From chemistry-request@server.ccl.net Tue Dec 17 16:37:39 2002 Received: from mtiwmhc13.worldnet.att.net ([204.127.131.117]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id gBHLbci21233 for ; Tue, 17 Dec 2002 16:37:39 -0500 Received: from dopetec ([138.23.156.82]) by mtiwmhc13.worldnet.att.net (InterMail vM.5.01.05.xx 201-253-122-126-xxx-20020920) with ESMTP id <20021217213738.LVFU20029.mtiwmhc13.worldnet.att.net@dopetec> for ; Tue, 17 Dec 2002 21:37:38 +0000 From: "Donald Keidel" To: Subject: How to restart Opt and SCF in Gaussian 98 Date: Tue, 17 Dec 2002 13:37:37 -0800 Message-ID: <004701c2a614$856041f0$529c178a@dopetec> MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_0048_01C2A5D1.773D01F0" X-Priority: 3 (Normal) X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook, Build 10.0.3416 X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2600.0000 Importance: Normal This is a multi-part message in MIME format. ------=_NextPart_000_0048_01C2A5D1.773D01F0 Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: 7bit Hello all, I am going to restart a job using the following line in my .com file. #P HF/6-31+G(d) SCF(Restart, qc, Maxcycle=500) Opt(Restart) is this the correct line to use to restart both the Opt and the SCF? Also, how can I determine if either the Opt or the SCF procedure have finished? Thank you in advance for all the help. Don ------------------------------------------------------------------------ --------------------------------------- Donald J. Keidel University of California, Riverside Department of Biochemistry and Molecular Biology Riverside, CA 92521 phone: (909) 787-5493 fax: (909) 787-4434 dkeidel397@att.net webpage: www.biochemistry.ucr.edu/gru/gradstudents/don_keidel/index.htm ------=_NextPart_000_0048_01C2A5D1.773D01F0 Content-Type: text/html; charset="us-ascii" Content-Transfer-Encoding: quoted-printable

Hello all,

I am going to restart a job using the following line = in my .com file.

#P HF/6-31+G(d) SCF(Restart, qc, Maxcycle=3D500) = Opt(Restart)

is this the correct line to use to restart both the = Opt and the SCF? Also, how can I determine if either the Opt or the SCF = procedure have finished? Thank you in advance for all the = help.

Don

------------------------------------------------------= ---------------------------------------------------------
Donald J. Keidel
University of California, Riverside
Department of Biochemistry and Molecular Biology
Riverside, CA = 92521
phone: (909) 787-5493
fax: (909) 787-4434
dkeidel397@att.net
webpage: www.biochemistry.ucr.edu/gru/gradstudents/don_keidel/index.htm<= /span>

