From owner-chemistry@ccl.net Mon Aug 1 02:12:01 2011 From: "krati joshi kjjulie.joshi..gmail.com" To: CCL Subject: CCL:G: How to run compound jobs (opt+NMR) in gaussian03 Message-Id: <-45181-110801020944-26847-uI5//pLZ2i53IGGjdybXWg,server.ccl.net> X-Original-From: "krati joshi" Date: Mon, 1 Aug 2011 02:09:41 -0400 Sent to CCL by: "krati joshi" [kjjulie.joshi:_:gmail.com] Dear all, I want to run a compound job i.e.optimization followed by NMR calculation using gaussian 03 programm but i dont know how to prepare a proper input for it. So if anybody knows anything about it pls tell me, it will help me alot. Thanks in advance. KRATI JOSHI Catalysis Division, National Chamical laboratory Dr. Homi Bhabha road,Pune(Maharashtra),India Email, kjjulie.joshi-at-gmail.com From owner-chemistry@ccl.net Mon Aug 1 07:46:00 2011 From: "Jean Jules FIFEN julesfifen : gmail.com" To: CCL Subject: CCL:G: How to calculate IP,EA,EN using Gaussian Message-Id: <-45182-110801074023-1715-MnPY/Jhf2STiXIsAFjJ1Hg . server.ccl.net> X-Original-From: Jean Jules FIFEN Content-Type: multipart/alternative; boundary=bcaec54faf6852f9a304a9701852 Date: Mon, 1 Aug 2011 13:40:16 +0200 MIME-Version: 1.0 Sent to CCL by: Jean Jules FIFEN [julesfifen|*|gmail.com] --bcaec54faf6852f9a304a9701852 Content-Type: text/plain; charset=ISO-8859-1 Find relevant information in the following paper (Comp. Theor. Chem. 2011, 966, 232). For electronegativities calculations, you can use Pearson formula for which the electonegativity is defined as, ki=(IP+PA)/2. Hope this would help. On 14 July 2011 19:50, christina jenifer g christinamsc__gmail.com < owner-chemistry|ccl.net> wrote: > > Sent to CCL by: "christina jenifer g" [christinamsc]![gmail.com] > Dear all, > > I am wondering if anyone of you performed the following calculations > from Gaussian output. How to calculate ionization potential, electron > affinity and electro negativity values from Gaussian output files and > suggest me the desired key word in order to calculate these values from > output file. > > Any comments on this matter would be greatly appreciated > > Thanks in advance > > By > > CHRISTINA> > > -- Jean Jules FIFEN University of Douala, Cameroon, Laboratory of Fundamental Physics. --bcaec54faf6852f9a304a9701852 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Find relevant information in the following paper (Comp. Theor. Chem. 2011, = 966, 232). For electronegativities calculations, you can use Pearson formul= a for which the electonegativity is defined as, ki=3D(IP+PA)/2.
Hope th= is would help.

On 14 July 2011 19:50, christina jenifer g <= a href=3D"http://christinamsc__gmail.com">christinamsc__gmail.com <owner-chemistry= |ccl.net> wrote:

Sent to CCL by: "christina jenifer g" [christinamsc]![gmail.com]
Dear all,

=A0 =A0 =A0 =A0I am wondering if anyone of you performed the following cal= culations from Gaussian output. How to calculate ionization potential, elec= tron affinity and electro negativity values from Gaussian output files and = suggest me the desired key word in order to calculate these values from out= put file.

=A0 =A0 =A0 =A0Any comments on this matter would be greatly appreciated
Thanks in advance

By

CHRISTINA



-=3D This is automatically added to each message by the mailing script =3D-=
E-mail to subscribers: CHEMISTRY|ccl.n= et or use:
=A0 =A0 =A0http://www.ccl.net/cgi-bin/ccl/send_ccl_message

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=A0 =A0 =A0http://www.ccl.net/cgi-bin/ccl/send_ccl_message

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--
Jean Jules FIFEN
Un= iversity of Douala, Cameroon,
Laboratory of Fundamental Physics.

