From chemistry-request@server.ccl.net Thu Apr 10 21:44:31 2003 Received: from mx1.ustc.edu.cn ([218.22.21.1]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h3B1iU310701 for ; Thu, 10 Apr 2003 21:44:30 -0400 Received: from dxl ([202.38.82.79]) by mx1.ustc.edu.cn (8.8.7/8.8.6) with ESMTP id JAA25724 for ; Fri, 11 Apr 2003 09:26:37 +0800 Message-Id: <200304110126.JAA25724@mx1.ustc.edu.cn> Date: Fri, 11 Apr 2003 9:28:32 +0800 From: ¶¡Ñ¸À× Reply-To: dxl@mail.ustc.edu.cn To: CCls Subject: RE: question: EA of O2 Organization: Öйú¿Æ´óÑ¡¼ü»¯Ñ§ÊµÑéÊÒ X-mailer: FoxMail 4.0 beta 2 [cn] Mime-Version: 1.0 Content-Type: multipart/mixed; boundary="=====000_Dragon028458805546_=====" This is a multi-part message in MIME format. --=====000_Dragon028458805546_===== Content-Type: text/plain; charset="GB2312" Content-Transfer-Encoding: base64 RGVhciBBbGyjug0KDQqhoaGhVGhhbmsgeW91ICxEYXZpZCBTaG9iZSENCglUaGUgNi0zMTErK0cq KiBpcyB0aGUgb25seSBiYXNpcyBJIHRyaWVkIHdpdGggZGlmZnVzZSBmdW5jdGlvbnMuIFNvIEkg dGhpbmsgDQoJdGhpcyBpcyB0aGUgbW9zdCBpbXBvcnRhbnQgcG9pbnQuIA0KDQoJTm93IEkgdGVz dCBhdWctY2MtcFZUWiwgYW5kIGFsc28gZ290IGEgcXVpdGUgZ29vZCByZXN1bHQuCQ0KDQogCQkJ CQ0KoaGhoaGhoaGhoaGhoaGhoaGhoaGhoaGhoaGhoURpbmcgWHVubGVpDQqhoaGhoaGhoaGhoaGh oaGhoaGhoaGhoaGhoaGhMjAwMy0wNC0xMQ0KX19fX19fX19fX19fX19fX19fX19fX19fX19fX19f X19fX19fX19fX19fX19fXw0KRGluZyBYdW5sZWksIFBoLkQuIENhbmRpZGF0ZQ0KT3BlbiBMYWJv cmF0b3J5IG9mIEJvbmQgU2VsZWN0aXZlIENoZW1pc3RyeQ0KVW5pdmVyc2l0eSBvZiBTY2llbmNl ICYgVGVjaG5vbG9neSBvZiBDaGluYQ0KSGVmZWksIEFuaHVpIDIzMDAyNiwgUC5SLkNoaW5hDQpU ZWwuOiAwMDg2LTU1MS0zNjAzNDE4DQpGYXguOiAwMDg2LTU1MS0zNjAyOTY5DQpFLW1haWw6IGR4 bEBtYWlsLnVzdGMuZWR1LmNuDQpIdHRwOi8vd3d3LmJzYy51c3RjLmVkdS5jbi9+ZHhsDQpfX19f X19fX19fX19fX19fX19fX19fX19fX19fX19fX19fX19fX19fX19fX19fX19fX19fX19fX19fX19f X19fX19fX19fX19fX19fX19fX19fX19fX19fX19fXwkNCglNeSBuZXh0IHF1ZXN0aW9uOiBJcyA2 LTMxMSsrRyoqIHRoZSBvbmx5IGJhc2lzIHlvdSB0cmllZCB3aXRoIGRpZmZ1c2UgZnVuY3Rpb25z ICh1c3VhbGx5IGluZGljYXRlZCBieSBhICcrJyBpbiB0aGUgbmFtZSk/ICAgVGhlc2UgYXJlIHVz dWFsbHkgbmVjZXNzYXJ5IGZvciBhbnkgY2FsY3VsYXRpb24gaW52b2x2aW5nIGFuaW9ucy4gIA0K DQpZb3UgbWlnaHQgYWxzbyB3YW50IHRvIGNoZWNrIGZvciBzcGluIGNvbnRhbWluYXRpb24uICAN Cg0KLS1EYXZpZCBTaG9iZSANCg0KDQo= --=====000_Dragon028458805546_===== Content-Type: image/gif; name="LittleBoy.GIF" Content-Transfer-Encoding: base64 Content-Disposition: FoxmailIcon; filename="LittleBoy.GIF" R0lGODlhIAAgANQAAGCXzwCAgGBnYP/IkPzJmpFjPBsNA2Q8HxQDACIGAk4HADYDAA0AAP///wAA ANPT05KSkm5ubmVlZUZGRiUlJRgYGBEREQ8PDwcHBwMDAwAAAAAAAAAAAAAAAAAAAAAAACH/C05F VFNDQVBFMi4wAwEAAAAh/sJodHRwOi8vd3d3LnJ0bHNvZnQuY29tL2FuaW1hZ2ljLwoKQ3JlYXRl ZCB3aXRoIEFuaW1hZ2ljIEdJRiBWIDEuMjJhCmJ5IFJpZ2h0IHRvIExlZnQgU29mdHdhcmUgSW5j LgoKVG8gc3VwcHJlc3MgdGhpcyBtZXNzYWdlIGluIHRoZSByZWdpc3RlcmVkIHZlcnNpb24KdW5j aGVjayAiT3B0aW9ucyB8IEFuaW1hZ2ljIGNvbW1lbnQgZnJhbWUiCgAh+QQJGQABACwAAAAAIAAg AAAF1mAgjmRpnmiqrqrjvjCLugNsO3LpDPz91rgcggf07XqyYa/nI9ZWytqy6HQGT1HrtEq8mhjc 45b7NImB5DTSrP6py6UoLfweLEwGpuBcJ95LYEANYm5vfyQOeQ4Ng12LfFyHIw5gi41AApdqkiIO CUxdjJppnAGBYYyQBQUERAoleW2QRAWuJFmOfbW1rySnfVy7A70jsV3ARAc8xCO/RXNkC8rDWGGz ZAgpzsgD2Srbfd4rCZ/ALjki5OXWXjKWoz2D6AEvooM2ojEtAADvqfz+BgE0EQIAIfkECRkAAQAs AAAAACAAIAAABc5gII5kaZ5oqq6q474wi7oDbDty6Qz8/da4HIIH9O16smGv5yPWVsrasuh0Bk9R 67RKvJoY3OOW+zSJgeQ00qz+qculKC38HixMhum5TryXwFKBVHV+JA55R2KJhGZgMFt7XIUjDglM XZhvkyKAYW5OBQUERAoleW2RRAWkJFldqVWrq6UknXxcsgO0I6eZtwMHPLsjtkVzZAvBulievwgp xb8DzyrRfNQrCZa3Ljki2tueXjIODeaR5eMrL+bnNu0xLQAA5e0NDvP18PkmIQAh+QQJGQABACwA AAAAIAAgAAAF02AgjmRpnmiqrqrjvjCLug9sO3LpPPz91rgchgf07XqyYa/nI9ZWytqy6HQGT1Hr tEq8mjLc45b7NImB5DTSrP6py6UoLfx+VEwWpuRcJ95LYEANYm5vfyQOeQ4Ng12LfFyHIw5gi41A EpdqkiIOF0xdjJppnAGBYYyQERFOFCV5bZBErDyuI1mOfaystiOnfVy7D70isF3ARBO1X1U2m8rD WGGyZBgpv8g81irYwNsrF5/ALjki4eLTXjKWoz2D5QEvooM2ojEtEBDsqfn7g/0mQgAAOw== --=====000_Dragon028458805546_=====-- From chemistry-request@server.ccl.net Thu Apr 10 16:20:07 2003 Received: from marcy.nas.nasa.gov ([129.99.113.17]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h3AKK6304978 for ; Thu, 10 Apr 2003 16:20:06 -0400 Received: from localhost (ioana@localhost) by marcy.nas.nasa.gov (8.11.7+Sun/8.11.6/NAS 8.11.6-5n) with ESMTP id h3AKJtP07432; Thu, 10 Apr 2003 13:19:55 -0700 (PDT) Date: Thu, 10 Apr 2003 13:19:55 -0700 (PDT) From: Ioana Cozmuta To: Pradipta Bandyopadhyay cc: chemistry@ccl.net