From chemistry-request@server.ccl.net Thu Nov 22 03:07:47 2001 Received: from mx01.uni-tuebingen.de ([134.2.3.11]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id fAM87kB29317 for ; Thu, 22 Nov 2001 03:07:46 -0500 Received: from Helena (helena.pharm.chemie.uni-tuebingen.de [134.2.68.136]) by mx01.uni-tuebingen.de (8.9.3/8.9.3) with SMTP id JAA21415 for ; Thu, 22 Nov 2001 09:07:45 +0100 Message-Id: <3.0.6.32.20011122090814.007aedd0@cpbnc01.mail.uni-tuebingen.de> X-Sender: cpbnc01@cpbnc01.mail.uni-tuebingen.de X-Mailer: QUALCOMM Windows Eudora Light Version 3.0.6 (32) Date: Thu, 22 Nov 2001 09:08:14 +0100 To: chemistry@ccl.net From: Christoph Nimptsch Subject: Re: CCL:Convert MOs between G98/Jaguar and GAMESS In-Reply-To: <3BFC04E0.F9A581B5@asc.hpc.mil> Mime-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id fAM87lB29318 At 14:47 21.11.01 -0500, XIAOFENG FRANK DUAN wrote: > Hi, all! I'd like to convert MOs from G98/Jaguar calculations to GAMESS's > $vec format. Does any one know where to find a program or scripts to do so? > Thanks! Have you tried Babel? It is free and can convert a number of file formats into each other. http://www.eyesopen.com/babel.html Hope it helps, Christoph Nimptsch ------------------------------------------ Christoph Nimptsch Apotheker Pharmazeutisches Institut Arbeitskreis Prof. Kovar Universität Tübingen Auf der Morgenstelle 8 D-72076 Tuebingen Tel.: 07071/2978794 mailto:christoph.nimptsch@uni-tuebingen.de ------------------------------------------ From chemistry-request@server.ccl.net Thu Nov 22 04:22:04 2001 Received: from mail.takas.lt ([212.59.31.66]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id fAM9M2B30748 for ; Thu, 22 Nov 2001 04:22:03 -0500 Received: from olegas ([212.59.14.111]) by mail.takas.lt with Microsoft SMTPSVC(5.0.2195.2966); Thu, 22 Nov 2001 11:18:54 +0200 Message-ID: <00ae01c1733f$8b3dedb0$550f3bd4@olegas> From: "Olegas Eicher-Lorka" To: Subject: Mysterious G98W output: The Summary!! Date: Thu, 22 Nov 2001 11:18:29 +0100 MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_00A8_01C17347.69A7A030" X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 5.50.4807.1700 X-MIMEOLE: Produced By Microsoft MimeOLE V5.50.4807.1700 X-OriginalArrivalTime: 22 Nov 2001 09:18:55.0020 (UTC) FILETIME=[B54C76C0:01C17336] This is a multi-part message in MIME format. ------=_NextPart_000_00A8_01C17347.69A7A030 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Dear CCLers, We recieved a number of answers telling us what the mysterious output = was, to thos who haven't a clue what I'm talking about here's the = original post: > When doing B3LYP Opt's (using #P) we've only recently started to get = this in the output file: >=20 > Isotropic Fermi Contact Couplings > Atom a.u. MegaHertz Gauss 10(-4) = cm-1 > 1 C(13) 0.00908 10.21192 3.64387 = 3.40633 > 2 C(13) -0.00326 -3.66731 -1.30859 = -1.22328 > 3 H 0.00155 6.93828 2.47575 = 2.31436 > 4 H 0.00017 0.77599 0.27689 = 0.25884 > 5 H 0.00017 0.77424 0.27627 = 0.25826 > 6 S(33) 0.18303 62.86418 22.43151 = 20.96923 > 7 H 0.00016 0.73397 0.26190 = 0.24483 > 8 H 0.00017 0.73965 0.26392 = 0.24672 > 9 Cu(63) 0.89938 1066.75970 380.64649 = 355.83273 > 10 Cu(63) 0.89702 1063.96061 379.64770 = 354.89906 >=20 > Just one simple question... what exactly is all of this, it looks a = bit 'NMRish" is it? Not a bad guess, as it turns out, as according to Uwe Richter = (uwe@fmp-berlin.de): >Pretty close! You might have noticed that you obtain this output only = for open shell calculations (ROHF or UHF/UDFT). The first column (a.u.) = is >simply the calculated spin density at the nuclei. From these values, = the hyperfine coupling constants (ESR) are calculated in various units. = This >conversion, although straightforward (just a couple of constants) is = quite a pain if you do it by hand (thank you, GAUSSIAN). The Fermi = Contact Terms >are also printed when the FIELD keyword is used in conjunction with = UHF/UDFT. From those, NMR J-coupling constants can be calculated. >Unfortunately, this must be done by hand ;-(.=20 This was helpful, but Vasile Chis (vchis@phys.ubbcluj.ro), stated = something blindingly obvious that we had overlooked: >Your input molecule is a paramagnetic one and by default the isotropic = hyperfine coupling constants are calculated and exprimed in a.u., MHz=20 >Gauss and cm^-1, for all the nuclei with non-zero spin. In the case of = carbon nucleus, the Hyperfine coupling constant is calculated for 13^C=20 >instead of 12^C with zero nuclear spin. So, this "ESRish" output it's = not due to the P option in the route but to=20 >the odd electron in your molecule. Thanks Vasile! We read Jim Stoner's (jstoner@du.edu) response will great = joy (especially Olegas, as he's not used to being called "Professor") = for his full details: Yes, these are magnetic resonance parameters. When one requests a #P = output, G98 dumps this table to the log file. It is the isotropic = hyperfine interaction constant, a_0 in different units for each of the = nuclei in the Z-matrix. For EPR, in solution, a_0 splits the Zeeman = interaction into 2(I+1) lines. A rather painfully complete discussion = can be found in Weil, Bolton, and Wertz, "Electron Paramagnetic = Resonance: Elementary Theory and Practical Applications" 1994 (ISBN = 0-471-57234-9). If you are interested in the observable, it is the sum = of the isotropic and anisotropic hyperfines. You can get the complete = anisotropic hyperfine coupling if you use keyword, PROP=3DEPR. The = output will have the matrix constants in different units and the = direction cosines of the anisotropic interaction. And thanks Jim, I suddenly remembered the Weil book from my undergrad = years, painful is similar to how I would describe it. And finally a = reply from the G-Man (csd@gaussian.com (Cust. Service Doug)): >When you run an open shell calculation using spin unrestricted = formalism it is simple to define a spin density and evaluate the >spin density at the nuclear positions which gives the fermi contact. = The static portion of the hyperfine splitting can be derived from=20 >this. Check out Exercise 6.8 in the second edition of Exploring = Chemistry with Electronic Structure Methods. A copy was sent >with the G98 distribution or additional copies can be ordered from = Gaussian. Sorry Doug, but we're in Lithuania and we're used to buying our software = > from "alternative" sources, which normally means no books, guides etc. = So when we recieved G98W to make us feel at home, we burnt all the = literature. Thanks everyone: Simon and Olegas One more question, the "humourous" quotes at the bottom of the G98 = output have stopped being "humourous"- how do I switch them off? ------=_NextPart_000_00A8_01C17347.69A7A030 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable
Dear CCLers,
We recieved a number of answers telling us what the=20 mysterious  output was, to thos who haven't a clue what I'm talking = about=20 here's the original post:
 