--bcaec54faf6852f9a304a9701852-- From owner-chemistry@ccl.net Mon Aug 1 08:42:00 2011 From: "Arindam Ganguly arindamganguly{=}gmail.com" To: CCL Subject: CCL:G: Polymer FTIR/Raman spectral simulation using Gaussian 03W Message-Id: <-45183-110801084120-22005-W30/KHsYu3Lb8/rvJed+Ng!^!server.ccl.net> X-Original-From: "Arindam Ganguly" Date: Mon, 1 Aug 2011 08:41:15 -0400 Sent to CCL by: "Arindam Ganguly" [arindamganguly(~)gmail.com] Dear CCL Users, Good afternoon and hope this message reaches you all well. I have question which is quite obvious from the subject of the message. Has anyone used Gaussian 03W for Polymer FTIR/Raman spectra simulation? Any guidance and references will be really helpful. I would also be grateful if anyone of you would be willing to share input files? Thank you all very much for your support. Sincerely, Arindam From owner-chemistry@ccl.net Mon Aug 1 09:17:01 2011 From: "Arindam Ganguly arindamganguly#,#gmail.com" To: CCL Subject: CCL:G: How to calculate IP,EA,EN using Gaussian Message-Id: <-45184-110801083640-8667-aS9SvV6ofK5rabxRfTBA5w#server.ccl.net> X-Original-From: Arindam Ganguly Content-Type: multipart/alternative; boundary=20cf303f6c5a7dc8de04a970e130 Date: Mon, 1 Aug 2011 08:36:31 -0400 MIME-Version: 1.0 Sent to CCL by: Arindam Ganguly [arindamganguly^_^gmail.com] --20cf303f6c5a7dc8de04a970e130 Content-Type: text/plain; charset=ISO-8859-1 Dear Jean, Could you please indicate the full journal name of (Comp. Theor. Chem. ). Thank you. Sincerely, Arindam On Mon, Aug 1, 2011 at 7:40 AM, Jean Jules FIFEN julesfifen : gmail.com < owner-chemistry*o*ccl.net> wrote: > Find relevant information in the following paper (Comp. Theor. Chem. 2011, > 966, 232). For electronegativities calculations, you can use Pearson formula > for which the electonegativity is defined as, ki=(IP+PA)/2. > Hope this would help. > > On 14 July 2011 19:50, christina jenifer g christinamsc__gmail.com < > owner-chemistry,ccl.net> wrote: > >> >> Sent to CCL by: "christina jenifer g" [christinamsc]![gmail.com] >> Dear all, >> >> I am wondering if anyone of you performed the following >> calculations from Gaussian output. How to calculate ionization potential, >> electron affinity and electro negativity values from Gaussian output files >> and suggest me the desired key word in order to calculate these values from >> output file. >> >> Any comments on this matter would be greatly appreciated >> >> Thanks in advance >> >> By >> >> CHRISTINA** >> E-mail to subscribers: CHEMISTRY,ccl.net or use:>> >> E-mail to administrators: CHEMISTRY-REQUEST,ccl.net or use>> **>> >> >> > > > -- > Jean Jules FIFEN > University of Douala, Cameroon, > Laboratory of Fundamental Physics. > > -- Arindam Ganguly, Ph.D. Postdoctoral Researcher University of Michigan, Ann Arbor Phone:-816-419-1806 http://www.linkedin.com/in/arindamganguly --20cf303f6c5a7dc8de04a970e130 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Dear Jean,
Could you please indicate the full journal name of (Comp. Theor= . Chem.=A0). Thank you.
Sincerely,
Arindam

On Mon, Aug 1,= 2011 at 7:40 AM, Jean Jules FIFEN julesfifen : gmail.com <owner-chemistry*o*ccl.net> wrote:
Find relevant information in the following = paper (Comp. Theor. Chem. 2011, 966, 232). For electronegativities calculat= ions, you can use Pearson formula for which the electonegativity is defined= as, ki=3D(IP+PA)/2.
Hope this would help.

On 14 July 2011 19:50, christina jenifer g <= a href=3D"http://christinamsc__gmail.com" target=3D"_blank">christinamsc__g= mail.com <owner-chemistry,ccl.net> wrote:

Sent to CCL by: "christina jenifer g" [christinamsc]![gmail.com]
Dear all,

=A0 =A0 =A0 =A0I am wondering if anyone of you performed the following cal= culations from Gaussian output. How to calculate ionization potential, elec= tron affinity and electro negativity values from Gaussian output files and = suggest me the desired key word in order to calculate these values from out= put file.

