From owner-chemistry@ccl.net Tue Jul 7 09:47:01 2015 From: "Kaushik Hatua kaushikhatua]~[yahoo.in" To: CCL Subject: CCL:G: Vibrational polarizability and hyperpolarizability Message-Id: <-51507-150707094220-25214-s4VanK6GbQQAs3dUB5tbsQ,,server.ccl.net> X-Original-From: Kaushik Hatua Content-Type: multipart/alternative; boundary="_400306F6-76BA-49AE-8DF1-FC3B5F466CAC_" Date: Tue, 7 Jul 2015 19:12:00 +0530 MIME-Version: 1.0 Sent to CCL by: Kaushik Hatua [kaushikhatua _ yahoo.in] --_400306F6-76BA-49AE-8DF1-FC3B5F466CAC_ Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="Windows-1252" Dear all Can anybody provide the exact working equation of vibrational contribution = to polarizability and hyperpolarizability calculated by Gaussian 09 during = RAMAN calculation. I have lot of reference regarding this but i am confused= which one is used by Gaussian ? Any help would be appreciated. Sent from Nokia Lumia = --_400306F6-76BA-49AE-8DF1-FC3B5F466CAC_ Content-Transfer-Encoding: quoted-printable Content-Type: text/html; charset="Windows-1252"

Dear all
Can anybody provide the exact working = equation of vibrational contribution to polarizability and hyperpolarizabil= ity calculated by Gaussian 09 during RAMAN calculation. I have lot of refer= ence regarding this but i am confused which one is used by Gaussian ? Any h= elp would be appreciated.

Sent from Nokia Lumia

<= /html>= --_400306F6-76BA-49AE-8DF1-FC3B5F466CAC_-- From owner-chemistry@ccl.net Tue Jul 7 11:34:01 2015 From: "Rana, Anup rana~~chemie.uni-siegen.de" To: CCL Subject: CCL:G: How to get ACID plot by AICD and g09 binary Message-Id: <-51508-150707113247-11098-ZybRhjhzkf1PcfbBeBGiIw::server.ccl.net> X-Original-From: "Rana, Anup" Content-Language: en-US Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="us-ascii" Date: Tue, 7 Jul 2015 15:32:30 +0000 MIME-Version: 1.0 Sent to CCL by: "Rana, Anup" [rana#%#chemie.uni-siegen.de] Hi all, I want to plot ACID map to visualize aromaticity. For that, I already have AICD-1.5.7.1 program from Prof. Herges and I have already done NMR computation by NMR=CSGT IOp(10/93=1) keywords by gaussian 09 D.01 (binary). So, gaussian generated one .log file and one data file. As far I know, from gaussian 09 help, that the data file can be processed by stand alone AICD program. My question is that how to do so? I could not find any detail manual for the program. Whatever I understood from the AICD script, in the root directory of the program, that gaussian should be patched with AICD program and for that I should have source code. Unfortunately I dont have it; I have only binary. So, how to get ACID plot by using AICD and g09 binary? Thank you in advance. With best regards, Anup Rana From owner-chemistry@ccl.net Tue Jul 7 12:09:01 2015 From: "Elliot Menkah elliotsmenkah^^^hotmail.com" To: CCL Subject: CCL: Drawing Chemical structures and Equations Message-Id: <-51509-150707081331-20213-i/zFGsH0VoQlUseq2EigBg .. server.ccl.net> X-Original-From: Elliot Menkah Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="utf-8" Date: Tue, 7 Jul 2015 12:09:11 +0000 MIME-Version: 1.0 Sent to CCL by: Elliot Menkah [elliotsmenkah() hotmail.com] Hello Everyone, Does anyone know any free chemistry software in linux ( such as chem draw) that can help you draw chemical structures and equations? Thank you. Kind Regards, Elliot -- Elliot S. Menkah Research Student - Computational Chemistry/ Computational Material Science Theoretical and Computational Chemistry Dept. of Chemistry Kwame Nkrumah UNiversity of Sci. and Tech. Kumasi Ghana Tel: +233 243-055-717 Alt Email: elliotsmenkah]=[gmail.com elliotsmenkah]=[hotmail.com From owner-chemistry@ccl.net Tue Jul 7 13:13:00 2015 From: "Victor Rosas Garcia rosas.victor~~gmail.com" To: CCL Subject: CCL: Drawing Chemical structures and Equations Message-Id: <-51510-150707131039-1124-gSlq1Z5AIowg+fgLKvNiNw=server.ccl.net> X-Original-From: Victor Rosas Garcia Content-Type: multipart/alternative; boundary=089e014946b29d3f3e051a4c1953 Date: Tue, 7 Jul 2015 12:10:33 -0500 MIME-Version: 1.0 Sent to CCL by: Victor Rosas Garcia [rosas.victor~~gmail.com] --089e014946b29d3f3e051a4c1953 Content-Type: text/plain; charset=UTF-8 yes. You can try BKchem, chemtool, easychem, gchempaint and xdrawchem. Hope this helps Victor 2015-07-07 7:09 GMT-05:00 Elliot Menkah elliotsmenkah^^^hotmail.com < owner-chemistry[a]ccl.net>: > > Sent to CCL by: Elliot Menkah [elliotsmenkah() hotmail.com] > Hello Everyone, > Does anyone know any free chemistry software in linux ( such as chem > draw) that can help you draw chemical structures and equations? > > Thank you. > > Kind Regards, > Elliot > > -- > Elliot S. Menkah > Research Student - Computational Chemistry/ Computational Material Science > Theoretical and Computational Chemistry > Dept. of Chemistry > Kwame Nkrumah UNiversity of Sci. and Tech. > Kumasi > Ghana > > Tel: +233 243-055-717 > > Alt Email: elliotsmenkah#gmail.com > elliotsmenkah#hotmail.com> > > --089e014946b29d3f3e051a4c1953 Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable

