if anyone knows of a graphic visualization software program that has similar capabilities to Molekel that is compatible with Gaussian 03? > Thankyou. > Petrina > -- Masahiko Suenaga alohascc||mbox.nc.kyushu-u.ac.jp From owner-chemistry@ccl.net Wed Jul 26 22:49:00 2006 From: "jerome * scs.uiuc.edu" To: CCL Subject: CCL:G: Graphic visualization software compatible with G03 Message-Id: <-32263-060726211445-12870-pzYVOMTxrbtVkkD1ukl2+g|,|server.ccl.net> X-Original-From: jerome()scs.uiuc.edu Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="utf-8"; format=flowed Date: Wed, 26 Jul 2006 19:34:32 -0500 Mime-Version: 1.0 Sent to CCL by: jerome : scs.uiuc.edu > Sent to CCL by: "Petrina Kamya" [kpetrina2|-|yahoo.com] > I am wondering if anyone knows of a graphic visualization software program that has similar capabilities to Molekel that is compatible with Gaussian 03? Try Gabedit: http://lasim.univ-lyon1.fr/allouche/gabedit/ From owner-chemistry@ccl.net Wed Jul 26 23:24:00 2006 From: "Lalinda N Palliyaguru lalinda|temple.edu" To: CCL Subject: CCL:G: How to include effective core potentials in Gau. Message-Id: <-32264-060725115702-19570-s3MeTf3BJvDvEX8NgB5rVw##server.ccl.net> X-Original-From: "Lalinda N Palliyaguru" Date: Tue, 25 Jul 2006 11:56:59 -0400 Sent to CCL by: "Lalinda N Palliyaguru" [lalinda#%#temple.edu] Dear Sir I am trying to do a CIS calculation for the excited states for CH2BrI, I would like to use effective core potentials for Halogens, Could you please tell me where to include those potentials in the gaussian job file? thanks Lalinda Palliyaguru From owner-chemistry@ccl.net Wed Jul 26 23:58:00 2006 From: "Joaquin Barroso Flores joaco_barroso\a/yahoo.com" To: CCL Subject: CCL:G: Molecular orbital energies plot Message-Id: <-32265-060726231146-7302-KaY3O9JjCUb0BClTSpjHFw^^^server.ccl.net> X-Original-From: Joaquin Barroso Flores Content-Transfer-Encoding: 8bit Content-Type: multipart/alternative; boundary="0-1486014701-1153968297=:40347" Date: Wed, 26 Jul 2006 21:44:57 -0500 (CDT) MIME-Version: 1.0 Sent to CCL by: Joaquin Barroso Flores [joaco_barroso^^^yahoo.com] --0-1486014701-1153968297=:40347 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit Hi, One of the latest versions of gaussview (in case you are usign Gaussian) can display some nice MO diagrams. Joaqu�n "C. Garoufalis garoufal__physics.upatras.gr" escribi�: Sent to CCL by: "C. Garoufalis" [garoufal__physics.upatras.gr] You can also use Origin with a data file of the form: 1 -87.121 1 -87.120 1 . 1 . 1 . 1 -80.205 1 -80.016 Do a scater graph and then choose very small symbol size an choose the option "drop line horizontally" I guess that you can also follow the same method with Excell Mpourmpakis Giannis gbourb . chemistry.uoc.gr wrote: > Sent to CCL by: Mpourmpakis Giannis [gbourb*chemistry.uoc.gr] > You can try the Origin program. Use the symbol "line" instead the square > and you can plot > the levels. Best regards, > Giannis > > > > Agalya Govindasamy agalya81|,|gmail.com wrote: > > >> Sent to CCL by: "Agalya Govindasamy" [agalya81(-)gmail.com] >> I have molecular orbital energies of some systems and i want to plot them >> in a single figure and compare the energy levels. I am not able to do >> this using Excel. Could anyone please tell if there is any software to make >> molecular orbital energy level plots.> >> >> >> >> >> >> > > > > -- ------------------------------------------------- Dr. Christos S. Garoufalis Dept. of Physics, Univ. of Patras, Greece email: garoufal(-)physics.upatras.gr Tel. +30 2610 997729 -------------------------------------------------http://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt__________________________________________________ Correo Yahoo! Espacio para todos tus mensajes, antivirus y antispam �gratis! Reg�strate ya - http://correo.yahoo.com.mx/ --0-1486014701-1153968297=:40347 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: 8bit

Hi,

One of the latest versions of gaussview (in case you are usign Gaussian) can display some nice MO diagrams.

Joaqu�n

"C. Garoufalis garoufal__physics.upatras.gr" <owner-chemistry^^ccl.net> escribi�:

Sent to CCL by: "C. Garoufalis" [garoufal__physics.upatras.gr]

You can also use Origin with a data file of the form:

1 -87.121
1 -87.120
1 .
1 .
1 .
1 -80.205
1 -80.016

Do a scater graph and then choose very small symbol size an choose the
option "drop line horizontally"

I guess that you can also follow the same method with Excell

Mpourmpakis Giannis gbourb . chemistry.uoc.gr wrote:
> Sent to CCL by: Mpourmpakis Giannis [gbourb*chemistry.uoc.gr]
> You can try the Origin program. Use the symbol "line" instead the square
> and you can plot
> the levels. Best regards,
> Giannis
>
>
>
> Agalya Govindasamy agalya81|,|gmail.com wrote:
>
>
>> Sent to CCL by: "Agalya Govindasamy" [agalya81(-)gmail.com]
>> I have molecular orbital energies of some systems and i want to plot them
>> in a single figure and compare the energy levels. I am not able to do
>> this using Excel. Could anyone please tell if there is any software to make
>> molecular orbital energy level plots.>
>>
>>
>>
>>
>>
>>
>
>
>
>

--
-------------------------------------------------
Dr. Christos S. Garoufalis
Dept. of Physics, Univ. of Patras, Greece
email: garoufal(-)physics.upatras.gr
Tel. +30 2610 997729
-------------------------------------------------

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