From chemistry-request@server.ccl.net Wed Aug 15 04:15:16 2001 Received: from smtp1.dti.ne.jp ([202.216.228.36]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f7F8FEv18778 for ; Wed, 15 Aug 2001 04:15:15 -0400 Received: from b159504364 (PPP91.fukuoka-ip.dti.ne.jp [211.132.92.91]) by smtp1.dti.ne.jp (8.9.3/3.7W) with SMTP id RAA05763 for ; Wed, 15 Aug 2001 17:15:12 +0900 (JST) Message-ID: <00f801c12561$7bca5e80$5b5c84d3@b159504364> From: "TELKUNI" To: Subject: True Parameter of VWN Functional of Gaussian98W Date: Wed, 15 Aug 2001 17:08:35 +0900 MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 5.00.2615.200 X-MimeOLE: Produced By Microsoft MimeOLE V5.00.2615.200 Hello! CCLers I'm leaning the correlation functional "VWN " and try to use it on Gaussian98W. I would like to know true G98W's VWN parameter. According to the original paper of VWN (S. H. Vosko, L. Wilk, and M. Nusair: Can. J. Phys. vol.58, 1200 (1980)), the functional employs the parameters as follows: x0(x-zero) = -0.409286, b = 13.0720, c = 42.7298 (in Section4). But the other books and articles, there are different combination of parameters, for example(paramagnetic state): x0 = -0.10498, b = 3.72744, c = 12.9352 (by Density Functional Theory And Its Application - Japanese). I think G98W might employ the original paper's parameters, but I don't know the articles nor method to check it. If you know the method(for example: using IOp option) or articles, please teach me. All responses, I will appreciate. I will summarize them and send to CCL. Best regards, Telkuni ---------------------------------------------- Telkuni Tsuru Kyushyu Electronic Technology and Research telkuni@venus.dti.ne.jp ---------------------------------------------- From chemistry-request@server.ccl.net Wed Aug 15 08:32:45 2001 Received: from mail2.zrz.tu-berlin.de ([130.149.4.14]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f7FCWiv13606 for ; Wed, 15 Aug 2001 08:32:44 -0400 Received: from mailszrz.zrz.tu-berlin.de ([130.149.4.11]) by mail2.zrz.tu-berlin.de with esmtp (exim-3.32) id 15Wzqg-0002nu-00; Wed, 15 Aug 2001 14:32:38 +0200 Received: from natrium.chem.tu-berlin.de ([130.149.169.143]) by mailszrz.zrz.tu-berlin.de with esmtp (exim-3.32) id 15Wzqg-0005vf-00; Wed, 15 Aug 2001 14:32:38 +0200 Mime-Version: 1.0 X-Sender: chwu0531@mailszrz.zrz.tu-berlin.de Message-Id: In-Reply-To: <00f801c12561$7bca5e80$5b5c84d3@b159504364> References: <00f801c12561$7bca5e80$5b5c84d3@b159504364> Date: Wed, 15 Aug 2001 14:32:37 +0200 To: "TELKUNI" From: Christoph van =?iso-8859-1?Q?W=FCllen?= Subject: Re: CCL:True Parameter of VWN Functional of Gaussian98W Cc: chemistry@ccl.net Content-Type: text/plain; charset="iso-8859-1" ; format="flowed" Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id f7FCWjv13607 1.) Gaussian VWN functional uses the parameters given in *table* 3 of the VWN paper. These parameters approximate the RPA results, not the Monte-Carlo results! These parameters are used for the closed-shell and completely spin-polarized (only alpha spin electrons) cases. 2.) Gaussian VWN does not use the RPA spin stiffness parameters to inter- polate between these two cases, but uses the interpolation valid for the exchange energy of a uniform electron gas. (I do not know what happened that they chose this option). With the TZ basis sets of Ahlrichs and Schafer you should get the following energies Atom: He(ground state) He(1s2s Triplet) N Atom(Quartet) HF -2.85989543 -1.79100228 -54.40232895 LDA3 -2.86994363 -1.77391426 -54.26495985 LDA5 -2.83256107 -1.73613023 -54.13356852 BLYP -2.90460692 -1.79477978 -54.58993091 B3LYP -2.91302754 -1.80220154 -54.60420134 Things to note: (1) open shell calculations done