yes. You can try BKchem, chemtool, easychem, gch= empaint and xdrawchem.

Hope this helps

Victor
=

2015-07-07 = 7:09 GMT-05:00 Elliot Menkah elliotsmenkah^^^hotmail.com <owner-chemistry[a]ccl.net>:

Sent to CCL by: Elliot Menkah [elliotsmenkah() hotmail.com]
Hello Everyone,
Does anyone know any free chemistry software in linux ( such as chem
draw) that can help you draw chemical structures and equations?

Thank you.

Kind Regards,
Elliot

--
Elliot S. Menkah
Research Student - Computational Chemistry/ Computational Material Science<= br> Theoretical and Computational Chemistry
Dept. of Chemistry
Kwame Nkrumah UNiversity of Sci. and Tech.
Kumasi
Ghana

Tel: +233 243-055-717

Alt Email: elliotsmenkah#gmail.com
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-0800 MIME-Version: 1.0 Sent to CCL by: John Keller [jwkeller(-)alaska.edu] --001a11381404b6d457051a4de8fb Content-Type: text/plain; charset=UTF-8 Hi Elliott, ChemAxon has free version of MarvinSketch for Windows, Mac, and Linux. I installed the latest version on a 64-bit CentOS 6.5 system with no problems. I even has a ChemDraw skin. John Keller On Tue, Jul 7, 2015 at 4:09 AM, Elliot Menkah elliotsmenkah^^^hotmail.com < owner-chemistry]*[ccl.net> wrote: > > Sent to CCL by: Elliot Menkah [elliotsmenkah() hotmail.com] > Hello Everyone, > Does anyone know any free chemistry software in linux ( such as chem > draw) that can help you draw chemical structures and equations? > > Thank you. > > Kind Regards, > Elliot > > -- > Elliot S. Menkah > Research Student - Computational Chemistry/ Computational Material Science > Theoretical and Computational Chemistry > Dept. of Chemistry > Kwame Nkrumah UNiversity of Sci. and Tech. > Kumasi > Ghana > > Tel: +233 243-055-717 > > Alt Email: elliotsmenkah#gmail.com > elliotsmenkah#hotmail.com> > > --001a11381404b6d457051a4de8fb Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable

Hi Elliott,

ChemAxon has free version of MarvinSketch = for Windows, Mac, and Linux. I installed the latest version on a 64-bit Cen= tOS 6.5 system with no problems. I even has a ChemDraw skin.

John= Keller

On Tue, Jul 7, 2015 at 4:09 AM, Elliot Menkah elliotsmenka= h^^^hotmail.com <owner-chemistry]*[= ccl.net> wrote:

Sent to CCL by: Elliot Menkah [elliotsmenkah() hotmail.com]
Hello Everyone,
Does anyone know any free chemistry software in linux ( such as chem
draw) that can help you draw chemical structures and equations?

Thank you.