> When doing B3LYP Opt's (using #P) we've only = recently=20 started to get this in the output file:
>=20
>           = ;            = =20 Isotropic Fermi Contact Couplings
>     =20 Atom           &nb= sp;    =20 a.u.      =20 MegaHertz      =20 Gauss      10(-4) = cm-1
>   =20 1 =20 C(13)           &n= bsp; =20 0.00908     =20 10.21192      =20 3.64387       = 3.40633
>   =20 2 =20 C(13)           &n= bsp;=20 -0.00326      = -3.66731     =20 -1.30859      = -1.22328
>   =20 3 =20 H            =      =20 0.00155      =20 6.93828      =20 2.47575       = 2.31436
>   =20 4 =20 H            =      =20 0.00017      =20 0.77599      =20 0.27689       = 0.25884
>   =20 5 =20 H            =      =20 0.00017      =20 0.77424      =20 0.27627       = 0.25826
>   =20 6 =20 S(33)           &n= bsp; =20 0.18303      = 62.86418     =20 22.43151      = 20.96923
>   =20 7 =20 H            =      =20 0.00016      =20 0.73397      =20 0.26190       = 0.24483
>   =20 8 =20 H            =      =20 0.00017      =20 0.73965      =20 0.26392       = 0.24672
>   =20 9 =20 Cu(63)           &= nbsp;=20 0.89938    1066.75970    =20 380.64649     355.83273
>   10  = Cu(63)           &= nbsp;=20 0.89702    1063.96061    =20 379.64770     354.89906
>
> Just one = simple=20 question... what exactly is all of this, it looks a bit 'NMRish" is=20 it?
 