Subject: Re: CCL:Matlab!! In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi Pradipta, I am not sure if I understand it right, if you want to plot the potential V at each set of coordinates (x,y,z) then you already have a 4D function. So you would need something like the 3 coordinates and a color for the 4th value. I know AVS can do that but you have to learn how to use it. Regarding matlab. Let's say you have indeed 3 columns of data: x, y, z or z, y, and V. The way I do it is I read all data in one matrix and then split that in three (of course you can read it in four but you can only plot 3 at a time Here is a piece I am using: close all; clear all; fid = fopen('datafile.dat', 'r'); a = fscanf(fid, '%g'); fclose(fid); n = size(a,1)/3; for i = 1 : n x(i) = b(3 * i - 2); y(i) = b(3 * i - 1); z(i) = b(3 * i); end; plot3(x, y, z, '.'); grid on; (you need a graphical display with this last option so in case you ssh do not forgot to forward it). I think however that you should try and use something else. If you are generating the electrostatic potential from a Delphi calculation the InsightII interface has the possibility to let you plot that. Alternatively you may use VMD to do this plots. Below is an e-mail from John Stone from the VMD list. Hope this is of some help for you, Ioana ********************************* John Stone escreveu: > Dear Vlad, > There are two VMD scripts available which may be of interest to you > since you have access to Delphi. One is "potsel" which calculates > potential for an atom selection in VMD, and the other is "potsurf" which > colors a surface representation in VMD by the potential values supplied > by Delphi. These two scripts should be a good starting point for you to > get VMD working with Delphi. > > The two scripts are here: > http://www.ks.uiuc.edu/Research/vmd/script_library/scripts/potsel/ > http://www.ks.uiuc.edu/Research/vmd/script_library/scripts/potsurf/ > > Along the same lines, I believe that Nathan Baker's APBS package comes > with some scripts to allow it to work with VMD. It is available for > free, and they've got a web portal setup for running jobs on the NPACI > machines: > http://agave.wustl.edu/apbs/ > > Thanks, From chemistry-request@server.ccl.net Fri Apr 11 07:15:34 2003 Received: from puga.vdu.lt ([193.219.38.32]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h3BBFY303082 for ; Fri, 11 Apr 2003 07:15:34 -0400 Received: from amavis by puga.vdu.lt with scanned-ok for chemistry@ccl.net id 193wUx-0001QP-00; Fri, 11 Apr 2003 13:15:11 +0200 Received: from vaidila.vdu.lt ([193.219.38.52] ident=mail) by puga.vdu.lt with esmtp for chemistry@ccl.net id 193wUx-0001QE-00; Fri, 11 Apr 2003 13:15:11 +0200 Received: from vejas.vdu.lt ([193.219.38.82] helo=localhost) by vaidila.vdu.lt with esmtp for chemistry@ccl.net id 193wVX-0007BZ-00; Fri, 11 Apr 2003 13:15:47 +0200 Date: Fri, 11 Apr 2003 14:15:31 +0300 From: Arturas X-Mailer: The Bat! (v1.44) UNREG / CD5BF9353B3B7091 Reply-To: Arturas Organization: SemteX X-Priority: 3 (Normal) Message-ID: <105166948198.20030411141531@vaidila.vdu.lt> To: CCL Subject: Coordination compouds Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Virus-Scanned: by AMaViS snapshot-20020300 Hello CCL'ers, Can anybody point to info about structure and chemistry of dimers of Fe(X)5, where X - any monodentate ligand (CN or other.) Also, what the best QM/MM and ab initio software to calculate transition metal cpmplexes (not GAMESS,GAUSSIAN) ? -- Best regards, Arturas Z. From chemistry-request@server.ccl.net Fri Apr 11 07:42:50 2003 Received: from smtp4.dti.ne.jp ([202.216.228.39]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h3BBgn303760 for ; Fri, 11 Apr 2003 07:42:49 -0400 Received: from oemcomputer (PPP25.fukuoka-ip.dti.ne.jp [211.132.92.25]) by smtp4.dti.ne.jp (3.08s) with SMTP id h3BBgkiP024113 for ; Fri, 11 Apr 2003 20:42:48 +0900 (JST) Message-ID: <000b01c3001e$facd8e20$195c84d3@oemcomputer> From: "Telkuni" To: Subject: Gaussian98W's IOp list Date: Fri, 11 Apr 2003 20:39:14 +0900 MIME-Version: 1.0 Content-Type: text/plain; charset="iso-2022-jp" Content-Transfer-Encoding: 7bit X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 5.50.4133.2400 X-MimeOLE: Produced By Microsoft MimeOLE