Kind Regards,
Elliot

--
Elliot S. Menkah
Research Student - Computational Chemistry/ Computational Material Science<= br> Theoretical and Computational Chemistry
Dept. of Chemistry
Kwame Nkrumah UNiversity of Sci. and Tech.
Kumasi
Ghana

Tel: +233 243-= 055-717

Alt Email: elliotsmenkah#gmail.com
=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0elliotsmenkah#hotmail.com

-=3D This is automatically added to each message by the mailing script =3D-=
To recover the email address of the author of the message, please ch= ange
E-mail to subscribers: CHEMISTRY]*[ccl.n= et or use:
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--001a11381404b6d457051a4de8fb-- From owner-chemistry@ccl.net Tue Jul 7 17:20:01 2015 From: "Elliot Menkah elliotsmenkah ~~ hotmail.com" To: CCL Subject: CCL: Drawing Chemical structures and Equations Message-Id: <-51513-150707170753-3459-4FMTU538Fn6zfcXyHph0OA(-)server.ccl.net> X-Original-From: Elliot Menkah Content-Type: multipart/alternative; boundary="------------020609030701060109080004" Date: Tue, 7 Jul 2015 21:07:43 +0000 MIME-Version: 1.0 Sent to CCL by: Elliot Menkah [elliotsmenkah:-:hotmail.com] --------------020609030701060109080004 Content-Type: text/plain; charset="utf-8" Content-Transfer-Encoding: 7bit Thank you all for the invaluable information. Kind Regards, Elliot On 07/07/2015 07:20 PM, John Keller jwkeller^_^alaska.edu wrote: > Hi Elliott, > ChemAxon has free version of MarvinSketch for Windows, Mac, and Linux. > I installed the latest version on a 64-bit CentOS 6.5 system with no > problems. I even has a ChemDraw skin. > John Keller > > > On Tue, Jul 7, 2015 at 4:09 AM, Elliot Menkah > elliotsmenkah^^^hotmail.com > > wrote: > > > Sent to CCL by: Elliot Menkah [elliotsmenkah() hotmail.com > ] > Hello Everyone, > Does anyone know any free chemistry software in linux ( such as chem > draw) that can help you draw chemical structures and equations? > > Thank you. > > Kind Regards, > Elliot > > -- > Elliot S. Menkah > Research Student - Computational Chemistry/ Computational Material > Science > Theoretical and Computational Chemistry > Dept. of Chemistry > Kwame Nkrumah UNiversity of Sci. and Tech. > Kumasi > Ghana > > Tel: +233 243-055-717 > > Alt Email: elliotsmenkah#gmail.com > elliotsmenkah#hotmail.com > > > > -= This is automatically added to each message by the mailing > script =- > To recover the email address of the author of the message, please > change > E-mail to subscribers: CHEMISTRY*o*ccl.net > or use:> > E-mail to administrators: CHEMISTRY-REQUEST*o*ccl.net > or use> Conferences: > http://server.ccl.net/chemistry/announcements/conferences/> > > -- Elliot S. Menkah Research Student - Computational Chemistry/ Computational Material Science Theoretical and Computational Chemistry Dept. of Chemistry Kwame Nkrumah UNiversity of Sci. and Tech. Kumasi Ghana Tel: +233 243-055-717 Alt Email: elliotsmenkah ~~ gmail.com elliotsmenkah ~~ hotmail.com --------------020609030701060109080004 Content-Type: text/html; charset="utf-8" Content-Transfer-Encoding: quoted-printable

Thank you all for the invaluable information.

Kind Regards=2C
Elliot

On 07/07/2015 07:20 PM=2C John Keller jwkeller^_^alaska.edu wrote:

Hi Elliott=2C
ChemAxon has free version of MarvinSketch for Windows=2C Mac= =2C and Linux. I installed the latest version on a 64-bit CentOS 6.5 system with no problems. I even has a ChemDraw skin.

John Keller

On Tue=2C Jul 7=2C 2015 at 4:09 AM=2C El= liot Menkah elliotsmenkah^^^hotmail.com &= lt=3Bo= wner-chemistry*o*ccl.net>=3B wrote:

Sent to CCL by: Elliot Menkah [elliotsmenkah() hotmail.com]
Hello Everyone=2C
Does anyone know any free chemistry software in linux ( such as chem
draw) that can help you draw chemical structures and equations?

Thank you.