spin-unrestricted. Hartree-Fock results given for comparison (if they do not agree, something is wrong with the basis set). (2) The three examples cover the three cases (spin-unpolarized, completely spin-polarized, partially spin-polarized) mentioned above (the inter- polation problem only shows up for the N atom). (3) LDA3 = the LDA functional implemented in Gaussian LDA5 = the LDA functional used by the rest of us (i.e. SVWN5 in G98) (4) B3LYP contains LDA3 (I guess this is the right choice, since B3LYP was 'invented' by the Gaussian developers). (5) I implemented these functionals in my own program and got the same results, the only way to *really* know what is implemented in G98. (6) I suggest that my numbers are checked by others, so that our community knowns which functional is which. Please use highly accurate numerical grids. If the reference numbers should be obtained with another basis set, please make a suggestion. From chemistry-request@server.ccl.net Wed Aug 15 09:00:48 2001 Received: from t12mail.lanl.gov ([128.165.22.99]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f7FD0lv14164 for ; Wed, 15 Aug 2001 09:00:48 -0400 Received: from MatCha (ts-usr-136.lanl.gov [128.165.7.136]) by t12mail.lanl.gov (8.9.1a/8.9.1) with SMTP id HAA25630; Wed, 15 Aug 2001 07:00:44 -0600 (MDT) Content-Type: text/plain; charset="iso-8859-1" From: Matt Challacombe Reply-To: MChalla@LANL.Gov Organization: Group T-12, Los Alamos National Lab To: "TELKUNI" , Subject: Re: CCL:True Parameter of VWN Functional of Gaussian98W Date: Wed, 15 Aug 2001 05:52:01 -0600 X-Mailer: KMail [version 1.2] References: <00f801c12561$7bca5e80$5b5c84d3@b159504364> In-Reply-To: <00f801c12561$7bca5e80$5b5c84d3@b159504364> MIME-Version: 1.0 Message-Id: <0108150552010V.02205@MatCha> Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id f7FD0mv14165 Right, you will want to have a look at the very helpfull paper: @article{Hertwig97, author = {R. H. Hertwig and W. Koch}, title = {On the parameterization of the local correlation functional. What is Becke-3-LYP?}, journal = {Chem. Phys. Lett.}, year = {1997 }, volume = 268, number = {5-6}, pages = {345-351}, month = {APR 18} } Good luck! -Matt PS. This is your brain. This is your brain on VWN, any questions? -- a quote from the MESA dft module On Wednesday 15 August 2001 02:08 am, TELKUNI wrote: > Hello! CCLers > > I'm leaning the correlation functional "VWN " and try to use it on > Gaussian98W. I would like to know true G98W's VWN parameter. > > According to the original paper of VWN (S. H. Vosko, L. Wilk, and M. > Nusair: Can. J. Phys. vol.58, 1200 (1980)), the functional employs the > parameters as follows: x0(x-zero) = -0.409286, b = 13.0720, c = 42.7298 (in > Section4). > > But the other books and articles, there are different combination of > parameters, for example(paramagnetic state): x0 = -0.10498, b = 3.72744, c > = 12.9352 (by Density Functional Theory And Its Application - Japanese). > > I think G98W might employ the original paper's parameters, but I don't > know the articles nor method to check it. If you know the method(for > example: using IOp option) or articles, please teach me. > > All responses, I will appreciate. > I will summarize them and send to CCL. > > > Best regards, > Telkuni > > > ---------------------------------------------- > Telkuni Tsuru > > Kyushyu Electronic Technology and Research > > telkuni@venus.dti.ne.jp > ---------------------------------------------- > > > -= This is automatically added to each message by mailing script =- > CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins > MAILSERV@ccl.net -- HELP CHEMISTRY or HELP SEARCH > CHEMISTRY-SEARCH@ccl.net -- archive search | Gopher: gopher.ccl.net > 70 Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: > jkl@ccl.net -- Matt Challacombe, Ph.D. http://www.t12.lanl.gov/~mchalla/ Los Alamos National Laboratory email: MChalla@LANL.Gov Group T-12, Mail Stop B268 phone: (505) 665-5905 Los Alamos, New Mexico 87545 fax: (505) 665-3909 From chemistry-request@server.ccl.net Wed Aug 15 10:04:10 2001 Received: from igor.urz.unibas.ch ([131.152.1.3]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f7FE4Av15209 for ; Wed, 15 Aug 2001 10:04:10 -0400 Received: from unibas.ch (filou.chemie.unibas.ch [131.152.112.19]) by igor.urz.unibas.ch (PMDF V6.0-24 #41480) with ESMTP id <0GI4004BV4EXET@igor.urz.unibas.ch> for chemistry@ccl.net; Wed, 15 Aug 2001 16:04:09 +0200 (MET DST) Date: Wed, 15 Aug 2001 16:03:08 +0200 From: Stanislav Ivan Subject: Force Field To: chemistry@ccl.net Message-id: <3B7A811C.ECFAB7B8@unibas.ch> MIME-version: 1.0 X-Mailer: Mozilla 4.75 [en] (WinNT; U) Content-type: text/plain; charset=us-ascii Content-transfer-encoding: 7bit X-Accept-Language: en Dear CCLers, I am PhD student and I am just starting calculations using Force Field methods. Could you please advice/suggest me some basic references about Force Field with the description of basic methods (AMBER, MM2 etc.) and their preformance on different systems (proteins,DNA, general organic systems), reliability of such calculations, .... Thanks in advance. Stanislav Ivan Institute of Organic Chemistry Basel Switzerland From chemistry-request@server.ccl.net Wed Aug 15 10:25:42 2001 Received: from earth.ox.ac.uk (root@[163.1.22.6]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f7FEPgv15603 for ; Wed, 15 Aug 2001 10:25:42 -0400 Received: from pauling.earth.ox.ac.uk (pauling [163.1.22.22]) by earth.ox.ac.uk (8.9.3+Sun/8.9.1) with ESMTP id PAA02591 for ; Wed, 15 Aug 2001 15:25:38 +0100 (BST) From: Keith Refson MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Message-ID: <15226.34400.843223.871821@gargle.gargle.HOWL> Date: Wed, 15 Aug 2001 15:25:36 +0100 To: Computational Chemistry List CCL Subject: Potential parameter fitting X-Mailer: VM 6.95-rfhacked under 21.1 (patch 12) "Channel Islands" XEmacs Lucid I'm searching for software to perform potential parameter fitting of simple forms (ie lennard-jones, buckingham forms possibly with charges) to a tabulated set of points representing an energy hypersurface for simple ions or small molecules? Does anyone there know of any software which is able to do this in a reasonably flexible manner? I'm hoping for something simpler and more flexible than the old "roll your own energy and derivative routine" for plugging into a general least-squares fit program. I'm sure this wheel must have been invented many times.... Keith Refson -- Dr Keith Refson, "Paradigm is a word too often used by those who would Dept of Earth Sciences like to have a new idea but cannot think of one." Parks Road, -- Mervyn King, Deputy Governor, Bank of England Oxford OX1 3PR, UK Keith.Refson@ Tel: 01865 272026 earth.ox.ac.uk Fax: 01865 272072 From chemistry-request@server.ccl.net Wed Aug 15 07:04:40 2001 Received: from server.mldnet.com (root@[212.56.192.20]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f7FB4av12202 for ; Wed, 15 Aug 2001 07:04:37 -0400 Received: from ppp-212.56.193.101.mldnet.com (ppp-212.56.193.101.mldnet.com [212.56.193.101]) by server.mldnet.com (8.9.3/8.9.3) with ESMTP id OAA09810 for ; Wed, 15 Aug 2001 14:04:04 +0300 Date: Sat, 15 Sep 2001 13:42:44 +0300 From: Mike Peleah X-Mailer: The Bat! (v1.53d) Reply-To: Mike Peleah X-Priority: 3 (Normal) Message-ID: <402572553.20010915134244@yahoo.com> To: chemistry@ccl.net Subject: NMR and EPR sofware MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear chemistry, Is there any (free) software to predict H1 NMR and/or EPR spectra on the base of quantum chemical calculations? The most interesting for me is software compatible with PC GAMESS and/or ArgusLab. Best regards, Mike mailto:MikePeleah@yahoo.com From chemistry-request@server.ccl.net Wed Aug 15 11:34:36 2001 Received: from aloha.unl.edu ([129.93.36.9]) by server.ccl.net (8.11.0/8.11.0) with SMTP id f7FFYav17304 for ; Wed, 15 Aug 2001 11:34:36 -0400 Received: from localhost by aloha.unl.edu (AIX 3.2/UCB 5.64/4.03) id AA10611; Wed, 15 Aug 2001 10:21:25 -0500 Date: Wed, 15 Aug 2001 10:21:25 -0500 (CDT) From: ggallup@aloha.unl.edu Reply-To: ggallup@aloha.unl.edu To: chemistry@ccl.net Subject: Valence Bond Package Available In-Reply-To: <3B7A811C.ECFAB7B8@unibas.ch> Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII An occasional query about the availability of a Valence Bond package has appeared on this list. I would like to announce the availability of the University of Nebraska CRUNCH package. The source code, compilation scripts, and the user manual are bundled as a gzipped tar archive for down-loading at http://phy-ggallup.unl.edu/crunch/ . Separate copies of the user manual in pdf or postscript format and the general README file are also available for perusal. G. A. Gallup Voice: 402-435-6967 Department of Chemistry FAX: 402-435-6823 University of Nebraska-Lincoln Email: ggallup@aloha.unl.edu or Lincoln, NE 68588-0304 ggallup1@unl.edu From chemistry-request@server.ccl.net Wed Aug 15 11:50:01 2001 Received: from qtp.ufl.edu ([128.227.89.3]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f7FFo1v17759 for ; Wed, 15 Aug 2001 11:50:01 -0400 Received: from pc1 (pc1 [128.227.192.187]) by qtp.ufl.edu (8.9.1a/8.9.1) with SMTP id LAA27854; Wed, 15 Aug 2001 11:50:12 -0400 (EDT) Message-ID: <030d01c125a2$c63a8c60$bbc0e380@qtp.ufl.edu> From: "Stefan Fau" To: "David Magers" Cc: "CCL - all" References: Subject: Re: CCL:reported decimal accuracy in cartesian displacement vectors inG98 Date: Wed, 15 Aug 2001 11:55:57 -0400 MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 5.00.2314.1300 X-MimeOLE: Produced By Microsoft MimeOLE V5.00.2314.1300 Hi David, the keyword you are looking for is # ... freq(hpmodes) I believe in G94 it was named slightly different. Gaussian has a lot of information on-line at http://www.gaussian.com/techinfo.htm including detailed descriptions of all the keywords. If in doubt, you can also read the headers of the source code (check the link you are interested in and link1). Stefan ______________________________________________________________________ Dr. Stefan Fau | fau@qtp.ufl.edu Quantum Theory Project | (352) 392-6714 University of Florida Gainesville, FL 32611-8435 From chemistry-request@server.ccl.net Wed Aug 15 12:24:23 2001 Received: from qtp.ufl.edu ([128.227.89.3]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f7FGONv18398 for ; Wed, 15 Aug 2001 12:24:23 -0400 Received: from pc1 (pc1 [128.227.192.187]) by qtp.ufl.edu (8.9.1a/8.9.1) with SMTP id MAA28205; Wed, 15 Aug 2001 12:24:08 -0400 (EDT) Message-ID: <033701c125a7$87e59220$bbc0e380@qtp.ufl.edu> From: "Stefan Fau" To: "Alexander Kulak" Cc: "CCL - all" References: Subject: CCL:Re:1,5-Diaminotetrazole aminogroup structure Date: Wed, 15 Aug 2001 12:29:53 -0400 MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 5.00.2314.1300 X-MimeOLE: Produced By Microsoft MimeOLE V5.00.2314.1300 Hi Alexander, Prof. Norrby raised valid points. However, there also seems to be a problem with respect to the basis set you used. It appears that molecules with many (or maybe neighboring) nitrogen atoms are not described well enough by split