V5.50.4133.2400 Hello, CCLers. Does anyone have Gaussian98W's IOp list? (I'm using verA.7) I always utilize Gaussian's IOp page http://www.gaussian.com/iops.htm , but it is not available now. The IOp functions which I especially like to know are 30=1/8; 8/6=1,10=1,23=2,27=262144000/1; 9/27=262144000,41=6,42=1,48=2/14; . (These are concerning the TDDFT.) ...Any responses I'll appreciate and summarize them. Thanks in advance. ---------------------------------------------------- Telkuni Tsuru telkuni@venus.dti.ne.jp From chemistry-request@server.ccl.net Fri Apr 11 08:29:09 2003 Received: from dedalus.lcc.ufmg.br ([150.164.65.10]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h3BCT8305462 for ; Fri, 11 Apr 2003 08:29:08 -0400 Received: from dedalus.lcc.ufmg.br (loopback [127.0.0.1]) by dedalus.lcc.ufmg.br (8.12.8p1/8.12.8) with ESMTP id h3BCN73q027102; Fri, 11 Apr 2003 09:23:07 -0300 Received: from localhost (amolive@localhost) by dedalus.lcc.ufmg.br (8.12.8p1/8.12.8/Submit) with ESMTP id h3BCN6F2027100; Fri, 11 Apr 2003 09:23:06 -0300 Date: Fri, 11 Apr 2003 09:23:06 -0300 (BSC) From: andre mauricio de oliveira X-X-Sender: amolive@dedalus To: Sergio Manzetti cc: chemistry@ccl.net Subject: Re: CCL:MOPAC format from mol file In-Reply-To: <00f801c2ff89$58bb5670$a259f081@uio.no> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII dear Dr Manzetti, You should replace `KEYWORDS GO HERE` for the suitable keywords needed for your calculus (see keywords list in MOPAC manual). Regards. On Thu, 10 Apr 2003, Sergio Manzetti wrote: > Hi, I try to generate a MOPAC calculation of NADP, but when I try with the input file it says unrecognized keyword, or atom ill defined...below is the MOPAC input for NADP, can anyone see something missing? Thanks. > > Sergio > > KEYWORDS GO HERE > C 0.0000000 0 0.000000 0 0.000000 0 0 0 0 0.0000 > C 1.4909987 1 0.000000 0 0.000000 0 1 0 0 0.0000 > C 1.4589154 1 120.833751 1 0.000000 0 1 2 0 0.0000 > C 1.5952887 1 104.179711 1 -123.629997 1 1 2 3 0.0000 > C 1.4327690 1 118.649162 1 -177.109970 1 4 1 2 0.0000 > C 1.4961080 1 107.216845 1 -161.441326 1 5 4 1 0.0000 > C 1.4141955 1 113.692259 1 -69.678566 1 6 5 4 0.0000 > C 1.4861497 1 114.497941 1 51.716667 1 6 5 4 0.0000 > C 1.4452941 1 111.437239 1 74.248685 1 8 6 5 0.0000 > C 1.5054733 1 103.365827 1 -166.496868 1 8 6 5 0.0000 > C 1.4574546 1 111.809306 1 -86.763311 1 10 8 6 0.0000 > C 1.4501824 1 106.004635 1 161.480085 1 7 6 5 0.0000 > C 1.4742222 1 107.653685 1 -139.809374 1 12 7 6 0.0000 > C 1.3833969 1 128.944472 1 66.940975 1 13 12 7 0.0000 > C 1.2992633 1 112.520808 1 178.715024 1 14 13 12 0.0000 > C 1.3880497 1 104.385214 1 -0.091869 1 15 14 13 0.0000 > C 1.4212055 1 132.803663 1 -178.929926 1 16 15 14 0.0000 > C 1.3238100 1 121.797140 1 0.190214 1 17 16 15 0.0000 > C 1.3672524 1 118.021273 1 -179.725459 1 17 16 15 0.0000 > C 1.3491634 1 120.848602 1 -0.066268 1 19 17 16 0.0000 > C 1.3502274 1 125.054262 1 -0.679602 1 20 19 17 0.0000 > C 1.3539457 1 111.183849 1 0.730735 1 16 15 14 0.0000 > O 1.5778419 1 110.549256 1 126.272978 1 1 2 3 0.0000 > N 1.5977684 1 134.654605 1 -121.941769 1 23 1 2 0.0000 > N 1.4758096 1 110.162467 1 -56.814322 1 24 23 1 0.0000 > N 1.5009081 1 105.285562 1 72.156186 1 24 23 1 0.0000 > N 1.5660166 1 104.006219 1 -178.870480 1 24 23 1 0.0000 > N 1.4258156 1 118.281226 1 69.379294 1 27 24 23 0.0000 > N 1.5245626 1 111.272573 1 175.371156 1 28 27 24 0.0000 > N 1.4342420 1 110.854111 1 -60.335961 1 29 28 27 0.0000 > N 1.5326307 1 114.247710 1 57.889983 1 29 28 27 0.0000 > N 1.4234219 1 112.607565 1 144.895209 1 31 29 28 0.0000 > N 1.5163852 1 105.507122 1 -95.103814 1 31 29 28 0.0000 > N 1.4066321 1 113.843089 1 -150.480848 1 33 31 29 0.0000 > N 1.4146388 1 111.185567 1 114.063306 1 30 29 28 0.0000 > N 1.4537538 1 111.078782 1 -139.680558 1 35 30 29 0.0000 > N 1.4161479 1 118.169858 1 79.144271 1 36 35 30 0.0000 > N 1.4306551 1 116.150232 1 -179.373873 1 37 36 35 0.0000 > N 1.4574762 1 121.740928 1 -178.042998 1 38 37 36 0.0000 > N 1.2482388 1 120.855729 1 167.276205 1 39 38 37 0.0000 > N 1.3598312 1 121.250981 1 -10.757352 1 39 38 37 0.0000 > N 1.4154049 1 118.632746 1 0.854415 1 38 37 36 0.0000 > N 1.3635670 1 123.585731 1 -1.005756 1 42 38 37 0.0000 > N 1.3617566 1 118.413749 1 