From chemistry-request@server.ccl.net Thu Aug 1 05:32:53 2002 Received: from aspirine.u-strasbg.fr (IDENT:root@[130.79.84.250]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g719Wqf12267 for ; Thu, 1 Aug 2002 05:32:52 -0400 Received: from pharma.u-strasbg.fr (lead2.u-strasbg.fr [130.79.85.21]) (authenticated) by aspirine.u-strasbg.fr (8.10.2/8.10.2) with ESMTP id g719HAh01310 for ; Thu, 1 Aug 2002 11:17:10 +0200 Message-ID: <3D490042.1090307@pharma.u-strasbg.fr> Date: Thu, 01 Aug 2002 11:32:50 +0200 From: Antoine Logean Reply-To: alogean@aspirine.u-strasbg.fr Organization: CNRS - ULP - ETHZ User-Agent: Mozilla/5.0 (Windows; U; Windows NT 5.1; fr-FR; rv:0.9.4.1) Gecko/20020314 Netscape6/6.2.2 X-Accept-Language: fr-fr, en MIME-Version: 1.0 To: chemistry@ccl.net Subject: chemical "distance" between two amino acids Content-Type: text/plain; charset=us-ascii; format=flowed Content-Transfer-Encoding: 7bit Dear all, I am searching a way to quantify the physico-chemical differences between two amino acids, a king of chemical "distance", that can be represented just by an integer value. I am sure this was already be done. Does any one know web resources covering this subject ? Thanks Antoine From chemistry-request@server.ccl.net Thu Aug 1 05:56:54 2002 Received: from century.fen.bilkent.edu.tr ([139.179.97.100]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g719uqf12922 for ; Thu, 1 Aug 2002 05:56:52 -0400 Received: from fen.bilkent.edu.tr (fenII-121.fen.bilkent.edu.tr [139.179.97.239]) by century.fen.bilkent.edu.tr (8.9.1/8.9.1) with ESMTP id MAA07054 for ; Thu, 1 Aug 2002 12:52:27 +0300 (EET DST) Message-ID: <3D49066E.6080609@fen.bilkent.edu.tr> Date: Thu, 01 Aug 2002 12:59:10 +0300 From: Ulrike Salzner Organization: Bilkent University User-Agent: Mozilla/5.0 (Windows; U; Win98; en-US; rv:0.9.4) Gecko/20011128 Netscape6/6.2.1 X-Accept-Language: en-us MIME-Version: 1.0 To: chemistry@ccl.net Subject: pyramidalization of amides Content-Type: text/plain; charset=us-ascii; format=flowed Content-Transfer-Encoding: 7bit Hello, I am reviewing a thesis which deals with pyramidalization in amides, S, Se anlogues and amids in larger ring systems. Substituent effects are analyzed and compared with AIM and NBO. All of these systems have inversion barriers smaller than ammonia, some of them are planar. Thus, like ammonia, these molecules probably violate the Born-Oppenheimer approximation. How reliable are standard calculations (B3LYP/6-31G*, MP2/6-31G*) of bond angles, i.e. degree of pyramidalization? Should trends be ok? I would appreciate oppinions on this. Sincerely, Ulrike Salzner From chemistry-request@server.ccl.net Thu Aug 1 12:35:30 2002 Received: from wrzx35.rz.uni-wuerzburg.de ([132.187.3.35]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g71GZTf25438 for ; Thu, 1 Aug 2002 12:35:29 -0400 Received: from wrzx34.rz.uni-wuerzburg.de (wrzx34.rz.uni-wuerzburg.de [132.187.3.34]) by wrzx35.rz.uni-wuerzburg.de (8.8.8/8.8.8/uniwue-MM-1.05) with ESMTP id SAA25027 for ; Thu, 1 Aug 2002 18:35:24 +0200 (MET DST) Received: from localhost (localhost [127.0.0.1]) by wrzx34.rz.uni-wuerzburg.de (Postfix) with ESMTP id 11CC25F66 for ; Thu, 1 Aug 2002 18:35:24 +0200 (CEST) Received: from wrzx07.rz.uni-wuerzburg.de (wrzx07.rz.uni-wuerzburg.de [132.187.1.7]) by wrzx34.rz.uni-wuerzburg.de (Postfix) with ESMTP id A582E6272 for ; Thu, 1 Aug 2002 18:35:23 +0200 (CEST) Received: from WACD55 (wacd55.chemie.uni-wuerzburg.de [132.187.24.155]) by wrzx07.rz.uni-wuerzburg.de (Postfix) with ESMTP id 9EFF62D5 for ; Thu, 1 Aug 2002 18:35:23 +0200 (CEST) From: "Dominik Auer" To: chemistry@ccl.net Date: Thu, 1 Aug 2002 18:35:58 +0200 MIME-Version: 1.0 Subject: Gaussian 2GB limit with ReiserFS Message-ID: <3D497F8E.14899.1081F9E0@localhost> Priority: normal X-mailer: Pegasus Mail for