valence plus polarization basis sets like 6-31G(d) or cc-pVDZ. This was illustrated on the example of N6. Various authors found structures close to C2h using split valence basis sets. Upon addition of diffuse functions (aug-cc-pVDZ) or when using cc-pVTZ, the molecule was calculated to have C2h symmetry. We believe the interaction of lone pairs to be responsible for the phenomenon. See M. Tobita, R.J. Bartlett, J. Phys. Chem. A 2001, 105, 4107 and references cited therein. Stefan ______________________________________________________________________ Dr. Stefan Fau | fau@qtp.ufl.edu Quantum Theory Project | (352) 392-6714 University of Florida Gainesville, FL 32611-8435 From chemistry-request@server.ccl.net Wed Aug 15 12:24:59 2001 Received: from iris.iupui.edu ([134.68.220.32]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f7FGOxv18413 for ; Wed, 15 Aug 2001 12:24:59 -0400 Received: from macgw.chem.iupui.edu (macgw.chem.iupui.edu [134.68.137.71]) by iris.iupui.edu (8.9.3/8.9.3/IUPUIPO.20010613) with SMTP id LAA28190; Wed, 15 Aug 2001 11:24:57 -0500 (EST) Message-ID: Date: 15 Aug 2001 11:27:52 -0500 From: "Boyd" Subject: re: force fields To: "Ivan, Stanislav" Cc: "OSC CCL" X-Mailer: Mail*Link SMTP for Quarterdeck Mail; Version 4.1.0 Dear Stanislav, Regarding your request for information on force fields, you might want to check out Reviews in Computational Chemistry. This book series has had a number of chapters on force fields, molecular mechanics, and simulations. Two of these chapters are: I. Pettersson and T. Liljefors, in Reviews in Computational Chemistry, VCH, New York, 1996, Vol. 9, pp. 167-189. Molecular Mechanics Calculated Conformational Energies of Organic Molecules: A Comparison of Force Fields. M. Jalaie and K. B. Lipkowitz, in Reviews in Computational Chemistry, Wiley-VCH, New York, 2000, Vol. 14, pp. 441-486. Appendix: Published Force Field Parameters for Molecular Mechanics, Molecular Dynamics, and Monte Carlo Simulations. Good luck, Don Donald B. Boyd, Ph.D. Editor, Reviews in Computational Chemistry http://chem.iupui.edu/rcc/rcc.html Gordon Research Conferences on Computational Chemistry http://chem.iupui.edu/rcc/grccc.html Department of Chemistry Indiana University-Purdue University at Indianapolis Indianapolis, Indiana 46202-3274, U.S.A. E-mail boyd@chem.iupui.edu From chemistry-request@server.ccl.net Wed Aug 15 12:42:00 2001 Received: from ribotargets.com ([194.129.39.11]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f7FGfxv18896 for ; Wed, 15 Aug 2001 12:41:59 -0400 Received: from szilva by echo.ribotargets.com with local (Exim 3.13 #1) id 15X3he-00022l-00; Wed, 15 Aug 2001 16:39:34 +0000 Date: Wed, 15 Aug 2001 16:39:34 +0000 From: Szilveszter Juhos To: Keith Refson Cc: CHEMISTRY@ccl.net Subject: Re: CCL:Potential parameter fitting Message-ID: <20010815163934.B6464@echo.ribotargets.com> References: <15226.34400.843223.871821@gargle.gargle.HOWL> Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Disposition: inline User-Agent: Mutt/1.2.5i In-Reply-To: <15226.34400.843223.871821@gargle.gargle.HOWL>; from Keith.Refson@earth.ox.ac.uk on Wed, Aug 15, 2001 at 03:25:36PM +0100 On Wed, Aug 15, 2001 at 03:25:36PM +0100, Keith Refson wrote: > I'm searching for software to perform potential parameter fitting > of simple forms (ie lennard-jones, buckingham forms possibly with gnuplot can do a pretty good job at the beginning. With some shell-scripting you can do it even in batch mode. http://www.ucc.ie/gnuplot/gnuplot-faq.html Szilva From chemistry-request@server.ccl.net Wed Aug 15 13:27:49 2001 Received: from mail.chem.tamu.edu (IDENT:root@[165.91.176.8]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f7FHRmv20137 for ; Wed, 15 Aug 2001 13:27:49 -0400 Received: from [165.91.177.236] (account fan HELO mail.chem.tamu.edu) by mail.chem.tamu.edu (CommuniGate Pro SMTP 3.4.7) with ESMTP id 222890 for chemistry@ccl.net; Wed, 15 Aug 2001 12:23:11 -0500 Sender: fan@ccl.net Message-ID: <3B7AB16D.B1D12F27@mail.chem.tamu.edu> Date: Wed, 15 Aug 2001 12:29:17 -0500 From: Huajun Fan X-Mailer: Mozilla 4.76C-SGI [en] (X11; I; IRIX 6.5 IP32) X-Accept-Language: en MIME-Version: 1.0 CC: chemistry@ccl.net Subject: question about ONIOM method References: <804576578.20010809231305@bancorp.ru> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear CCLers, I would like to do an oniom calculations with two layers on and Ir complex. Since none of the examples Gaussian given used any general basis, I wonder how I can input pseudo into the high layer atoms, like Ir. Here is my attempt to use gen and pseudo, but results in an error (both list below, more details/questions are at the end of this email). Does anyone out there has any suggest/advice/experience ont this? ANything is appreciated. THanks in advance!! ===input=== %Chk=oniom_1a.chk %nproc=4 %mem=80000000 #p oniom(b3lyp/gen:uff) pseudo=read scf=(maxcycle=256 conver=6) iop(6/7=3) gfinput opt=(maxcycle=256) 1a in ONIOM method 0 1 atom specifications ... ... atom specifications Ir S 3 1.00 0.2350000000D+01 -0.1678464000D+01 0.1582000000D+01 0.2095255000D+01 ... ... **** 6 7 9 10 11 12 13 14 15 16 17 18 19 sto-3g **** Ir P 0 lanl2dz ===end of input=== ===error== ... ... (Enter /usr/local/g98/l301.exe) Standard basis: VSTO-3G (5D, 7F) Atomic number 77 exceeds maximum of 54 in STO -- maximum used. Basis set in the form of general basis input: 1 0 SP 3 1.00 0.8910101433D+00 -0.3842642607D+00 -0.3481691526D+00 0.4797538759D+00 -0.1972567438D+00 0.6290323690D+00 0.2119157236D+00 0.1375495512D+01 0.6662832743D+00 ... ... PSEUDOPOTENTIAL PARAMETERS ==================================== WANTED AN INTEGER AS INPUT. FOUND A FLOATING POINT NUMBER AS INPUT. S 3 1.00 ? Error termination via Lnk1e in /usr/local/g98/l301.exe. ==== It looks G98 is asking for an integer for potention on Ir. However, it was reading the Ir valence basis set (the number right after "atom specifications", instead of reading from the end of the input file, where pseudo-potention is. Is there anything that I didn't specify right in the input file? Interestingly, in the middle of the output file (see above), G98 starts to use sto-3g for every atoms for second (high) layer. Is this causing hte problem and how I can fix it? Sorry for a long question and thank you all for your time reading it. huajun From chemistry-request@server.ccl.net Wed Aug 15 13:53:14 2001 Received: from xaver.org.chemie.tu-muenchen.de ([129.187.121.57]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f7FHrDv20741 for ; Wed, 15 Aug 2001 13:53:13 -0400 Received: (from guen@localhost) by xaver.org.chemie.tu-muenchen.de (SGI-8.9.3/8.9.3) id TAA99443 for chemistry@ccl.net; Wed, 15 Aug 2001 19:53:12 +0200 (MESZ) Message-Id: <200108151753.TAA99443@xaver.org.chemie.tu-muenchen.de> Date: Wed, 15 Aug 2001 19:53:11 +0200 From: Robert.Guenther@ch.tum.de Subject: Superimpose/Superposition cyclic peptides To: chemistry@ccl.net MIME-Version: 1.0 Content-Type: TEXT/plain; charset=us-ascii Dear CCL'ers, starting a new project on the conformational properties cyclic penta- and hexapeptides the following problem came up: I have about 50 different cyclopeptides with a known 3-dimensional conformation (either determined by experiments or obtained by strucutural calculation using molecular dynamics). My goal is to take these structures, cluster their backbone conformations and derive some conformational families. Unfortunately, the