From inge.muszynski@uni-tuebingen.de Tue Jun 16 02:30:54 1998 Received: from mx01.uni-tuebingen.de (root@mx01.uni-tuebingen.de [134.2.3.11]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id CAA17420 Tue, 16 Jun 1998 02:30:52 -0400 (EDT) Received: from poseidon.pharm.chemie.uni-tuebingen.de (poseidon.pharm.chemie.uni-tuebingen.de [134.2.68.21]) by mx01.uni-tuebingen.de (8.8.8/8.8.8) with SMTP id IAA02229 for ; Tue, 16 Jun 1998 08:30:34 +0200 Date: Tue, 16 Jun 1998 08:30:34 +0200 Message-Id: <199806160630.IAA02229@mx01.uni-tuebingen.de> X-Sender: cpcmu01@cpcmu01.mail.uni-tuebingen.de X-Mailer: Windows Eudora Light Version 1.5.2 Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" To: chemistry@www.ccl.net From: Inge Muszynski Subject: j param in AM1 Dear CCL'lers, I am working with the AM1-Hamiltonian in Mopac 6.0 implemented in the Tripos software SYBYL. While minimizing Iodophenole I recognized that the atom J had a POSITIVE partial charge of 0,137. Is this correct or could this be due to the fact that the atom J is only incompletely parameterized within AM1? (From the page 3-6 in the MOPAC-manual I concluded that this would not be the case). Could you please help me how to prove the parameterization of J and tell me where to find the file where atoms are parameterized. Many thanks in advance. Inge Muszynski From Jiri.Krechl@spechem.cz Tue Jun 16 08:09:15 1998 Received: from prg.traveller.cz (prg.traveller.cz [193.85.2.2]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id IAA18869 Tue, 16 Jun 1998 08:09:14 -0400 (EDT) Received: from ntt (gate.spechem.cz [193.85.250.177]) by prg.traveller.cz (8.8.5.EUnet/EUnet-CZ) with SMTP id OAA13337 for ; Tue, 16 Jun 1998 14:09:12 +0200 (MET DST) Message-ID: <002301bd991f$80e57840$b1fa55c1@ntt.spechem.cz> From: "Jiri Krechl" To: Subject: molecular mechanics Date: Tue, 16 Jun 1998 14:08:33 +0200 MIME-Version: 1.0 Content-Type: text/plain; charset="windows-1250" Content-Transfer-Encoding: 7bit X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 4.72.2106.4 X-MimeOLE: Produced By Microsoft MimeOLE V4.72.2106.4 I am looking for simple molecular mechanics procedure with source code available to public. Any information please directly to: Jiri.Krechl@spechem.cz Thanks JK From famoises@usc.es Tue Jun 16 11:00:33 1998 Received: from uscmail.usc.es (uscmail.usc.es [193.144.75.8]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id LAA20091 Tue, 16 Jun 1998 11:00:21 -0400 (EDT) Received: from localhost (famoises@localhost) by uscmail.usc.es (8.8.5/8.8.5) with SMTP id RAA25960 for ; Tue, 16 Jun 1998 17:00:06 +0200 (MET DST) Date: Tue, 16 Jun 1998 17:00:06 +0200 (MET DST) From: Moises Iglesias Gonzalez Reply-To: Moises Iglesias Gonzalez To: chemistry@www.ccl.net Subject: CoCu system Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear CCL's: We are looking for information about the system Co-Cu (Cobalt-Copper, the diatomic molecule). Mainly, We need optimized distance, vibrational frequencies and magnetic moment, but any additional information is welcome. Some recent experimental or theoretical paper or book will do. We know the book by Gerhard Herzberg "Molecular spectra and molecular structure", but it is very old so we would like to get newer data. Thanks in advance. ____________________________________ Moises Iglesias Depto. Fisica Aplicada Facultade de Fisica U. Santiago de Compostela Santiago de Compostela, A Corunna Spain. ____________________________________ From bruno@antas.agraria.uniss.it Tue Jun 16 