Windows (v4.01, DE v4.01-R3a) Content-type: text/plain; charset=US-ASCII Content-transfer-encoding: 7BIT Content-description: Mail message body X-Virus-Scanned: by AMaViS (Rechenzentrum Universitaet Wuerzburg) Hallo CCL we are having a problem with the 2GB limit on linux when doing g98 calculations (especially frequency calculations). Actually our used filesystem (ReiserFS) is supposed to allow files larger than 2GB, but calculations still keep crashing if the RWF- Files exceeds the 2GB margin. According to Gaussian the 2GB limit should no longer exist from Rev. A.7. We are using Rev. A.7 and a self compiled A.9, but on both versions the calculations keep crashing with the error: Erroneous write during file extend. write 159743 instead of 4096 On the other hand it is possible to create normal files larger 2GB, I have tested this with a small program. My questions are: 1.) Could the limitation come from (sub-)shell limitation since g98 is working (as far as I know) in korn-shell while we are using bash? If so how can I exceed the limit? 2.) Is it possible that the limit has not been corrected in A.7? Futhermore could it be caused by the fact, that our selfmade A.9 was build either with too old libraries or because it was build on a machine still having the 2GB limit? Somehow the limitation was then transferred into our binaries. If possible I need a permanently working solution, since I am the only one who knows how to maintain our systems. Thanks in advance Dominik Auer From chemistry-request@server.ccl.net Thu Aug 1 13:22:26 2002 Received: from mail2.fullerton.edu ([137.151.1.10]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g71HMOf26932 for ; Thu, 1 Aug 2002 13:22:24 -0400 Received: from viruswall1 (viruswall1.Fullerton.EDU [137.151.2.93]) by mail2.fullerton.edu (8.11.6/8.10.1) with SMTP id g71HM6k29426 for ; Thu, 1 Aug 2002 10:22:21 -0700 (PDT) Received: FROM e2k2.AD.FULLERTON.EDU BY viruswall1 ; Thu Aug 01 10:22:00 2002 -0700 X-MimeOLE: Produced By Microsoft Exchange V6.0.5762.3 content-class: urn:content-classes:message MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Subject: Segmentation fault error in Autodock Date: Thu, 1 Aug 2002 10:21:58 -0700 Message-ID: <4E4792C2A56F9242A6E1807025B2693E663DBE@e2k2.AD.FULLERTON.EDU> X-MS-Has-Attach: X-MS-TNEF-Correlator: Thread-Topic: Hint geometry optimization Thread-Index: AcI4xiIGoJgNwciMQ7e8hiOdFgs5OAAuZ9CA From: "Herron, Steven" To: Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id g71HMQf26933 Dear CCLers, I need some help with autodock. I keep getting a segmentation fault error when I run autodock. The error only occurs when I use the genetic algorithm and only on certain protein files. It is not the ligand file because the ligand docks successfully when I use a different protein. The protein and the ligand dock successfully when I use the Simulated Annealing algorithm, but I really like the Genetic algorithm with a local search (GALS). I cannot find the difference between the protein files that run and the ones that don't. I have also seen this occur when I try to add a co-factor to the protein file. Any assistance is appreciated Autodock runs initially but crashes once it starts the genetic algorithm (as shown below) ... ... BEGINNING LAMARCKIAN GENETIC ALGORITHM DOCKING Run: 1 / 10 Updating Second Time-dependent Seed Now. Seeds: 157989 1027642588 Date: Thu Jul 25 17:16:28 2002 (this is the end of the output file) Segmentation fault (core dumped) Thanks in Advance, Steven R. Herron sherron@fullerton.edu From chemistry-request@server.ccl.net Thu Aug 1 12:26:00 2002 Received: from ucismtp02.unitedcatalysts.com ([208.23.162.6]) by server.ccl.net (8.11.6/8.11.0) with SMTP id g71GQ0f25044 for ; Thu, 1 Aug 2002 12:26:00 -0400 Received: from 10.1.0.50 by ucismtp02.unitedcatalysts.com (InterScan