Kind Regards=2C
Elliot

--
Elliot S. Menkah
Research Student - Computational Chemistry/ Computational Material Science
Theoretical and Computational Chemistry
Dept. of Chemistry
Kwame Nkrumah UNiversity of Sci. and Tech.
Kumasi
Ghana

Tel: += 233 243-055-717

Alt Email: elliotsmenkah#gmail.com
=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0elliotsmenkah#hotmail.com

-=3D This is automatically added to each message by the mailing script =3D-
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Before posting=2C check wait time at: http://www.ccl.net

Job: http://www.ccl.net/jobs
Conferences: http://server.ccl.ne= t/chemistry/announcements/conferences/

Search Messages: http://www.ccl.net/c= hemistry/searchccl/index.shtml

=C2=A0 =C2=A0 =C2=A0 http://www.ccl.n= et/spammers.txt

RTFI: http://www.ccl.n= et/chemistry/aboutccl/instructions/

--=20
Elliot S. Menkah
Research Student - Computational Chemistry/ Computational Material Science
Theoretical and Computational Chemistry
Dept. of Chemistry
Kwame Nkrumah UNiversity of Sci. and Tech.
Kumasi
Ghana

Tel: +233 243-055-717

Alt Email: elliotsmenkah ~~ gmail.com
           elliotsmenkah ~~ hotmail.com

--------------020609030701060109080004-- From owner-chemistry@ccl.net Tue Jul 7 19:59:00 2015 From: "Nickolas Peter Burdick nburdick=-=reed.edu" To: CCL Subject: CCL: IRC of chirality swap tri-arylmethanols (like Ph3COH) from GAMESS Message-Id: <-51514-150707191411-4275-f/1wLbKI6HNCQJSswNteEQ+*+server.ccl.net> X-Original-From: "Nickolas Peter Burdick" Date: Tue, 7 Jul 2015 19:14:09 -0400 Sent to CCL by: "Nickolas Peter Burdick" [nburdick^reed.edu] Hi, I have been searching for transition states between helical chiral conformers of tri-arylmethanols. I have found some using Spartan and need to verify them with greater rigor. Since GAMESS is from the same lab that developed IRCs it seemed the logical place to look. I have run the test file exam11, which is a sample IRC calculation succesfully. I have been able to increase the number of points shown and change the direction along the imaginary frequency. I have been unsuccessful in performing IRC searches on my own, larger structures. An error that is reocurring is verbatim below, note that it shows in the command line, unlike my other issues which are just logged a the end of the output file. "C:\gamess.64>rungms dnest.inp > dnest.out PGFIO-F-231/formatted read/unit=5/error on data conversion. File name = C:\gamess.64\tmp\dnest.F05 formatted, sequential access record = 29 In source file hess.f, at line number 759" My tmp folder is empty afterwards and the output file only says: " GRADIENT OF THE ENERGY ---------------------- THE COARSE/FINE SCHWARZ SCREENINGS SKIPPED 2929/ 2026 BLOCKS. THE NUMBER OF GRADIENT INTEGRAL BLOCKS COMPUTED WAS 27130 ...... END OF 2-ELECTRON GRADIENT ...... STEP CPU TIME = 0.13 TOTAL CPU TIME = 0.5 ( 0.0 MIN) TOTAL WALL CLOCK TIME= 0.5 SECONDS, CPU UTILIZATION IS 100.00% job aborted: [ranks] message [0] process exited without calling finalize [1] terminated ---- error analysis ----- [0] on dhaulagiri C:\gamess.64\gamess.13-64.pgi.fast.exe ended prematurely and may have crashed. exit code 127 " With multiple attempts ending similarly, I reattempted with a diels-alder transition state, of which I am more confident in the saddle, so as to be sure that it wasn't just a fluke of shoddy input (although that is still my prime suspect). The above error message is from that DA TS; but it only differs from my previous error messages in that the sequential access record = 47, 48 or 49 instead. I have not been able to find hess.f or dnest.f05. I'm not at all familiar with fortran. I have tried writing my input files by hand, adapting the working exam11 file and with avagadro program. While I think I have circumvented my problems in finding the hessian matrix, perhaps there lies the problem. All of the tutorials that I have read (http://www.chemtube3d.com/ChemTube3DGuide.pdf and http://molecularmodelingbasics.blogspot.com/2009/10/get-reaction- intrinsic-reaction.html) indicate a $hess section of the output, which I have been unable to find. I have been copying the cartesian force constant matrix because it looked the most similar to the .hess file created by ORCA which i have also tried to use. I have been reading the GAMESS manual, but haven't found much beyond short descriptions of what each keyword does. I have searched it by keyword and index, but not yet exhaustively front to back, maybe I missed something. If you could point me towards a tutorial, forum or manual I would greatly appreciate it. Really anything would help. Thank you. (about me, just an upcoming senior undergrad working as a summer research assistant. Fairly fresh to these more rigorous computational techniques) Nick Burdick nburdick~~reed.edu 3203 SE woodstock blvd. MS 1433 From owner-chemistry@ccl.net Tue Jul 7 23:03:01 2015 From: "Salter-Duke, Brian James - brian.james.duke ~~ gmail.com" To: CCL Subject: CCL: IRC of chirality swap tri-arylmethanols (like Ph3COH) from GAMESS Message-Id: <-51515-150707222949-10861-tMzFEfjrpd8pX5/cyyFrpg~!