=A0 =A0 =A0 =A0Any comments on this matter would be greatly appreciated
Thanks in advance

By

CHRISTINA



-=3D This is automatically added to each message by the mailing script =3D-=
E-mail to subscribers: CHEMISTRY,ccl.net or use:
=A0 =A0 =A0http://www.ccl.net/cgi-bin/ccl/send_ccl_message

E-mail to administrators: CHEMISTRY-REQUEST,ccl.net or use
=A0 =A0 =A0http://www.ccl.net/cgi-bin/ccl/send_ccl_message

Subscribe/Unsubscribe:
=A0 =A0 =A0http://www.ccl.net/chemistry/sub_unsub.shtml

Before posting, check wait time at: http://www.ccl.net

Job: http://www.ccl.n= et/jobs
Conferences: http://server.ccl.net/chemistry/announcements/co= nferences/

Search Messages: http://www.ccl.net/chemistry/searchccl/index.shtml
=A0 =A0 =A0h= ttp://www.ccl.net/spammers.txt

RTFI: http://www.ccl.net/chemistry/aboutccl/instructions/





--
Jean Jules FIFEN
Univ= ersity of Douala, Cameroon,
Laboratory of Fundamental Physics.




--
Arindam Ganguly, Ph.D.<= br>Postdoctoral Researcher
University of Michigan, Ann Arbor
Phone:-8= 16-419-1806
http://www.linkedin.com/in/arindamganguly
--20cf303f6c5a7dc8de04a970e130-- From owner-chemistry@ccl.net Mon Aug 1 09:52:01 2011 From: "Dan Maftei dan.maftei{}uaic.ro" To: CCL Subject: CCL:G: Linux input / output Gaussian09 Message-Id: <-45185-110801060939-9374-bCIx+G3ltLy1bhp6NBoEIA ~~ server.ccl.net> X-Original-From: Dan Maftei Content-Type: multipart/mixed; boundary="------------010109050309090008070507" Date: Mon, 01 Aug 2011 13:09:27 +0300 MIME-Version: 1.0 Sent to CCL by: Dan Maftei [dan.maftei]-[uaic.ro] This is a multi-part message in MIME format. --------------010109050309090008070507 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 7bit Hy Henry, On Linux you may use Molden (http://www.cmbi.ru.nl/molden/). You may grab a copy of it's source code by FTP from here: ftp://ftp.cmbi.ru.nl/pub/molgraph/molden/molden5.0.tar.gz The source code may then be easily compiled on most Linux OS'es using gcc and gfortan. However, molden isn't a replacement for GaussView but has almost all the features needed for a vizualization software to work with Gaussian. If looking for a tool to generate the keyword section of a Gaussian input file, consider writing it by yourself, it's allways a better choice. When working with molden, I usually save the geometry in Gaussian z-matrix form and insert the route/keywords by hand in top of the generated file. Regards, Dan Maftei. Pe 31.07.2011 18:25, Henry Martinez hmartine-*-gmail.com a scris: > Sent to CCL by: "Henry Martinez" [hmartine+/-gmail.com] > Hi everyone, > What would be the best "replacement" in Linux to Gaussian viewto use with Gaussian 09 (of course > linux as well)? Some software that allow me to generate the input file for Gaussian09 and also see (in a > graphic way) the output file as well. So far The only one I know is Gabedit..any other? > Thanks a lot for the help> > -- Dan Maftei, Assistant Professor, Faculty of Chemistry/Department of Chemistry University Alexandru Ioan Cuza Iasi Bd. Carol 1, Nr. 11, 700506 Iasi, Romania Tel: +40 232 201307 E-mail(s): dan.maftei*|*chem.uaic.ro dan.maftei*|*uaic.ro --------------010109050309090008070507 Content-Type: application/pgp-keys; name="0xF59B8983.asc" Content-Transfer-Encoding: 7bit Content-Disposition: attachment; filename="0xF59B8983.asc" -----BEGIN PGP PUBLIC KEY BLOCK----- Version: GnuPG v2.0.14 (GNU/Linux) mQGiBEjrO0wRBACQkJChhDxP3N+/d5o1B/6TCA54b9w+qbhDnW7GK/wZDunsmEKY XVsAcWt+O32NHVekEyOBYetR8wctmyWogIjn9YZznk/PkQzZhqL6bD4MirXbyBvP MiII7iF1T+Ou7tiv7UbmpwRYX2Wb02ey51i0qdq9WQ1E+XATmifzXGGFIwCg3u/O +oyu37f+7hm92q1Ls20AxrsD/jN2Fh7yjl0erV4Sy/USe+CS+lKWZDAMkCFj5wTe +SqTPWtN0GKfiWeXjgUBCdRCktVfOEHjo0bcpnYpm7BY7hnGbD7+ceO2dSvCFRf2 NWmWpDgW6+zLKhuoMpVYwYtkGD0v9as14MQJyDyZewonP5mPwN/aMBA12iPOifQ4 Pgw9A/4mvsmoTLnSPkoauLoU+mRKbGFGBNUeLUFfzxLxcOei5BrRg3nKLW9p+sUZ tVdMPbpWSAf88HambwFR6TOwmwrX0pbRo5gucWga6txESPP8cw2FA9CTpSn+CrIO iqPRr+g48yoMYiWGT4t2PalrEgof+yyE+75It5Io7ihUzix2jbQkRGFuIE1hZnRl 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DOCK is a suite of programs for molecular docking. In version 6.5 a new scoring function Descriptor Score is available. It reports van der Waals and Coulombic energies, hydrogen bonds, and per-residue energy decomposition comparisons with a reference molecule. DOCK continues to provide a variety of other scoring methods including grid based, PB/SA, and GB/SA, as well as a simple interface to the AmberTools MD engine that enables receptor flexibility and a complete MM force field. For full information on what is new in DOCK 6.5, please visit: http://dock.compbio.ucsf.edu/DOCK_6/new_in_6.5.txt Sincerely, The DOCK Team Please visit us at the DOCK Web site. http://dock.compbio.ucsf.edu From owner-chemistry@ccl.net Mon Aug 1 11:18:00 2011 From: "Sanjay Bharathwaj computationalchemist*o*gmail.com" To: CCL Subject: CCL: Molecular Formula to Structures - Free ware Message-Id: <-45187-110801094802-10483-H0tu+uaeHM0I1qxhCdz/Pw-.-server.ccl.net> X-Original-From: Sanjay Bharathwaj Content-Type: multipart/alternative; boundary=001636c9262baefeff04a971e00c Date: Mon, 1 Aug 2011 15:47:52 +0200 MIME-Version: 1.0 Sent to CCL by: Sanjay Bharathwaj [computationalchemist- -gmail.com] --001636c9262baefeff04a971e00c Content-Type: text/plain; charset=ISO-8859-1 I didn't need any of these webpages. I am looking similar to MOLGEN for organometallic compounds. Please help. Best regards, Sanjay On 29 July 2011 16:07, Abhik Seal abhik1368*_*gmail.com < owner-chemistry-$-ccl.net> wroteHi > > > Why dont you use online tool http://cactus.nci.nih.gov/chemical/structure > and you can also use Opsin (http://opsin.ch.cam.ac.uk/) to > > thank you > > Abhik Seal > *OSDD CHEMINFORMATICS* > +919831682877 > http://osddcheminfo.webs.com > > > > On Fri, Jul 29, 2011 at 2:43 PM, Sanjay Bharathwaj computationalchemist+*+ > gmail.com wrote: > >> Dear Colleagues, >> >> I am looking for a program (free ware/or with full trial version for >> limited time) that can list the possible structures >> (organometallic compound) when the molecular formula is given. >> >> For example i know for organic molecules MOLGEN does this job. >> But that's not free as well. (molgen(dot)de) >> >> If you have any kind of codes/genetic algorithm that can do this >> job, please share your knowledge and your help will be acknowledged >> suitably. >> >> Best regards, >> Dr. Sanjay >> >> -- >> Regards, >> Dr. Sanjay Bharathwaj Kumar, >> Dharmendra Institute of Technology, >> India. >> > > -- Regards, Dr. Sanjay Bharathwaj Kumar, Dharmendra Institute of Technology, India. --001636c9262baefeff04a971e00c Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable I didn't need any of these webpages.
I am looking similar to MOLGEN= for organometallic compounds.
Please help.