0.448534 1 43 42 38 0.0000 > C 1.6104652 1 123.853336 1 -145.123171 1 11 10 8 0.0000 > C 1.5048751 1 109.327762 1 -91.096377 1 45 11 10 0.0000 > C 1.5109020 1 102.991438 1 29.325753 1 45 11 10 0.0000 > C 1.4871210 1 100.481918 1 147.314143 1 45 11 10 0.0000 > > Andre Mauricio de Oliveira VOICE +55-031-374-1325 +55-031-499-5765 FAX +55-031-499-5700 Laboratorio de QSAR e Modelagem Molecular Nucleo de Estudos em Quimica Medicinal (NEQUIM) NEQUIM's Homepage: http://www.qui.ufmg.br/~nequim Departamento de Quimica ICEx Federal University of Minas Gerais Av Antonio Carlos 6627 Pampulha ZIP CODE 31270-901 Belo Horizonte MG Brazil From chemistry-request@server.ccl.net Fri Apr 11 03:30:35 2003 Received: from ciril.fr ([193.50.27.66]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h3B7UY315935 for ; Fri, 11 Apr 2003 03:30:34 -0400 Received: from host20.lctn.uhp-nancy.fr (host20.lctn.uhp-nancy.fr [193.50.239.24]) by ciril.fr (8.12.9/8.12.9/Guy-01-04-2003) with ESMTP id h3B7UXc1023143; Fri, 11 Apr 2003 09:30:33 +0200 (METDST) Received: from lctn.uhp-nancy.fr (pt-xav.lctn.uhp-nancy.fr [193.50.239.125]) by host20.lctn.uhp-nancy.fr (AIX4.3/8.9.3/8.9.3) with ESMTP id JAA24598; Fri, 11 Apr 2003 09:20:27 +0200 Message-ID: <3E966E79.A16E2FB8@lctn.uhp-nancy.fr> Date: Fri, 11 Apr 2003 09:27:53 +0200 From: Xavier Assfeld X-Mailer: Mozilla 4.75 [fr] (Win98; U) X-Accept-Language: fr MIME-Version: 1.0 To: Damian A Scherlis Perel CC: chemistry@ccl.net Subject: Re: CCL:spin contamination References: Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit X-Scanned-By: arcturus.ciril.fr Hey, have you checked the HOMO-LUMO gap? If it is too small, the MP2 results will diverge, and it is better to use variational method instead of perturbation theory. Seeing your S**2 values, I wonder if the singlet state is really the ground state? Hope this helps. Damian A Scherlis Perel a écrit : > Dear all, > > I have performed UHF calculations on pi dimers which are > known to be singlet states, to eventually compute the MP2 > energies. I got the singlet UHF wave function, which > turned out to be unstable. The stable state, though, > about 0.1 hartree lower in E, exhibits a large extent > of spin contamination: > > S**2 before annihilation: 3.7642, after: 14.6554 > > Moreover, if MP2 is applied to both HF wave functions, the > UMP2 energy that results from the pure state, initially higher, > is lower than the corresponding to the contaminated state. > > I wonder what state is more reliable, if any, to get the > total energies. All comments will be appreciated. > > Thanks! > > ------------------------ > Damian Scherlis > Department of Materials Science & Engineering > Massachusetts Institute of Technology > damians@mit.edu > 617 253 6026 > > -= 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 -- ...Xav Ast. Pr. Xavier Assfeld Xavier.Assfeld@lctn.uhp-nancy.fr Laboratoire de Chimie théorique (T) 33 3 83 68 43 74 Université Henri Poincaré (F) 33 3 83 68 43 71 F-54506 Nancy B.P. 239 http://www.lctn.uhp-nancy.fr From chemistry-request@server.ccl.net Fri Apr 11 02:57:02 2003 Received: from ns.ciac.jl.cn ([202.98.16.1]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h3B6uq315322 for ; Fri, 11 Apr 2003 02:56:55 -0400 Received: from zhang1 (localhost [127.0.0.1]) by ns.ciac.jl.cn (8.9.1/8.9.1) with SMTP id PAA22925 for ; Fri, 11 Apr 2003 15:00:21 +0800 (CST) Message-Id: <200304110700.PAA22925@ns.ciac.jl.cn> From: "zjwu" To: "chemistry@ccl.net" Subject: PCM frequency calculation X-mailer: Foxmail 4.2 [cn] Mime-Version: 1.0 Content-Type: multipart/alternative; boundary="=====002_Dragon728447207021_=====" Date: Fri, 11 Apr 2003 14:57:40 +0800 This is a multi-part message in MIME format. --=====002_Dragon728447207021_===== Content-Type: text/plain; charset="GB2312" Content-Transfer-Encoding: 7bit Dear cclers, Does anybody know how to run PCM frequency calculation on PCM optimized geometry? I have tried to run PCM frequency calculation with the keywords: #B3LYP/6-31g(d,p) freq=numer scrf=(pcm or cpcm, solvent=water) but it seems the frequency calculation never stops. Any suggestions are appreciated. Regards, Zhijian Wu --=====002_Dragon728447207021_===== Content-Type: text/html; charset="GB2312" Content-Transfer-Encoding: 7bit