E-Mail VirusWall NT); Thu, 01 Aug 2002 12:21:52 -0400 Received: from lvlxch01.unitedcatalysts.com ([10.16.100.88]) by lvlmail.unitedcatalysts.com (PMDF V6.0-24 #41777) with ESMTP id <0H06002GSANZ0M@lvlmail.unitedcatalysts.com>; Thu, 01 Aug 2002 12:19:11 -0400 (EDT) Received: by lvlxch01.unitedcatalysts.com with Internet Mail Service (5.5.2653.19) id ; Thu, 01 Aug 2002 12:22:34 -0400 Content-return: allowed Date: Thu, 01 Aug 2002 12:22:34 -0400 From: "Shobe, Dave" Subject: RE: pyramidalization of amides To: "'Ulrike Salzner'" Cc: "'CCL'" Message-id: <157A51F55AAAD3119CD70008C7B1629D01C15EFA@lvlxch01.unitedcatalysts.com> MIME-version: 1.0 X-Mailer: Internet Mail Service (5.5.2653.19) 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 g71GQ0f25045 My opinion: the calculations will be valid, if interpreted properly. I tend to think of such systems as "obeying" a modified, three-level Born-Oppenheimer approximation. In the standard two-level Born-Oppenheimer approximation, the nuclei are frozen, with the electrons treated in quantum mechanical fashion, giving the familiar potential energy surface. However, once we have that potential energy surface, we can use it to give the nuclei a quantum treatment: that is what we do when calculating zero-point and thermal energies. However, hydrogen compounds can be better treated with a three way distinction between electrons, hydrogen nuclei (especially if they are protons, i.e. 1H), and then the heavier nuclei. One calculates the potential energy surface in the usual fashion (freezing all nuclei and allowing quantum mechanical treatment of electrons). However, once that potential energy surface is calculated, the hydrogen atoms would be treated quantum mechanically while other nuclei are still frozen. A new heavy atom potential energy surface is thus generated, and wavefunctions and probability distributions are calculated for the hydrogen nuclei. There was an article in Accounts of Chemical Research a few years ago in which this was done for water clusters. Back to your question: a planar amide is still distinguished from a pyramdialized amide in having a one-minimum or two-minima potential energy surface for the amide hydrogen. These produce one-maximum or two-maxima probability distributions (respectively) for the hydrogen nuclei. Experimental geometries typically come from diffraction studies, which actually measure these probability distributions since the results are averaged among the molecules in the sample. Thus, the experimental geometries should correspond to the minima found by B3LYP/6-31G* and the like. --David Shobe Süd-Chemie Inc. phone (502) 634-7409 fax (502) 634-7724 email dshobe@sud-chemieinc.com Don't bother flaming me: I'm behind a firewall. -----Original Message----- From: Ulrike Salzner [mailto:salzner@fen.bilkent.edu.tr] Sent: Thursday, August 01, 2002 5:59 AM To: chemistry@ccl.net Subject: CCL:pyramidalization of amides Hello, I am reviewing a thesis which deals with pyramidalization in amides, S, Se anlogues and amids in larger ring systems. Substituent effects are analyzed and compared with AIM and NBO. All of these systems have inversion barriers smaller than ammonia, some of them are planar. Thus, like ammonia, these molecules probably violate the Born-Oppenheimer approximation. How reliable are standard calculations (B3LYP/6-31G*, MP2/6-31G*) of bond angles, i.e. degree of pyramidalization? Should trends be ok? I would appreciate oppinions on this. Sincerely, Ulrike Salzner -= 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 Wed Jul 31 18:31:34 2002 Received: from jester.ti.com ([192.94.94.1]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g6VMVYf13849 for ; Wed, 31 Jul 2002 18:31:34 -0400 Received: from dlep6.itg.ti.com ([157.170.188.9]) by jester.ti.com (8.11.6/8.11.6) with