------=_NextPart_000_0048_01C2A5D1.773D01F0-- From chemistry-request@server.ccl.net Wed Dec 18 09:34:26 2002 Received: from mail1.cc.huji.ac.il ([132.64.1.17]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id gBIEYOi01824 for ; Wed, 18 Dec 2002 09:34:25 -0500 Received: from 127.0.0.1 (localhost.localdomain [127.0.0.1]) by mail1.cc.huji.ac.il (Postfix) with SMTP id B38093FE3A; Wed, 18 Dec 2002 13:46:17 +0200 (IST) Received: by mail1.cc.huji.ac.il (Postfix, from userid 31998) id 8C6A33FE44; Wed, 18 Dec 2002 13:45:37 +0200 (IST) Received: from VMS.HUJI.AC.IL (vms.huji.ac.il [128.139.4.12]) by mail1.cc.huji.ac.il (Postfix) with SMTP id 073323FE43 for ; Wed, 18 Dec 2002 13:45:37 +0200 (IST) Received: by HUJIVMS via SMTP(132.64.98.82_39771) (HUyMail-V7f2); Wed, 18 Dec 2002 13:45:37 +0200 Received: by HUJIVMS via SMTP(132.64.98.82_39771) (HUyMail-V7f2); Wed, 18 Dec 2002 13:45:36 +0200 Message-Id: <5.1.0.14.0.20021218134210.00a78030@pob.huji.ac.il> X-Sender: ivan@pob.huji.ac.il X-Mailer: QUALCOMM Windows Eudora Version 5.1 Date: Wed, 18 Dec 2002 13:49:04 +0200 To: chemistry@ccl.net From: Ivan Aprahamian Subject: Question Mime-Version: 1.0 Content-Type: multipart/mixed; boundary="=====================_11205212==_" X-Spam-Status: No, hits=0.7 required=5.8 tests=AWL,SPAM_PHRASE_00_01 version=2.43 X-Spam-Level: --=====================_11205212==_ Content-Type: text/plain; charset="us-ascii"; format=flowed To whom may it concern, I was wondering what will be the best way to run calculations on a molecule that contains a cycopropyl anion which has an inverted carbon; please see the attached illustration. Thank you in advance ivan .................................... Ivan Aprahamian Department of Organic Chemistry, The Hebrew University of Jerusalem, Jerusalem, 91904, Israel. Tel: ++ 972-2-6586272/258 Fax: ++ 972-2-6527547 E-mail: ivan@pob.huji.ac.il --=====================_11205212==_ Content-Type: image/gif; name="cyclo.gif"; x-mac-type="47494666"; x-mac-creator="4A565752" Content-Transfer-Encoding: base64 Content-Disposition: attachment; filename="cyclo.gif" R0lGODlhXgCeAPcAAAAAAIAAAACAAICAAAAAgIAAgACAgMDAwMDcwNTQyAAAAP///////wAAAP8A AP//AAD/AAD//wAA//8A/wAAAP///////wAAAP8AAP//AAD/AAD//wAA//8A/wAAAP///////wAA AP8AAP//AAD/AAD//wAA//8A/wAAAP///////wAAAP8AAP//AAD/AAD//wAA//8A/wAAAP////// /wAAAP8AAP//AAD/AAD//wAA//8A/wAAAP///////wAAAP8AAP//AAD/AAD//wAA//8A/wAAAP// /////wAAAP8AAP//AAD/AAD//wAA//8A/wAAAP///////wAAAP8AAP//AAD/AAD//wAA//8A/wAA AP///////wAAAP8AAP//AAD/AAD//wAA//8A/wAAAP///////wAAAP8AAP//AAD/AAD//wAA//8A /wAAAP///////wAAAP8AAP//AAD/AAD//wAA//8A/wAAAP///////wAAAP8AAP//AAD/AAD//wAA //8A/wAAAP///////wAAAP8AAP//AAD/AAD//wAA//8A/wAAAP///////wAAAP8AAP//AAD/AAD/ /wAA//8A/wAAAP///////wAAAP8AAP//AAD/AAD//wAA//8A/wAAAP///////wAAAP8AAP//AAD/ AAD//wAA//8A/wAAAP///////wAAAP8AAP//AAD/AAD//wAA//8A/wAAAP///////wAAAP8AAP// AAD/AAD//wAA//8A/wAAAP///////wAAAP8AAP//AAD/AAD//wAA//8A/wAAAP///////wAAAP8A