Dear cclers,

Does anybody know how to run PCM frequency calculation on PCM optimized geometry? I have tried to run PCM frequency calculation with the keywords:

#B3LYP/6-31g(d,p) freq=numer scrf=(pcm or cpcm, solvent=water)

but it seems the frequency calculation never stops. Any suggestions are appreciated.

Regards,

Zhijian Wu

--=====002_Dragon728447207021_=====-- From chemistry-request@server.ccl.net Fri Apr 11 03:14:30 2003 Received: from tigris.klte.hu ([193.6.138.33]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h3B7ET315594 for ; Fri, 11 Apr 2003 03:14:29 -0400 Received: from cthulhu (193.6.133.59) by tigris.klte.hu (MX V5.1-A Vn6f) with SMTP; Fri, 11 Apr 2003 09:56:49 +0200 Message-ID: <002001c2fffa$43de1550$3b8506c1@cthulhu> From: "Tamas E. Gunda" To: "Sergio Manzetti" , References: <00f801c2ff89$58bb5670$a259f081@uio.no> Subject: Re: CCL:MOPAC format from mol file Date: Fri, 11 Apr 2003 09:16:26 +0200 MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_001D_01C3000B.073AA530" X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 5.50.4920.2300 X-MimeOLE: Produced By Microsoft MimeOLE V5.50.4920.2300 This is a multi-part message in MIME format. ------=_NextPart_000_001D_01C3000B.073AA530 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable MOPAC files begin with three data lines, the first is for the key words, = which say to the program what to do, how to do etc, consult with the = MOPAC or target program documentation. The next two lines may contain additional info, then the coordinate = section follows: EF GNORM=3D0.100 MMOK GEO-OK AM1 MULLIK PULAY . . C 0.000000 0 0.000000 0 0.000000 0 0 0 0 C 1.408173 1 0.000000 0 0.000000 0 1 0 0 C 1.389786 1 119.080032 1 0.000000 0 2 1 0 C 1.397278 1 120.531311 1 0.000000 1 3 2 1 .... =20 By the way, you coordinates look somehow corrupted, they contain two = molecules and a lonely O atom (H2O?), all the atoms of the second one = are N atoms. With regards Tamas E. Gunda ---------------------------------------------- Prof. Tamas E. Gunda Department of Pharmaceutical Chemistry Medical and Health Center University of Debrecen, POBox 36 H-4010 Debrecen, Hungary tamasgunda@tigris.klte.hu ----- Original Message -----=20 From: Sergio Manzetti=20 To: chemistry@ccl.net=20 Sent: Thursday, April 10, 2003 19:46 Subject: CCL:MOPAC format from mol file Hi, I try to generate a MOPAC calculation of NADP, but when I try with = the input file it says unrecognized keyword, or atom ill defined...below = is the MOPAC input for NADP, can anyone see something missing? Thanks. Sergio KEYWORDS GO HEREC 0.0000000 0 0.000000 0 0.000000 0 0 0 0 0.0000C = 1.4909987 1 0.000000 0 0.000000 0 1 0 0 0.0000C 1.4589154 1 120.833751 1 = 0.000000 0 1 2 0 0.0000C 1.5952887 1 104.179711 1 -123.629997 1 1 2 3 = 0.0000C 1.4327690 1 118.649162 1 -177.109970 1 4 1 2 0.0000C 1.4961080 1 = 107.216845 1 -161.441326 1 5 4 1 0.0000C 1.4141955 1 113.692259 1 = -69.678566 1 6 5 4 0.0000C 1.4861497 1 114.497941 1 51.716667 1 6 5 4 = 0.0000C 1.4452941 1 111.437239 1 74.248685 1 8 6 5 0.0000C 1.5054733 1 = 103.365827 1 -166.496868 1 8 6 5 0.0000C 1.4574546 1 111.809306 1 = -86.763311 1 10 8 6 0.0000C 1.4501824 1 106.004635 1 161.480085 1 7 6 5 = 0.0000C 1.4742222 1 107.653685 1 -139.809374 1 12 7 6 0.0000C 1.3833969 = 1 128.944472 1 66.940975 1 13 12 7 0.0000C 1.2992633 1 112.520808 1 = 178.715024 1 14 13 12 0.0000C 1.3880497 1 104.385214 1 -0.091869 1 15 14 = 13 0.0000C 1.4212055 1 132.803663 1 -178.929926 1 16 15 14 0.0000C = 1.3238100 1 121.797140 1 0.190214 1 17 16 15 0.0000C 1.3672524 1 = 118.021273 1 -179.725459 1 17 16 15 0.0000C 1.3491634 1 120.848602 1 = -0.066268 1 19 17 16 0.0000C 1.3502274 1 125.054262 1 -0.679602 1 20 19 = 17 0.0000C 1.3539457 1 111.183849 1 0.730735 1 16 15 14 0.0000O = 1.5778419 1 110.549256 1 126.272978 1 1 2 3 0.0000N 1.5977684 1 = 134.654605 1 -121.941769 1 23 1 2 0.0000N 1.4758096 1 110.162467 1 = -56.814322 1 24 23 1 0.0000N 1.5009081 1 105.285562 1 72.156186 1 24 23 = 1 0.0000N 1.5660166 1 104.006219 1 -178.870480 1 24 23 1 0.0000N = 1.4258156 1 118.281226 1 69.379294 1 27 24 23 0.0000N 1.5245626 1 = 111.272573 1 175.371156 1 28 27 24 0.0000N 1.4342420 1 110.854111 1 = -60.335961 1 29 28 27 0.0000N 1.5326307 1 114.247710 1 57.889983 1 29 28 = 27 0.0000N 1.4234219 1 112.607565 1 144.895209 1 31 29 28 0.0000N = 1.5163852 1 105.507122 1 -95.103814 1 31 29 28 0.0000N 1.4066321 1 = 113.843089 1 -150.480848 1 33 31 29 0.0000N 1.4146388 1 111.185567 1 = 114.063306 1 30 29 28 0.0000N 1.4537538 1 111.078782 1 -139.680558 1 35 = 30 29 0.0000N 1.4161479 1 118.169858 1 79.144271 1 36 35 30 0.0000N = 1.4306551 1 116.150232 1 -179.373873 1 37 36 35 0.0000N 1.4574762 1 = 121.740928 1 -178.042998 1 38 37 36 0.0000N 1.2482388 1 120.855729 1 = 167.276205 1 39 38 37 0.0000N 1.3598312 1 121.250981 1 -10.757352 1 39 = 38 37 0.0000N 1.4154049 1 118.632746 1 0.854415 1 38 37 36 0.0000N = 1.3635670 1 123.585731 1 -1.005756 1 42 38 37 0.0000N 1.3617566 1 = 118.413749 1 0.448534 1 43 42 38 0.0000C 1.6104652 1 123.853336 1 = -145.123171 1 11 10 8 0.0000C 1.5048751 1 109.327762 1 -91.096377 1 45 = 11 10 0.0000C 1.5109020 1 102.991438 1 29.325753 1 45 11 10 0.0000C = 1.4871210 1 100.481918 1 147.314143 1 45 11 10 0.0000 ------=_NextPart_000_001D_01C3000B.073AA530 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable
MOPAC files begin with three data = lines, the first=20 is for the key words, which say to the program what to do, how to = do etc,=20 consult with the MOPAC or target program documentation.
 
The next two lines may contain = additional info,=20 then the coordinate section follows:
 
EF GNORM=3D0.100 MMOK GEO-OK AM1 MULLIK = PULAY
.
.
  C    0.000000  = 0   =20 0.000000  0    0.000000  0   =20 0   0   0
  C    = 1.408173 =20 1    0.000000  0    0.000000 =20 0    1   0   0
  = C   =20 1.389786  1  119.080032  1    = 0.000000 =20 0    2   1   0
  = C   =20 1.397278  1  120.531311  1    = 0.000000 =20 1    3   2   1
....
 
 
By the way, you coordinates look = somehow=20 corrupted, they contain two molecules and a lonely O atom (H2O?), = all the=20 atoms of the second one are N atoms.
 
With regards
 
Tamas E. Gunda
 
----------------------------------------------
Prof. Tamas E. Gunda
Department of=20 Pharmaceutical Chemistry
Medical and Health Center
University of = Debrecen,=20 POBox 36
H-4010 Debrecen, Hungary
tamasgunda@tigris.klte.hu
 
 
 
 
----- Original Message -----
From:=20 Sergio Manzetti
Sent: Thursday, April 10, 2003=20 19:46
Subject: CCL:MOPAC format from = mol=20 file

Hi, I try to generate a MOPAC = calculation of=20 NADP, but when I try with the input file it says unrecognized keyword, = or atom=20 ill defined...below is the MOPAC input for NADP, can anyone see = something=20 missing? Thanks.
 