11:40:35 1998 Received: from ssmain.uniss.it (ssmain.uniss.it [193.205.8.2]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id LAA20551 Tue, 16 Jun 1998 11:40:31 -0400 (EDT) Received: from frodo.agraria.uniss.it (frodo.agraria.uniss.it [193.205.10.80]) by ssmain.uniss.it with SMTP (8.8.8/8.8.8) id RAA03072; Tue, 16 Jun 1998 17:39:24 +0200 (METDST) Message-ID: <35868F15.482F@antas.agraria.uniss.it> Date: Tue, 16 Jun 1998 17:41:35 +0200 From: bruno manunza X-Mailer: Mozilla 3.01Gold (Win95; I) MIME-Version: 1.0 To: Jiri Krechl CC: chemistry@www.ccl.net Subject: Re: CCL:molecular mechanics References: <002301bd991f$80e57840$b1fa55c1@ntt.spechem.cz> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Jiri Krechl wrote: > > I am looking for simple molecular mechanics procedure with source code > available to public. Any information please directly to: > Jiri.Krechl@spechem.cz > Dear Jiri, have a look to the software page of our web site http://antas.agraria.uniss.it hope it helps Regards Bruno -- Dr Bruno Manunza DISAABA Univ. of Sassari V.le Italia 39 07100 Sassari ITALY phone 39 79 229215 fax 39 79 229276 e_mail bruno@antas.agraria.uniss.it http://antas.agraria.uniss.it From elewars@alchemy.chem.utoronto.ca Tue Jun 16 19:22:06 1998 Received: from alchemy.chem.utoronto.ca (alchemy.chem.utoronto.ca [142.150.224.224]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id TAA23446 Tue, 16 Jun 1998 19:22:05 -0400 (EDT) Received: (from elewars@localhost) by alchemy.chem.utoronto.ca (8.7.4/8.7.3) id TAA12694 for chemistry@www.ccl.net; Tue, 16 Jun 1998 19:22:05 -0400 (EDT) Date: Tue, 16 Jun 1998 19:22:05 -0400 (EDT) From: "E. Lewars" Message-Id: <199806162322.TAA12694@alchemy.chem.utoronto.ca> To: chemistry@www.ccl.net Subject: BASIS SET OPTIMIZATION--HOW? 1998 June 15 Hello, Could someone please outline (just outline) how the ab initio basis sets of popular programs like Gaussian are optimized nowadays (best alphas and contraction coefficients): are these varied for a set of small molecules till the values which give the lowest energies are found? Or are they optimized for *atoms* ? Thanks E. Lewars ==================== From ep7@dent.okayama-u.ac.jp Tue Jun 16 23:03:15 1998 Received: from deews1.dent.okayama-u.ac.jp (deews1.dent.okayama-u.ac.jp [150.46.202.36]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id XAA24703 Tue, 16 Jun 1998 23:02:58 -0400 (EDT) From: ep7@dent.okayama-u.ac.jp Received: from [150.46.140.80] (yobou2.dent.okayama-u.ac.jp [150.46.140.80]) by deews1.dent.okayama-u.ac.jp (8.8.8/3.6W) with SMTP id MAA28405 for ; Wed, 17 Jun 1998 12:04:10 +0900 (JST) Message-Id: <199806170304.MAA28405@deews1.dent.okayama-u.ac.jp> Date: Wed, 17 Jun 1998 12:20:13 +0900 To: CHEMISTRY@www.ccl.net Subject: Sumarry: L MIME-Version: 1.0 Content-Type: text/plain; charset=iso-2022-jp X-Mailer: Eudora-J(1.3.8.5-J13) I summarize for L. Thank you for everybody. From: gaussian.com!fox@lorentzian.com (Doug Fox) Subject: Re: L To: uunet!dent.okayama-u.ac.jp!ep7%lorentzian.com@uunet.uu.net (正村) Date: Mon, 8 Jun 1998 11:41:30 -0400 (EDT) X-Mailer: ELM [version 2.4 PL24] Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit X-UIDL: 2a27181a61c7442940f5837830f7bd4d Prof. Masamura, As I described before nearly linear segments are described as a pair of linear bends in place of a valence bend and dihedral which become ill defined at the linear geometry. These start out as bends in a pair of orthogonal reference planes, typically chosen so one is 180.0. As the molecule optimizes