Not a bad guess, as it turns out, as according to = Uwe Richter=20 (uwe@fmp-berlin.de):
 
>Pretty close!  You might have noticed that you obtain this = output=20 only for open shell calculations (ROHF or UHF/UDFT). The first column = (a.u.)=20 is
>simply the calculated spin density at the nuclei. From these = values,=20 the hyperfine coupling constants (ESR) are calculated in various units.=20 This
>conversion, although straightforward (just a couple of = constants) is=20 quite a pain if you do it by hand (thank you, GAUSSIAN). The Fermi = Contact=20 Terms
>are also printed when the FIELD keyword is used in = conjunction with=20 UHF/UDFT. From those, NMR J-coupling constants can be=20 calculated.
>Unfortunately, this must be done by hand ;-(.
 
This was helpful, but Vasile Chis (vchis@phys.ubbcluj.ro), stated = something=20 blindingly obvious that we had overlooked:
 
>Your input molecule is a paramagnetic one and by default the = isotropic=20 hyperfine coupling constants are calculated and exprimed in a.u., MHz=20
>Gauss and cm^-1, for all the nuclei with non-zero spin. In the = case of=20 carbon nucleus, the Hyperfine coupling constant is calculated for 13^C=20
>instead of 12^C with zero nuclear spin. So, this "ESRish" output = it's=20 not due to the P option in the route but to
>the odd electron in = your=20 molecule.
Thanks Vasile! We read Jim Stoner's (jstoner@du.edu) response will great = joy=20 (especially Olegas, as he's not used to being called "Professor") for = his full=20 details:
 
Yes,=20 these are magnetic resonance parameters. =20 When one requests a #P output, G98 dumps this table to the log = file.  It is the isotropic hyperfine=20 interaction constant, a_0 in different units for each of the nuclei in = the=20 Z-matrix.  For EPR, in = solution, a_0=20 splits the Zeeman interaction into 2(I+1) lines.  A rather painfully complete = discussion=20 can be found in Weil, Bolton, and Wertz, “Electron Paramagnetic = Resonance:  Elementary Theory and = Practical=20 Applications” 1994 (ISBN 0-471-57234-9). If you=20 are interested in the observable, it is the sum of the isotropic and = anisotropic=20 hyperfines.  You can get = the=20 complete anisotropic hyperfine coupling if you use keyword, PROP=3DEPR. =  The output will have the matrix = constants=20 in different units and the direction cosines of the anisotropic=20 interaction.
 
And thanks Jim, I suddenly remembered the Weil book from my = undergrad=20 years, painful is similar to how I would describe it. And finally a = reply from=20 the G-Man (csd@gaussian.com = (Cust. Service=20 Doug)):
 
>When you run an open shell calculation using spin unrestricted=20 formalism it is simple to define a spin density and evaluate = the
>spin=20 density at the nuclear positions which gives the fermi contact. The = static=20 portion of the hyperfine splitting can be derived from =
>this.  Check=20 out Exercise 6.8 in the second edition of Exploring Chemistry with = Electronic=20 Structure Methods.   A copy was sent
>with the G98 = distribution=20 or additional copies can be ordered from Gaussian.
Sorry Doug, but we're in Lithuania and we're used to buying our = software=20 > from "alternative" sources, which normally means no books, guides etc. = So when=20 we recieved G98W to make us feel at home, we burnt all the = literature.
 
Thanks everyone:
 
Simon and Olegas
 
One more question, the "humourous" quotes at the bottom of the G98 = output=20 have stopped being "humourous"- how do I switch them off?