Sergio
 
KEYWORDS GO HERE
C 0.0000000 0 =
0.000000 0 0.000000 0 0 0 0 0.0000
C 1.4909987 1 0.000000 0 =
0.000000 0 1 0 0 0.0000
C 1.4589154 1 120.833751 1 0.000000 0 =
1 2 0 0.0000
C 1.5952887 1 104.179711 1 -123.629997 1 1 2 3 =
0.0000
C 1.4327690 1 118.649162 1 -177.109970 1 4 1 2 =
0.0000
C 1.4961080 1 107.216845 1 -161.441326 1 5 4 1 =
0.0000
C 1.4141955 1 113.692259 1 -69.678566 1 6 5 4 =
0.0000
C 1.4861497 1 114.497941 1 51.716667 1 6 5 4 =
0.0000
C 1.4452941 1 111.437239 1 74.248685 1 8 6 5 =
0.0000
C 1.5054733 1 103.365827 1 -166.496868 1 8 6 5 =
0.0000
C 1.4574546 1 111.809306 1 -86.763311 1 10 8 6 =
0.0000
C 1.4501824 1 106.004635 1 161.480085 1 7 6 5 =
0.0000
C 1.4742222 1 107.653685 1 -139.809374 1 12 7 6 =
0.0000
C 1.3833969 1 128.944472 1 66.940975 1 13 12 7 =
0.0000
C 1.2992633 1 112.520808 1 178.715024 1 14 13 12 =
0.0000
C 1.3880497 1 104.385214 1 -0.091869 1 15 14 13 =
0.0000
C 1.4212055 1 132.803663 1 -178.929926 1 16 15 14 =
0.0000
C 1.3238100 1 121.797140 1 0.190214 1 17 16 15 =
0.0000
C 1.3672524 1 118.021273 1 -179.725459 1 17 16 15 =
0.0000
C 1.3491634 1 120.848602 1 -0.066268 1 19 17 16 =
0.0000
C 1.3502274 1 125.054262 1 -0.679602 1 20 19 17 =
0.0000
C 1.3539457 1 111.183849 1 0.730735 1 16 15 14 =
0.0000
O 1.5778419 1 110.549256 1 126.272978 1 1 2 3 =
0.0000
N 1.5977684 1 134.654605 1 -121.941769 1 23 1 2 =
0.0000
N 1.4758096 1 110.162467 1 -56.814322 1 24 23 1 =
0.0000
N 1.5009081 1 105.285562 1 72.156186 1 24 23 1 =
0.0000
N 1.5660166 1 104.006219 1 -178.870480 1 24 23 1 =
0.0000
N 1.4258156 1 118.281226 1 69.379294 1 27 24 23 =
0.0000
N 1.5245626 1 111.272573 1 175.371156 1 28 27 24 =
0.0000
N 1.4342420 1 110.854111 1 -60.335961 1 29 28 27 =
0.0000
N 1.5326307 1 114.247710 1 57.889983 1 29 28 27 =
0.0000
N 1.4234219 1 112.607565 1 144.895209 1 31 29 28 =
0.0000
N 1.5163852 1 105.507122 1 -95.103814 1 31 29 28 =
0.0000
N 1.4066321 1 113.843089 1 -150.480848 1 33 31 29 =
0.0000
N 1.4146388 1 111.185567 1 114.063306 1 30 29 28 =
0.0000
N 1.4537538 1 111.078782 1 -139.680558 1 35 30 29 =
0.0000
N 1.4161479 1 118.169858 1 79.144271 1 36 35 30 =
0.0000
N 1.4306551 1 116.150232 1 -179.373873 1 37 36 35 =
0.0000
N 1.4574762 1 121.740928 1 -178.042998 1 38 37 36 =
0.0000
N 1.2482388 1 120.855729 1 167.276205 1 39 38 37 =
0.0000
N 1.3598312 1 121.250981 1 -10.757352 1 39 38 37 =
0.0000
N 1.4154049 1 118.632746 1 0.854415 1 38 37 36 =
0.0000
N 1.3635670 1 123.585731 1 -1.005756 1 42 38 37 =
0.0000
N 1.3617566 1 118.413749 1 0.448534 1 43 42 38 =
0.0000
C 1.6104652 1 123.853336 1 -145.123171 1 11 10 8 =
0.0000
C 1.5048751 1 109.327762 1 -91.096377 1 45 11 10 =
0.0000
C 1.5109020 1 102.991438 1 29.325753 1 45 11 10 =
0.0000
C 1.4871210 1 100.481918 1 147.314143 1 45 11 10 =
0.0000
------=_NextPart_000_001D_01C3000B.073AA530-- From chemistry-request@server.ccl.net Fri Apr 11 08:39:40 2003 Received: from dedalus.lcc.ufmg.br ([150.164.65.10]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h3BCdd305870 for ; Fri, 11 Apr 2003 08:39:39 -0400 Received: from dedalus.lcc.ufmg.br (loopback [127.0.0.1]) by dedalus.lcc.ufmg.br (8.12.8p1/8.12.8) with ESMTP id h3BCXc3q047152; Fri, 11 Apr 2003 09:33:38 -0300 Received: from localhost (amolive@localhost) by dedalus.lcc.ufmg.br (8.12.8p1/8.12.8/Submit) with ESMTP id h3BCXWm8047150; Fri, 11 Apr 2003 09:33:38 -0300 Date: Fri, 11 Apr 2003 09:33:26 -0300 (BSC) From: andre mauricio de oliveira X-X-Sender: amolive@dedalus To: Ioana Cozmuta cc: Computational Chemistry List Subject: Re: CCL:question about DNA In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear Dr Cozmuta, 1. Usually minor/major grooves width can be measured as the distance between P-P atoms in nearest residues in both chains. Some free programs (like 3DNA and Curves) make it automatically when PDB file is furnished. C4` - C4` are also taken as the reference distance for grooves width, but results are similar to those w/ P-P. 2. Program Curves and 3DNA also calculate other parameters, some of them more suitable for evaluating distortion than helicity itself. See: (1) Calladine, C. R. & Drew, H. R. (1984) "A base-centered explanation of the B-to-A transition in DNA," J. Mol. Biol. 178, 773-782. (2)Fratini, A. V., Kopka, M. L., Drew, H. R. & Dickerson, R. E. (1982) "Reversible bending and helix geometry in a B-DNA dodecamer: CGCTAATTCGCG," J. Biol. Chem. 24, 14686-14707. (3) Dickerson, R. E., Goodsell, D. S., Neidle, S. A. ....The tyrany of the lattice.... Proc. Natl. Acad. Sci. USA (1994) 91, 3579-83. Best regards. On Wed, 9 Apr 2003, Ioana Cozmuta wrote: > Hi CCL users, > > > I've run Molecular Dynamics for a single stranded nucleic acid homopolymer > in water with the initial configuration being helical and the final sort > of bulky. > I was thinking that a way to characterize the "distortion" is to > follow during the dynamics the values of the minor/major grooves and also > the helicity. > I have two questions: > 1. Between which atoms exactly one should measure the minor/major grooves > 2. What is the best way to calculate the helicity of a strand? > > Any advice on this matter would be appreciated. > > Thanks in advance, > Ioana > > > -= 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 > > > > > > Andre Mauricio de Oliveira VOICE +55-031-374-1325 +55-031-499-5765 FAX +55-031-499-5700 Laboratorio de QSAR e Modelagem Molecular Nucleo de Estudos em Quimica Medicinal (NEQUIM) NEQUIM's Homepage: http://www.qui.ufmg.br/~nequim Departamento de Quimica ICEx Federal University of Minas Gerais Av Antonio Carlos 6627 Pampulha ZIP CODE 31270-901 Belo Horizonte MG Brazil From