AP//AAD/AAD//wAA//8A/wAAAP///////wAAAP8AAP//AAD/AAD//wAA//8A/wAAAP///////wAA AP8AAP//AAD/AAD//wAA//8A/wAAAP///////wAAAP8AAP//AAD/AAD//wAA//8A/wAAAP////// /wAAAP8AAP//AP/78DpupYCAgP8AAAD/AP//AAAA//8A/wD//////yH5BAEAAAsALAAAAABeAJ4A AAj/ABcIHEiwoMGDCBMqXMiwocOHECNKnEixosWLGDNq3Mixo8ePIEOKtAig5MiTEwEIVImypUST LmMiZCmz5kqYC2jajEmTpc6dNnEC5TlUZsmeRV36HPgzKcqjTkFCXRn1ZNOmVUUKzcq1q9evOcGO xCp2I9myGc+ivah2bcW2blPG7Qh3LsS6dh3izctwL1+Ffv/OFMyWMEnDbxFTDKyYauOIjBtHVjxZ 8uOXlRFvvbxQZWbCnjkfnMo0rOibTJGaFv1T51LOWFWvtnzUpOvSj2MXlE15t8Hbknvqxh1cLe/T vwl+zgsceXLlzkf7jj6dOPXZjq9j3458+HXv1ME7/ye7fC357wnLlz2rXiz78IDhp5c/eHzn6G3b d4Wrnyt/+/e11F+ABNKF04AFzkdXdgjG15dWmz3V0HJCNQjZhIetZuFdeiV204YXYijXV3vVRRqI hXXo4HH7PYQXaWD59R5zHOZ0IF+B3cideSGiJliOufXYm4uwEXlZiaypeKSSSz542n9POhmlg1Mq 2B2VV9YHoHT0Vbell19ah99z6IE5JnTaZbdjlmpqxyJ9KLa45phxtljnfnf6F2Gac3bJZ5tpwshn nv79+RyhhRoq5p+IOrVnmYr2eaakkyraaFSXFvVopYZm6iigjEYKaqCRCkqqqJ4mlaqorLbq6quC BQEEADs= --=====================_11205212==_-- From chemistry-request@server.ccl.net Tue Dec 17 10:40:01 2002 Received: from mx3.trentu.ca ([206.248.118.2]) by server.ccl.net (8.11.6/8.11.0) with SMTP id gBHFe0i13493 for ; Tue, 17 Dec 2002 10:40:00 -0500 Received: (qmail 8918 invoked by uid 504); 17 Dec 2002 15:37:48 -0000 Received: from elewars@trentu.ca by mx3.trentu.ca by uid 501 with qmail-scanner-1.14 (fsecure: 4.15/4370/2002-12-13/2002-12-13. 2002-12-13/ Clear:. Processed in 0.4193 secs); 17 Dec 2002 15:37:48 -0000 X-Qmail-Scanner-Mail-From: elewars@trentu.ca via mx3.trentu.ca X-Qmail-Scanner: 1.14 (Clear:. Processed in 0.4193 secs) Received: from unknown (HELO trentu.ca) (206.248.117.30) by mx3.trentu.ca with SMTP; 17 Dec 2002 15:37:48 -0000 Message-ID: <3DFF45ED.39BAE639@trentu.ca> Date: Tue, 17 Dec 2002 10:42:38 -0500 From: elewars X-Mailer: Mozilla 4.79 [en] (WinNT; U) X-Accept-Language: en MIME-Version: 1.0 To: pop14848 , chemistry@ccl.net Subject: Re: CCL:calculated IR frequencies References: <200212171132190004.8A96B794@mailhub.uni-konstanz.de> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit 2002 Dec 17 Re calc and exp IR freqs, harmonic corrections and exp corrections: Harmonic freqs: K. P. Huber, G. Herzberg, "Molecular Spectra and Molecular Structure. IV. Constants of Diatomic Molecules", Van Nostrand Reinhold, New York, 1979. Calc freqs cf. raw exp. and harmonic: W. J. Hehre, L. Radom, P. v. R. Schleyer, J. A. Pople, "Ab Initio Molecular Orbital Theory", Wiley, New Yprk, 1986, pp 234-5. A. St-Amant, chapter 2, p 235, in "Reviews in Computational Chemistry, Vol. 7, K. B. Lipkowitz and D. B. Boys, Eds., VCH, New York, 1996. F. Jensen, "Introduction to Computational Chemistry", Wiley, New York, 1999, pp 271-4. Empirical correction of calc freqs to agree better with exp (probably the canonical paper): A. P. Scott, L. Radom, J. Phys. Chem., 1996, 100, 16502. E. Lewars ============ pop14848 wrote: > Hi, > > can someone point me to a paper discussing calculated IR frequencies vs. experimental frequencies? I am not