the structure may move away from linear and so the two angles are measured to remain orthonal, i.e. the reference planes effectively change. Clearly this has moved to a nearly 20 degree bend and you should look to the cartesian coordinates for these three atoms to get the exact valence angle. One quick way to do this is to read the structure back into G94 with %kjob l202 %chk=mychk # HF ChkBas Geom=AllCheck which will stop after evaluating the symmetry and structure printouts for the final geometry. If you have a graphical interface which can read this final structure you can use it to measure this angle as well. > >optimized > >structures. > > Please teach me. > > One year ago, I received answer. > > For nearly linear segments of a molecule, 175.0 degreees or higher. > the possibility exists that the angle will open out to 180 degrees and > cause a numerical instability. As a result we define this as a linear angle > and include the second, orthogonal bend as well, instead of the deheadral. > Thus you will see two entrries with the same trio of atoms labveled "L". > One should be 180.0 degrees and the other nearly 180.0. > > However, I can not understand above. > For example, > L(1,12,13)=179.5716 > L(1,12,13)=198.5946 > What is these ? > > Please replay to me. > > Masao Masamura > Preventive Dentistry > Okayama University Dental School > Shikata-cho, 2-5-1 > Okayama 700 > Japan > FAX: 81-86-235ー6714 > e-mail: ep7@dent.okayama-u.ac.jp > Douglas J. Fox Director of Technical Support help@gaussian.com Content-Type: text/plain; charset="us-ascii" Date: Thu, 11 Jun 1998 07:35:21 +0200 To: ep7@dent.okayama-u.ac.jp From: Per-Ola Norrby Subject: Re: CCL:L X-UIDL: 5f5e8c83b204b4f86ec59bd9f54629e5 Dear ??? (I couldn't see your name?) >L(4,12,13)=175.0254 >L(4,12,13)=187.3401 <=== I think L(4,12,13) = D(4,12,13,X) ? These are linear bends. I'm not exactly up to date on the details, but I believe that when an angle is close to 180 degrees, you cannot use the last dihedral, so instead you use two angles to position "4". This works, because the program internally keeps track of keeping them orthogonal. >D(14,13,4,3)=19.8277 <==== I can not understand: A(13,12,4)=180 ? You cannot have a dihedral including an angle close to 180, so when you have an intervening linear bend, only the first and last atom are used. These situations are common with acetylenes and allenes, and also with some metals. Best regards, Per-Ola Norrby ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ Per-Ola Norrby, peon@medchem.dfh.dk Royal Danish School of Pharmacy, Dept. of Med. Chem. Universitetsparken 2, DK-2100 Copenhagen, Denmark Tel: +45-35376777-506, +45-35370850, fax +45-35370922 Date: Mon, 15 Jun 1998 11:00:05 +0200 From: Stefan Fau Reply-To: fau@mailer.uni-marburg.de Organization: Philipps-Universit閣 Marburg X-Mailer: Mozilla 3.01Gold (Win95; I) To: ep7@dent.okayama-u.ac.jp Subject: Re: L Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable X-UIDL: 2e439c9dd6d60799ac6cf300b3a23c44 Hi ep7, L-angles are used, when the angle of an atom-triple is close to 180 degrees. The pair of L-angles belongs to two perpendicular planes (which intersect in a line 'parallel' to the atomic triple). I can't say anything about your peculiar dihedral angle, but since this output seems to be in redundant internal coordinates, there should be enough other dihedral angles that are ok. Stefan Fau Philipps-Universit閣 Marburg fau@mailer.uni-marburg.de From ep7@dent.okayama-u.ac.jp Tue Jun 16 23:10:18 1998 Received: from deews1.dent.okayama-u.ac.jp (deews1.dent.okayama-u.ac.jp [150.46.202.36]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id XAA24739 Tue, 16 Jun 1998 23:09:44 -0400 (EDT) From: ep7@dent.okayama-u.ac.jp Received: from [150.46.140.80] (yobou2.dent.okayama-u.ac.jp [150.46.140.80]) by deews1.dent.okayama-u.ac.jp (8.8.8/3.6W) with SMTP id MAA28445 for ; Wed, 17 Jun 1998 12:11:08 +0900 (JST) Message-Id: <199806170311.MAA28445@deews1.dent.okayama-u.ac.jp> Date: Wed, 17 Jun 1998 12:27:10 +0900 To: CHEMISTRY@www.ccl.net Subject: XYZ to Zmat MIME-Version: 1.0 Content-Type: text/plain; charset=iso-2022-jp X-Mailer: Eudora-J(1.3.8.5-J13) Thank you for everybody. Other persons are the same opinion. Date: Thu, 11 Jun 1998 08:10:00 -0400 From: Ned Martin Subject: XYZ to Zmat To: ep7@dent.okayama-u.ac.jp X-Mailer: Microsoft Outlook Express 4.71.1712.3 Content-type: text/plain; charset="iso-8859-1" Content-transfer-encoding: 7bit X-MSMail-Priority: Normal X-MimeOLE: Produced By Microsoft MimeOLE V4.71.1712.3 X-Priority: 3 X-UIDL: 9e0af511eaaab70825230d1f053cf471 Masao, Use the newzmat utility: newzmat -ixyz -ozmat filename.xyz filename.com Then enter the charge and multiplicity (default 0, 1) when prompted. The filenames may have any extensions; I used .xyz and .com as examples. Good luck. Ned ************************************************************************ Ned H. Martin, W.S. DeLoach Professor Tel: (910) 962-3453 Department of Chemistry Fax: (910) 962-3013 University of North Carolina at Wilmington Wilmington, NC 28403-3297 email: martinn@uncwil.edu ************************************************************************ From ep7@dent.okayama-u.ac.jp Tue Jun 16 23:19:47 1998 Received: from deews1.dent.okayama-u.ac.jp (deews1.dent.okayama-u.ac.jp [150.46.202.36]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id XAA24816 Tue, 16 Jun 1998 23:19:42 -0400 (EDT) From: ep7@dent.okayama-u.ac.jp Received: from [150.46.140.80] (yobou2.dent.okayama-u.ac.jp [150.46.140.80]) by deews1.dent.okayama-u.ac.jp (8.8.8/3.6W) with SMTP id MAA28506 for ; Wed, 17 Jun 1998 12:21:06 +0900 (JST) Message-Id: <199806170321.MAA28506@deews1.dent.okayama-u.ac.jp> Date: Wed, 17 Jun 1998 12:37:09 +0900 To: CHEMISTRY@www.ccl.net Subject: Summary: newzmat for mixing internal and cartesian coordinates MIME-Version: 1.0 Content-Type: text/plain; charset=iso-2022-jp X-Mailer: Eudora-J(1.3.8.5-J13) I summarized it. Use the newzmat utility: newzmat -icart -ozmat filename.com filename2.com From hinde@oxygen.chem.utk.edu Tue Jun 16 23:42:52 1998 Received: from oxygen.chem.utk.edu (OXYGEN.CHEM.UTK.EDU [128.169.96.190]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with SMTP id XAA24960 Tue, 16 Jun 1998 23:42:52 -0400 (EDT) Received: (from hinde@localhost) by oxygen.chem.utk.edu (950413.SGI.8.6.12/950213.SGI.AUTOCF) id XAA26407 for CHEMISTRY@www.ccl.net; Tue, 16 Jun 1998 23:40:36 -0400 Date: Tue, 16 Jun 1998 23:40:36 -0400 From: hinde@oxygen.chem.utk.edu (Robert Hinde) Message-Id: <199806170340.XAA26407@oxygen.chem.utk.edu> To: CHEMISTRY@www.ccl.net Subject: G: CalDSu error message I am trying to optimize a molecule at the BP86/aug-cc-pvdz level. After two optimization steps I get the following message: CalDSu: NOpAll= 0 NOpUse= 0 but NOpSet= 2. CalDSu cannot use requested symmetry level. Error termination via Lnk1e in /g94dir/g94/l502.exe. Can anyone tell me what this rather cryptic error message means? Or better yet, how to avoid it? :-) Robert Hinde Univ. of Tennessee rhinde@utk.edu