chemistry-request@server.ccl.net Fri Apr 11 08:10:06 2003 Received: from mail.kaist.ac.kr ([143.248.4.44]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h3BCA5304712 for ; Fri, 11 Apr 2003 08:10:05 -0400 Received: from ilsun (ilsun.kaist.ac.kr [143.248.37.227]) by mail.kaist.ac.kr (8.12.9/8.12.9) with SMTP id h3BC934s007785 for ; Fri, 11 Apr 2003 21:09:03 +0900 (KST) Message-ID: <015401c30023$46553330$e325f88f@ilsun> From: "Kwanyong Seo" To: "CCL" Subject: CCL: Problem about geometry optimization - StepSize option Date: Fri, 11 Apr 2003 21:09:59 +0900 MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_0151_01C3006E.B5F6AA70" X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 6.00.2720.3000 X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2600.0000 This is a multi-part message in MIME format. ------=_NextPart_000_0151_01C3006E.B5F6AA70 Content-Type: text/plain; charset="ks_c_5601-1987" Content-Transfer-Encoding: base64 RGVhciBhbGwsDQoNCkluaXRpYWxseSwgSSBwZXJmb3JtZWQgR2F1c3NpYW4gY2FsY3VsYXRpb24g Ynkgb3B0aW9uIHN1Y2ggYXMgbG93ZXIgcGFydC4NCiAgICAgICAgIyBVQjNMWVAvU1RPLTNHIFND RiAoQ29udmVyID0gNCkgT3B0IEZyZXEgVGVzdA0KQnV0LCAiTWF4aW11bSBGb3JjZSIgdmFsdWUg d2FzIG5vdCBjb252ZXJnZWQsIGFuZCBJIGNhbid0IG9wdGFpbiBnb29kIHJlc3VsdC4NClNvLCBJ IGhhdmUgd2FudGVkIHRvIHVzZSB0aGUgIlN0ZXBTaXplIiBvcHRpb24sIGFuZCBwZXJmb3JtZWQg Y2FsY3VsYXRpb24gYnkgZm9sbG93aW5nIG9wdGlvbi4NCiAgICAgICAgIyBVQjNMWVAvU1RPLTNH IFNDRiAoQ29udmVyID0gNCkgT3B0KFN0ZXBTaXplPTUpIEZyZXEgVGVzdA0KQnkgdGhlIHdheSwg c3ludGF4IGVycm9yIGhhcHBlbnMgY29udGludWFsbHkuIEkgY2FuJ3QgZmluZCBhIHJlYXNvbiB3 aHkgb2NjdXJlZCB0aGlzIGVycm9yLg0KRG8geW91ICBrbm93IGFib3V0IHRoaXMgcHJvYmxlbT8g SGVscCBtZSwgcGx6fiENCg0KVGhhbmsgeW91IGZvciByZWFkaW5nLiANCg0KUmVnYXJkcywNCkt3 YW55b25nDQoNCg0KDQorKysrKysrKysrKysrKysrKysrKysrKysrKysrKysrKysrKysrKysrKysr KysrKysrKysNCkt3YW55b25nIFNlbyA6IChFLW1haWwpIGN1cGlkQG1haWwua2Fpc3QuYWMua3Ig KGZpcnN0KQ0KICAgICAgICAgICAgICAgICAgICAgICAgICAgICAgICAgICAgICAgIGN1cGlkQGth aXN0LmFjLmtyDQogICAgICAgICAgICAgICAgICAgICAgICAgICAgKE1TTikgIGNoZW1pc3Rfc2t5 QGhvdG1haWwuY29tDQpNLlMuIGNhbmRpZGF0ZQ0KRGVwYXJ0bWVudCBvZiBDaGVtaXN0cnkNCktv cmVhIEFkdmFuY2VkIEluc3RpdHV0ZSBvZiBTY2llbmNlICYgVGVjaG5vbG9neQ0KMzczLTEsIEd1 c2VvbmctZG9uZywgWXVzZW9uZy1ndSwNClRhZWpvbiwgUmVwdWJsaWMgb2YgS29yZWEgDQozMDUt NzAxDQorKysrKysrKysrKysrKysrKysrKysrKysrKysrKysrKysrKysrKysrKysrKysrKysrKysN Cg0K ------=_NextPart_000_0151_01C3006E.B5F6AA70 Content-Type: text/html; 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Fri, 11 Apr 2003 09:33:01 -0400 Received: from mr1.wpafb.af.mil (root@localhost) by mr1.wpafb.af.mil with ESMTP id h3BDX1w01924 for ; Fri, 11 Apr 2003 09:33:01 -0400 (EDT) Received: from mvs3.wpafb.af.mil (mvs3.wpafb.af.mil [198.97.67.124]) by mr1.wpafb.af.mil with ESMTP id h3BDX1C01917 for ; Fri, 11 Apr 2003 09:33:01 -0400 (EDT) Received: from mvs3.wpafb.af.mil (localhost [127.0.0.1]) by mvs3.wpafb.af.mil (8.11.7/8.11.7) with ESMTP id h3BDX1V13928 for ; Fri, 11 Apr 2003 09:33:01 -0400 (EDT) Received: from fszhtv02.wpafb.af.mil (fszhtv02.wpafb.af.mil [129.48.28.35]) by mvs3.wpafb.af.mil (8.11.7/8.11.7) with ESMTP id h3BDX0o13921 for ; Fri, 11 Apr 2003 09:33:00 -0400 (EDT) Received: by fszhtv02 with Internet Mail Service (5.5.2653.19) id <2W5WL8DS>; Fri, 11 Apr 2003 09:26:18 -0400 Message-ID: <53A10F824E50D511820800508BDF3F22078BB2B2@fszhtv12.wpafb.af.mil> From: Trohalaki Steven Contr AFRL/MLPJ To: chemistry@ccl.net Subject: RE: Refs, H bond calcs 100 atoms Date: Fri, 11 Apr 2003 09:26:16 -0400 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2653.19) Content-Type: text/plain; charset="iso-8859-1" I'd add to the list of references "ACS Symposium Series 569: Modeling the Hydrogen Bond," Douglas A. Smith, editor, ACS, Washington DC, 1994, although it may a bit dated. Steve Trohalaki -----Original Message----- From: elewars [mailto:elewars@trentu.ca] Sent: Thursday, April 10, 2003 3:35 PM To: chemistry@ccl.net Subject: CCL:Refs, H bond calcs 100 atoms 2003 April 10 re the question about H bonds in a "supramolecular system...100 atoms". These refs may be helpful: Comparison of semiempirical and ab initio calculations on H bonds: J. J. Dannenberg, THEOCHEM, 1997, 401, 279. H bonding and DFT: M. Lozynski, D. Rusinska-Roszak, H.-G. Mack, J Phys Chem A, 1998, 102, 2899. A DFT study of a hydrogen bond: J. Spangett-Larson, Chem. Phys., 1999, 240, 51. "Understanding the hydrogen bond with Quantum Chemistry": M. S. Gordon, J. H. Jensen, Acc. Chem. Res., 1996, 29, 536. E. Lewars ==== -= 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 Fri Apr 11 11:17:29 2003 Received: from smtp10.atl.mindspring.net ([207.69.200.246]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h3BFHS311853 for ; Fri, 11 Apr 2003 11:17:28 -0400 Received: from [192.168.167.45] (helo=wamui07.slb.atl.earthlink.net) by smtp10.atl.mindspring.net with esmtp (Exim 3.33 #1) id 1940HQ-0007vI-00 for chemistry@ccl.net; Fri, 11 Apr 2003 11:17:28 -0400 Received: from [192.168.167.62] by EarthlinkWAM via HTTP; Fri Apr 11 11:17:28 EDT 2003 Message-ID: <120261.1050074248550.JavaMail.nobody@wamui07.slb.atl.earthlink.net> Date: Fri, 11 Apr 2003 11:19:39 -0400 (EDT) From: Zach To: chemistry@ccl.net Subject: OPLS or OPLS-AA parameter set for carboxylic acids and amines Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Earthlink Web Access Mail version 3.0 Hello, A specific problem that I am working on requires me to optimize structures for proteins in which the acidic/basic side chains of aminoacids like GLU,ASP, ARG, etc. are in their neutral form rather than in the customary COO- or NH2+ form. I am using TINKER at the moment and in