residue numbering within the cyclic peptides is somehow arbitary, thus preventing a simple atom-on-atom superimposing, e.g. the molecule cyclo-(Pro-Ala-Ala-Ala-Ala) could have the same conformation as cyclo-(Ala-Ala- Pro-Ala-Ala) but it is not detected by common superimposing fomralisms, because the numbering scheme of the residues is different (the Pro's have the number 1 and 3 respectively). Does anyone knows about a programm or formalism which could help me to tackle this problem? Any hint is appreciated and will be posted on CCL. Thanx in advance, Robert +---------------------------------------------------------------+ | Dr. Robert Guenther [e-mail:Robert.Guenther(at)ch.tum.de] |-+ | Institut fuer organische Chemie und Biochemie II, TU Muenchen |#| | Lichtenbergstr. 4, D-85747 Garching |#| +---------------------------------------------------------------+#| +----------------------------------------------------------------+ From chemistry-request@server.ccl.net Wed Aug 15 12:34:32 2001 Received: from mail-nb00s0.nbnet.nb.ca ([198.164.200.23]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f7FGYWv18677 for ; Wed, 15 Aug 2001 12:34:32 -0400 Received: from IP010166115218.mta.ca ([142.166.95.211]) by mail-nb00s0.nbnet.nb.ca (Post.Office MTA v3.5.3 release 223 ID# 0-68911U130000L130000S0V35) with ESMTP id ca for ; Wed, 15 Aug 2001 13:34:31 -0300 Message-Id: <5.0.2.1.0.20010815133423.00aab880@mailserv.mta.ca> X-Sender: mculf@mailserv.mta.ca X-Mailer: QUALCOMM Windows Eudora Version 5.0.2 Date: Wed, 15 Aug 2001 13:41:15 -0300 To: chemistry@ccl.net From: Miroslava Culf Subject: g98w vs g98 Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii"; format=flowed Dear All, I just noticed that there is an incredible difference in price for Gaussian 98 for Windows and for Unix (difference of about $11000). So I was wondering why is that? What are the advantages of running Gaussian 98 on say SGI or Sun vs. PC? Thanks very much, Miroslava Miroslava Culf Mount Allison University Canada tel: 506-853-8395 e-mail: mculf@mta.ca From chemistry-request@server.ccl.net Wed Aug 15 19:30:59 2001 Received: from ivory.trentu.ca ([192.75.12.103]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f7FNUxv05481 for ; Wed, 15 Aug 2001 19:30:59 -0400 Received: from trentu.ca ([204.225.13.50]) by trentu.ca (PMDF V5.2-32 #37862) with ESMTP id <01K76AAPZP4S001DGQ@trentu.ca> for chemistry@ccl.net; Wed, 15 Aug 2001 19:30:30 EDT Date: Wed, 15 Aug 2001 19:36:36 -0400 From: elewars Subject: Re: CCL:Force Field To: Stanislav Ivan , chemistry@ccl.net Message-id: <3B7B0784.ED5CDFD0@trentu.ca> MIME-version: 1.0 X-Mailer: Mozilla 4.7 [en] (WinNT; I) Content-type: text/plain; charset=us-ascii Content-transfer-encoding: 7bit X-Accept-Language: en References: <3B7A811C.ECFAB7B8@unibas.ch> Hello, You might read "Molecular Mechanics Across chemistry", by Rappe and Casewit, 1997. E. Lewars ===== Stanislav Ivan wrote: > Dear CCLers, > > I am PhD student and I am just starting calculations using Force Field > methods. > Could you please advice/suggest me some basic references about Force > Field with the description of basic methods (AMBER, MM2 etc.) and their > preformance on different systems (proteins,DNA, general organic > systems), reliability of such calculations, .... > Thanks in advance. > > Stanislav Ivan > Institute of Organic Chemistry > Basel > Switzerland > > -= This is automatically added to each message by mailing script =- > CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins > MAILSERV@ccl.net -- HELP CHEMISTRY or HELP SEARCH > CHEMISTRY-SEARCH@ccl.net -- archive search | Gopher: gopher.ccl.net 70 > Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net