<= div>Best regards,
Sanjay

On 29 = July 2011 16:07, Abhik Seal abhik1368*_*gmail.= com <ow= ner-chemistry-$-ccl.net> wroteHi=A0

Why dont you use online tool=A0http://cactus.nci.nih.go= v/chemical/structure=A0 and you can also use Opsin (http://opsin.ch.cam.ac.uk/) to=A0=

thank you=A0
=A0
Abhik Seal
OSDD CHEMINFORMATICS
+91983168= 2877
http://osddchem= info.webs.com



On Fri, Jul 29, 2011 at 2:43 PM, Sanjay = Bharathwaj computationalchemist+*+gmail.com <owner-chemistry,ccl.net> wrote:
Dear=A0Colleagues,

<= div> I am looking for a=A0program (free ware/or with full trial version for limi= ted time)=A0that can list the possible structures
(organometallic compound) when the molecular=A0formula=A0is given.

For example i know for organic molecules MOLGEN does = this job.
But that's not free as well. (molgen(dot)de)

If you have any kind of codes/genetic algorithm that can do = this=A0
job, please share your knowledge and your help will be ac= knowledged=A0
suitably.

Best regards,
Dr. Sanjay

--
= Regards,
Dr. Sanjay Bharathwaj Kumar,
Dharmendra Institute of Technol= ogy,
India.




--
Regards,
Dr. Sanjay = Bharathwaj Kumar,
Dharmendra Institute of Technology,
India.
--001636c9262baefeff04a971e00c-- From owner-chemistry@ccl.net Mon Aug 1 11:52:00 2011 From: "krati joshi kjjulie.joshi*|*gmail.com" To: CCL Subject: CCL:G: 3 layer ONIOM NMR calculations in G03 Message-Id: <-45188-110801113153-16693-GHa3AL4khZxupve5hNN5Dw-x-server.ccl.net> X-Original-From: "krati joshi" Date: Mon, 1 Aug 2011 11:31:50 -0400 Sent to CCL by: "krati joshi" [kjjulie.joshi##gmail.com] Dear all, I want to do a 3 layer ONIOM NMR calculation using G03 program but i dont know the right keywords for it so if anybody knows pls suggest me the right keywords for it. It will be helpfull. Thanks in advance. Regards Krati Joshi Catalysis Division,NCL Dr. Homi Bhabha road, Pune(Maharashtra) India. Email, Kjjulie.joshi-at-gmail.com From owner-chemistry@ccl.net Mon Aug 1 16:36:00 2011 From: "James Mao xjamesmao~!~gmail.com" To: CCL Subject: CCL:G: aim in Gaussian 09 Message-Id: <-45189-110801155214-18753-aUjhZwSqjs+q/vte+kBStw*o*server.ccl.net> X-Original-From: "James Mao" Date: Mon, 1 Aug 2011 15:52:10 -0400 Sent to CCL by: "James Mao" [xjamesmao _ gmail.com] Dear cclers, I am testing aim in Gaussian and always get something wrong. When I tried aim it seems fine. But when I want some more result and tried aim=all or aim=bondorder, it gives me different result. For example, for aim/aim=charge, I got: ------------------------------------------------ Attr. Number of electrons Charge total spin ------------------------------------------------ 1 9.615522 0.000000 -0.615522 2 0.373758 0.000000 0.626242 3 9.649922 0.000000 -0.649922 4 0.361198 0.000000 0.638802 ------------------------------------------------ Total 20.000400 0.000000 -0.000400 ------------------------------------------------ It seems fine. But when I changed to aim=all or aim=bondorder (nothing else was changed) I got: aim=all (or bondorder) ------------------------------------------------ Attr. Number of electrons Charge total spin ------------------------------------------------ 1 0.232472 0.000000 8.767528 2 0.066455 0.000000 0.933545 3 0.165134 0.000000 8.834866 4 0.101160 0.000000 0.898840 ------------------------------------------------ Total 0.565221 0.000000 19.434779 ------------------------------------------------ Why they are different? Here is my simple input: ********** #n RHF/3-21G sp aim test hf2 aim testing 0 1 F H 1 B1 F 1 B2 2 A2 H 3 B3 1 A3 2 D3 Variables: B1=0.93970242 B2=2.65221513 A2=131.44658578 B3=0.94166715 A3=1.21513049 D3=-179.80197662 ********** My Gaussian is 09w A-02, windows 7. I tried different molecules and had the same problem. Can anyone help me confirm it? Thanks. James University of Pittsburgh