particular the OPLS forcefield (united atoms). The problem is that this forcefield (or most of the ones that are used for proteins) does not have the parameters for C, O and H when in COOH. OPLS-AA, the all atoms version of OPLS, do have some of the parameters but not all of them (I can find the bond stretching params). I was wondering then if someone have the parameters or can point me to a source where these parameters have been published. Thank for your help. Zach From chemistry-request@server.ccl.net Fri Apr 11 11:35:14 2003 Received: from evans.univer.kharkov.ua ([80.92.225.132]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h3BFZB312566 for ; Fri, 11 Apr 2003 11:35:11 -0400 Received: from spin.univer.kharkov.ua (spin.univer.kharkov.ua [192.168.213.252]) by evans.univer.kharkov.ua (8.12.8p1/8.12.5) with SMTP id h3BFZ70b008672 for ; Fri, 11 Apr 2003 18:35:07 +0300 Received: by spin.univer.kharkov.ua with Microsoft Mail id <01C30059.1A2F9080@spin.univer.kharkov.ua>; Fri, 11 Apr 2003 18:35:18 +0200 Message-ID: <01C30059.1A2F9080@spin.univer.kharkov.ua> From: "sergey i. kotelevskii" To: "'CCL community'" Subject: FW: Coordination compouds Date: Fri, 11 Apr 2003 18:35:17 +0200 MIME-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id h3BFZE312571 Hallo Arturas, If not GAMESS, GAUSSIAN than why not MOLCAS? It is designed with heavy metals in mind (In particular this is true if your complexes are coloured, and you're interested in spin-orbit effects etc.) Best regards, S.Kotelevskii ---------- From: Arturas Sent: Friday, April 11, 2003 1:15 PM To: CCL Subject: CCL:Coordination compouds Hello CCL'ers, Can anybody point to info about structure and chemistry of dimers of Fe(X)5, where X - any monodentate ligand (CN or other.) Also, what the best QM/MM and ab initio software to calculate transition metal cpmplexes (not GAMESS,GAUSSIAN) ? -- Best regards, Arturas Z. **************************************************************************************** Serghey I. Kotelevskii, Department of Theoretical Chemistry and Astrochemistry, Research Institute for Chemistry, Kharkiv VNKarazin National University, Kharkiv, Ukraine E-mail: kotelevskiy@univer.kharkov.ua From chemistry-request@server.ccl.net Fri Apr 11 11:26:23 2003 Received: from evans.univer.kharkov.ua ([80.92.225.132]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h3BFQK312260 for ; Fri, 11 Apr 2003 11:26:21 -0400 Received: from spin.univer.kharkov.ua (spin.univer.kharkov.ua [192.168.213.252]) by evans.univer.kharkov.ua (8.12.8p1/8.12.5) with SMTP id h3BFQE0b000348 for ; Fri, 11 Apr 2003 18:26:14 +0300 Received: by spin.univer.kharkov.ua with Microsoft Mail id <01C30057.DC928350@spin.univer.kharkov.ua>; Fri, 11 Apr 2003 18:26:25 +0200 Message-ID: <01C30057.DC928350@spin.univer.kharkov.ua> From: "sergey i. kotelevskii" To: "'CCL community'" Subject: FW: Methods and basis sets to study hydrogen bonding Date: Fri, 11 Apr 2003 18:26:19 +0200 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 h3BFQN312264 Hi Nelson, Don't hesitate, use AM1 for potential energy surface! It often works fairly well even when DFT fails. See e.g. the case of H5O2+ when AM1 correctly predicts two minima: A.C. Testa, Spectroscopy Lett. 32 (1999), 819-828 while B3LYP favors equidistant structure. If you are interested in tunneling or similar quantum effects, take a look at mixed quantum/classical MD models like: O.V.Prezhdo and Yu.V.Pereverzev, J. Chem.Phys. 113 (2000), 6557-6565. Best regards, S. Kotelevskii > Dear All > > I'm trying to perform some electonic calculation in supramolecular systems, and > I´m interested in study intermolecular hydrogen bonds between two molecules. > Can anyone advice me for the best methods (and basis sets) to study hydrogen > bonding? Note that my system is composed of 100 atoms. > > Thanks > > Best regards > > __________________________________________________________ > O email preferido dos portugueses agora com > 100Mb de espaço e acesso gratuito à Internet > http://www.portugalmail.com/gold/ > > > **************************************************************************************** Serghey I. Kotelevskii, Department of Theoretical Chemistry and Astrochemistry, Research Institute for Chemistry, Kharkiv VNKarazin National University, Kharkiv, Ukraine E-mail: kotelevskiy@univer.kharkov.ua From chemistry-request@server.ccl.net Fri Apr 11 15:04:48 2003 Received: from mserver.wlu.ca ([192.54.242.16]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h3BJ4m319267 for ; Fri, 11 Apr 2003 15:04:48 -0400 Received: from dimant ([192.219.240.193]) by mserver.wlu.ca (8.10.1/8.10.1) with SMTP id h3BJ4bK09466 for ; Fri, 11 Apr 2003 15:04:37 -0400 (EDT) Message-ID: <005101c3005d$42ec5950$c1f0dbc0@Chemistry> From: "D. Goussev" To: Subject: paramagnetic species in equilibrium Date: Fri, 11 Apr 2003 15:05:04 -0400 Organization: Wilfrid Laurier University MIME-Version: 1.0 Content-Type: text/plain; charset="Windows-1252" Content-Transfer-Encoding: 7bit X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 6.00.2800.1106 X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2800.1106 Dear All: I am looking for examples (or references to) of chemical equilibria involving diamagnetic and (in the same system) paramagnetic species that can be either the isomers (ground states & intermediates) or transition states connecting them. Thank you in advance, Dmitri Dmitri G. Gusev Associate Professor Department of Chemistry Wilfrid Laurier University Waterloo, Ontario N2L 3C5 Canada Tel.: (519) 884-1970, 2736 FAX: (519) 746-0677 e-mail: dgoussev@wlu.ca