~server.ccl.net> X-Original-From: "Salter-Duke, Brian James -" Content-Disposition: inline Content-Type: text/plain; charset=us-ascii Date: Wed, 8 Jul 2015 12:29:37 +1000 MIME-Version: 1.0 Sent to CCL by: "Salter-Duke, Brian James -" [brian.james.duke(-)gmail.com] First, you would do better putting this to the GAMESS list. Second, it would help if we could see you input files. Third, dnest.F05 is what dnest.inp was before it was copied to tmp. hess.f is what gamess/source/hess.src becomes after preprocessing before being compiled. The error occurs reading the $HESS block in your input file. Brian. On Tue, Jul 07, 2015 at 07:14:09PM -0400, Nickolas Peter Burdick nburdick=-=reed.edu wrote: > > Sent to CCL by: "Nickolas Peter Burdick" [nburdick^reed.edu] > Hi, > > I have been searching for transition states between helical chiral > conformers of tri-arylmethanols. I have found some using Spartan and need > to verify them with greater rigor. Since GAMESS is from the same lab that > developed IRCs it seemed the logical place to look. I have run the test > file exam11, which is a sample IRC calculation succesfully. I have been > able to increase the number of points shown and change the direction > along the imaginary frequency. I have been unsuccessful in performing IRC > searches on my own, larger structures. An error that is reocurring is > verbatim below, note that it shows in the command line, unlike my other > issues which are just logged a the end of the output file. > > "C:\gamess.64>rungms dnest.inp > dnest.out > PGFIO-F-231/formatted read/unit=5/error on data conversion. > File name = C:\gamess.64\tmp\dnest.F05 formatted, sequential access > record = 29 > In source file hess.f, at line number 759" > > My tmp folder is empty afterwards and the output file only says: > " GRADIENT OF THE ENERGY > ---------------------- > THE COARSE/FINE SCHWARZ SCREENINGS SKIPPED 2929/ 2026 > BLOCKS. > THE NUMBER OF GRADIENT INTEGRAL BLOCKS COMPUTED WAS 27130 > ...... END OF 2-ELECTRON GRADIENT ...... > STEP CPU TIME = 0.13 TOTAL CPU TIME = 0.5 ( 0.0 MIN) > TOTAL WALL CLOCK TIME= 0.5 SECONDS, CPU UTILIZATION IS 100.00% > > job aborted: > [ranks] message > > [0] process exited without calling finalize > > [1] terminated > > ---- error analysis ----- > > [0] on dhaulagiri > C:\gamess.64\gamess.13-64.pgi.fast.exe ended prematurely and may have > crashed. exit code 127 > " > > With multiple attempts ending similarly, I reattempted with a diels-alder > transition state, of which I am more confident in the saddle, so as to be > sure that it wasn't just a fluke of shoddy input (although that is still > my prime suspect). The above error message is from that DA TS; but it > only differs from my previous error messages in that the sequential > access record = 47, 48 or 49 instead. > > I have not been able to find hess.f or dnest.f05. I'm not at all familiar > with fortran. I have tried writing my input files by hand, adapting the > working exam11 file and with avagadro program. > > While I think I have circumvented my problems in finding the hessian > matrix, perhaps there lies the problem. All of the tutorials that I have > read (http://www.chemtube3d.com/ChemTube3DGuide.pdf and > http://molecularmodelingbasics.blogspot.com/2009/10/get-reaction- > intrinsic-reaction.html) indicate a $hess section of the output, which I > have been unable to find. I have been copying the cartesian force > constant matrix because it looked the most similar to the .hess file > created by ORCA which i have also tried to use. > > I have been reading the GAMESS manual, but haven't found much beyond > short descriptions of what each keyword does. I have searched it by > keyword and index, but not yet exhaustively front to back, maybe I missed > something. > > > If you could point me towards a tutorial, forum or manual I would greatly > appreciate it. Really anything would help. Thank you. > > (about me, just an upcoming senior undergrad working as a summer research > assistant. Fairly fresh to these more rigorous computational techniques) > Nick Burdick > nburdick_._reed.edu > 3203 SE woodstock blvd. > MS 1433> -- Brian Salter-Duke (Brian Duke) Brian.Salter-Duke,monash.edu Adjunct Associate Professor Monash Institute of Pharmaceutical Sciences Monash University Parkville Campus, VIC 3052, Australia