 
 ------=_NextPart_000_00A8_01C17347.69A7A030-- From chemistry-request@server.ccl.net Thu Nov 22 07:28:49 2001 Received: from janus.hosting4u.net ([209.15.2.37]) by server.ccl.net (8.11.6/8.11.0) with SMTP id fAMCSmB01223 for ; Thu, 22 Nov 2001 07:28:48 -0500 Received: (qmail 1834 invoked from network); 22 Nov 2001 12:28:48 -0000 Received: from zeus.hosting4u.net (HELO proinformatix.com) (209.15.2.56) by mail-gate.hosting4u.net with SMTP; 22 Nov 2001 12:28:48 -0000 Received: from yersina ([202.138.16.2]) by proinformatix.com ; Thu, 22 Nov 2001 06:28:45 -0600 Reply-To: From: "Sergio Manzetti" To: "Chemistry Discussion G" Subject: Revised full movie of the Na+/K+ pump Date: Thu, 22 Nov 2001 22:33:46 -0800 Message-ID: <001101c173e8$cf5055c0$02108aca@yersina> MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit X-Priority: 3 (Normal) X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook, Build 10.0.2627 Importance: Normal X-MimeOLE: Produced By Microsoft MimeOLE V5.00.2919.6700 X-Rcpt-To: Dear colleagues, I am embarrased to inform that last time I notified you all about my movies, I had only uploaded 10 seconds of the Na+/K+ pump movie by mistake, which is originally around 3min. I have noticed that some of you (attempted to) watch it, and even linked to it. Assuming a disappointment in those who watched it, I invite you all to look at the FULL version of it, which can be quite entertaining (personal judgement...), to bring up "disappointment to appointment". The link is (still): http://www.proinformatix.com/atpase.html Cheers for fears Sergio ________________________________________________________________________ _______________________________ Sergio Manzetti Research Scholar Centre of Molecular Biotechnology/ Supercomputer Facility Queensland University of Technology 2 George St. BRISBANE 4000 QLD AUSTRALIA email: s.manzetti@student.qut.edu.au Tlf: +61 7 3864 1434 www: http://www.life.sci.qut.edu.au/html/research/cmgenetics.html www2: http://www.its.qut.edu.au/hpc/ From chemistry-request@server.ccl.net Thu Nov 22 10:38:17 2001 Received: from Salicet.ucd.ie ([137.43.1.23]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id fAMFcGB04501 for ; Thu, 22 Nov 2001 10:38:16 -0500 X-Confirm-reading-to: Laurence.Cuffe@ucd.ie X-PMrqc: 1 Received: from CONVERSION-DAEMON.Salicet.ucd.ie by Salicet.ucd.ie (PMDF V6.0-025 #36961) id <0GN700F01KRAOZ@Salicet.ucd.ie> for chemistry@ccl.net; Thu, 22 Nov 2001 15:38:13 +0000 (GMT) Received: from elvira.ucd.ie ([137.43.24.26]) by Salicet.ucd.ie (PMDF V6.0-025 #36961) with ESMTP id <0GN700E4LKR3NN@Salicet.ucd.ie> for chemistry@ccl.net; Thu, 22 Nov 2001 15:37:52 +0000 (GMT) Date: Thu, 22 Nov 2001 15:38:07 +0000 From: Laurence Cuffe Subject: Re: CCL:Mysterious G98W output: The Summary!! In-reply-to: <00ae01c1733f$8b3dedb0$550f3bd4@olegas> To: chemistry@ccl.net Message-id: <3BFD1BDF.19867.12A9CC0@localhost> Organization: University College Dublin X-Mailer: Pegasus Mail for Win32 (v3.12c) Content-type: TEXT/PLAIN Priority: normal Date sent: Thu, 22 Nov 2001 11:18:29 +0100 From: Olegas Eicher-Lorka Subject: CCL:Mysterious G98W output: The Summary!! To: chemistry@ccl.net >Sorry Doug, but we're in Lithuania and we're used to buying our software > from "alternative" sources, which normally means no books, guides etc. So when we recieved G98W to make us feel at home, we burnt all the literature. > >Thanks everyone: > >Simon and Olegas > >One more question, the "humourous" quotes at the bottom of the G98 output have stopped being "humourous"- how do I switch them off? In view of your source of the software you may have copy protection problems with this feature, however if you delete the file L1.exe from your system it should get rid of the quotes. This step is NOT recommended if the software comes from a legitimate source. All the best Laurence Cuffe All the best > > > >