intersted in differences between DFT and HF/MP2 calculations but the general reasons of the overestimated IR-frequencies due to harmonic fundamentals instead of anharmonicity aswell as too short bond-length (in HF calcilations) etc. > In fact a paper not only disussion a mediate factor of about 0.9 but also discussing the difference of this factor from calculated frequence to frequence in one molecule would be perfekt (like 0.90 for one one normal mode, 0.93 for the next) > > Thanks in advance > > Eike Huebner > > -= This is automatically added to each message by mailing script =- > CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins > Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net From chemistry-request@server.ccl.net Tue Dec 17 22:27:42 2002 Received: from smtp.dicp.ac.cn ([159.226.238.50]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id gBI3Rfi26339 for ; Tue, 17 Dec 2002 22:27:41 -0500 Received: from apple ([159.226.159.204]) by smtp.dicp.ac.cn (8.11.6/8.11.6) with SMTP id gBI3ReY22837 for ; 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Tue, 17 Dec 2002 19:29:21 -0500 Received: from mailscan-out2.cac.washington.edu (mailscan-out2.cac.washington.edu [140.142.33.17]) by mxout5.cac.washington.edu (8.12.1+UW01.12/8.12.1+UW02.11) with SMTP id gBI0THpB021511 for ; Tue, 17 Dec 2002 16:29:17 -0800 Received: FROM smtp.washington.edu BY mailscan-out2.cac.washington.edu ; Tue Dec 17 16:29:17 2002 -0800 Received: from donald ([128.95.128.116]) by smtp.washington.edu (8.12.1+UW01.12/8.12.1+UW02.11) with SMTP id gBI0TGmX000923 for ; Tue, 17 Dec 2002 16:29:16 -0800 Message-ID: <009401c2a62b$be78af60$74805f80@donald> From: "Carsten Detering" To: Subject: Amber and antechamber Date: Wed, 18 Dec 2002 01:23:52 +0100 Organization: University of Washington MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_0091_01C2A634.202AC7E0" X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 6.00.2600.0000 X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2600.0000 This is a multi-part message in MIME format. ------=_NextPart_000_0091_01C2A634.202AC7E0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Hi all, I have yet another question concerning Amber7: I finally got along with LEaP, which assigned Amber99 charges to my RNA = allright. I get no error message loading the molecule as a PDB file into = LEaP. Unfortunately, I cannot save it from LEaP as a mol2 file. So I = saved it as an AmberPrep file, which I then converted to a mol2 file, = using antechamber. However, this only wrote the first nucleotide, and = not the entire RNA. Does anyone have an idea how to do that??? I appreciate your help. Cheers, Carsten ~~~~~~~~~~~~~~~~~~~~~~~~~~~ Carsten Detering, Ph.D. University of Washington Seattle, WA 98195 Phone 206-543-5081 Fax 206-685-8665 email detering@u.washington.edu ~~~~~~~~~~~~~~~~~~~~~~~~~~~ ------=_NextPart_000_0091_01C2A634.202AC7E0 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable

Hi all,

I have yet another question concerning Amber7:

I finally got along with LEaP, which assigned Amber99 charges = to my=20 RNA allright. I get no error message loading the molecule as a PDB = file=20 into LEaP. Unfortunately, I cannot save it from LEaP as a mol2 file. So = I saved=20 it as an AmberPrep file, which I then converted to a mol2 file, using=20 antechamber. However, this only wrote the first nucleotide, and not the = entire=20 RNA. Does anyone have an idea how to do that???

I appreciate your help.

Cheers, Carsten

~~~~~~~~~~~~~~~~~~~~~~~~~~~
Carsten Detering, = Ph.D.
University of=20 Washington
Seattle, WA 98195
Phone 206-543-5081
Fax=20 206-685-8665
email detering@u.washington.edu~~~~~~~~~~~~~~~~~~~~~~~~~~~

------=_NextPart_000_0091_01C2A634.202AC7E0-- From chemistry-request@server.ccl.net Wed Dec 18 16:47:46 2002 Received: from cornell.edu ([132.236.56.6]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id gBILlki11332 for ; Wed, 18 Dec 2002 16:47:46 -0500 Received: from cornell.edu (lock.ccmr.cornell.edu [128.84.241.198]) by cornell.edu (8.9.3/8.9.3) with ESMTP id QAA27346 for ; Wed, 18 Dec 2002 16:47:45 -0500 (EST) Sender: cc236@cornell.edu Message-ID: <3E00ED01.65843C02@cornell.edu> Date: Wed, 18 Dec 2002 16:47:46 -0500 From: Connie Chang X-Mailer: Mozilla 4.79 [en] (X11; U; Linux 2.4.18-10smp i686) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net Subject: Gaussian98W and hessian again.... Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi -- I was wondering if someone could answer two questions I have about Gaussian's output where the hessian is concerned... I obtained the hessian from the archive portion of the output file starting from NImag=0|| and ending at ||. I read this is as lower triangular matrix and filled in the blanks. THen I converted it to units of erg/cm^2 and divided by the mass (my molecule contains all of the same atoms). Then I diagonalize this matrix to get the eigenvalues and eigenvectors. My question is -- Why don't the eigenvectors I get this way match the eigenvectors given by the output part of the file: 6 7 8 9 10 AG BU AG BG AU Frequencies --- 133.7777 217.8831 219.3526 220.1136 220.5401 Reduced masses --- 12.0000 12.0000 12.0000 12.0000 12.0000 Force constants --- 0.1265 0.3356 0.3402 0.3426 0.3439 IR Intensities --- 0.0000 0.0109 0.0000 0.0000 0.0086 Raman Activities --- 0.0000 0.0000 0.0000 0.0000 0.0000 Depolarizations --- 0.0000 0.0000 0.0000 0.0000 0.0000 Coord Atom Element: 1 1 6 0.06549 0.02995 -0.02972 0.00000 0.00000 2 1 6 0.00350 -0.02940 0.01482 0.00000 0.00000 3 1 6 0.00000 0.00000 0.00000 0.04056 -0.03387 1 2 6 0.06720 -0.00807 0.00067 0.00000 0.00000 2 2 6 0.00539 -0.02838 -0.00791 0.00000 0.00000 3 2 6 0.00000 0.00000 0.00000 -0.00920 0.00683 1 3 6 -0.05283 -0.00382 0.00879 0.01422 -0.01471 2 3 6 0.02203 0.00592 0.00998 -0.00374 0.00309 3 3 6 0.00014 -0.00365 0.00415 -0.01084 0.00751 etc.etc.? I need the entire eigenvector matrix and not just 3*N-6 translation/rotational modes. The eigenvalues seem to match up fine, but the eigenvectors are different. Am I somehow scrambling the atom order or something? I've heard that Gaussian prints out the hessian as well using some IOP option. Does anyone know the exact option? Thanks, Connie From chemistry-request@server.ccl.net Wed Dec 18 19:59:34 2002 Received: from ultra.chem.ucsb.edu ([128.111.114.119]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id gBJ0xYi14651 for ; Wed, 18 Dec 2002 19:59:34 -0500 Received: from localhost (bushnell@localhost) by ultra.chem.ucsb.edu (8.12.3/8.12.3) with ESMTP id gBJ0xTCM012227; Wed, 18 Dec 2002 16:59:30 -0800 (PST) Date: Wed, 18 Dec 2002 16:59:29 -0800 (PST) From: John Bushnell To: wangyan cc: "chemistry@ccl.net" Subject: Re: CCL:Help : about the convergence of the molecule which contain Fe atom In-Reply-To: <200212180327.gBI3ReY22837@smtp.dicp.ac.cn> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-Virus-Scanned: by amavisd-milter (http://amavis.org/) Hi, The problem you appear to be having is with the geometry optimization convergence using B3LYP rather than the SCF convergence. You should probably do "opt = calcFC" to start the geometry optimization in a good direction. Yes, this can be expensive, but you will save in wasted oscillations (as you saw) later. In extreme cases, opt = CaclAll may be needed, which is of course extremely expensive (effectively doing a frequency calculation at every step of the optimization). - John On Wed, 18 Dec 2002, wangyan wrote: > Dear CCLer: > I am optimizating a zeolite cluster. In this cluster a silicon atom was substituted by a Fe atom. > I know that the molecules which contains Fe atom is diffuclt to > convergence , so I had tried my ways. at last I only finish my > optimiation completely using hf/sto-g. The following s is my process : > 1 Do a single point caculation with hf/sto-3g 2 by guess=read , finish > a optimization . This is iput file : #p hf/sto-3g > SCF(conver=6,maxcyc=500) guess=read > popt(z-matrix,maxcyc=200) 3.then with input file : #p hf/sto-3g > SCF(conver=6,maxcyc=500) guess=read popt(z-matrix,maxcyc=200) .It > also finish completely. But , when I using ub3lyp/sto-sg to optimize , > the question appears . this is my input file : #p UB3LYP/sto-3g > SCF(conver=6,maxcyc=500) geom=check guess=read > popt(z-matrix,maxcyc=200). At begining , the optimization is good and > have got a yes convergence in RMS force.But after it got a yes > convergence in RMS force, the optimation came back to very bad > convergence situation. The maximum force, the RMS force , the maximum > displacement and RMS displacement are all about 0.1. The bad > convergence oscillate many cycles. my question is how to do to finish > this optimization? Any suggestion is welcome. Thank you in advance. > wangyan >