ESMTP id g6VMVVe26620; Wed, 31 Jul 2002 17:31:31 -0500 (CDT) Received: from dlep6.itg.ti.com (localhost [127.0.0.1]) by dlep6.itg.ti.com (8.9.3/8.9.3) with ESMTP id RAA12976; Wed, 31 Jul 2002 17:31:30 -0500 (CDT) Received: from dlep98.itg.ti.com (dlep98.itg.ti.com [157.170.134.104]) by dlep6.itg.ti.com (8.9.3/8.9.3) with ESMTP id RAA12952; Wed, 31 Jul 2002 17:31:29 -0500 (CDT) Received: from dlee70.itg.ti.com (dlee70.itg.ti.com [157.170.135.145]) by dlep98.itg.ti.com (8.9.3/8.9.3) with ESMTP id RAA17389; Wed, 31 Jul 2002 17:31:29 -0500 (CDT) Received: by dlee70.itg.ti.com with Internet Mail Service (5.5.2653.19) id <3C91KY5T>; Wed, 31 Jul 2002 17:31:29 -0500 Message-ID: <118C57C6AD4DD61198900002A5F386A80197D082@dlee18.itg.ti.com> From: "Matz, Phillip" To: Hatice Can , chemistry@ccl.net Subject: RE: VERY LARGE Checkpoint file Date: Wed, 31 Jul 2002 17:31:26 -0500 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2653.19) Content-Type: text/plain I can say that the size of the checkpoint file should not be the problem. I have run jobs where the checkpoint file is >150MB. How are you setting up your route line to request the geometry be read from the checkpoint file? Or, more to the point, how do you know the problem is the checkpoint file? Regards, Phil Matz -----Original Message----- From: Hatice Can [mailto:alphacan2000@yahoo.com] Sent: Tuesday, July 30, 2002 11:46 AM To: chemistry@ccl.net Subject: CCL:VERY LARGE Checkpoint file Dear All, I am using Gaussian98 for CASSCF calculations. I have a problem with reusing the checkpoint file.The size of checkpoint file is over 6MB. When I want to call it for using the geometry of molecule in another calculation, the file can not be opened. I will be glad for all the suggestions or advices. Thank you and best regards, Hatice __________________________________________________ Do You Yahoo!? Yahoo! Health - Feel better, live better http://health.yahoo.com -= 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 Thu Aug 1 05:08:16 2002 Received: from web12308.mail.yahoo.com ([216.136.173.106]) by server.ccl.net (8.11.6/8.11.0) with SMTP id g7198Gf11657 for ; Thu, 1 Aug 2002 05:08:16 -0400 Message-ID: <20020801090815.37245.qmail@web12308.mail.yahoo.com> Received: from [202.141.71.240] by web12308.mail.yahoo.com via HTTP; Thu, 01 Aug 2002 02:08:15 PDT Date: Thu, 1 Aug 2002 02:08:15 -0700 (PDT) From: Anirban To: chemistry@ccl.net MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Hi!! I have been trying to do MD simulation with DLPOLY software for TIP4P water model. As an initial configuration I am using coordinates which I have used as input for SPC/E model and which created no problem in giving the published results(SPC/E) .The difference between the inputs in case of the two models are that TIP4P has an additional site whose coordinates I calculated by using the coordinates from SPC/E case. Now the problem is whenever I run MD for TIP4P I always end up with 'NANQ' in place of energies and other terms in the output file.I have taken care of the FIELD & the CONTROL file as required for TIP4P model. Could somebody please suggest how can I get rid of this problem / where am I going wrong ?? Thanks! Anirban __________________________________________________ Do You Yahoo!? Yahoo! Health - Feel better, live better http://health.yahoo.com From chemistry-request@server.ccl.net Thu Aug 1 10:09:49 2002 Received: from hqix.hydroqual.com ([207.241.200.195]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g71E9mf19855 for ; Thu, 1 Aug 2002 10:09:48 -0400 Received: by HQIX with Internet Mail Service (5.5.2653.19) id ; Thu, 1 Aug 2002 10:08:37 -0400 Message-ID: <21E773485C55D21184F900C0F01502C9017F6E9F@HQIX> From: dominic ditoro To: "'Yubo Fan'" , CHEMISTRY@ccl.net Subject: RE: share memory problem for G98 on Linux Date: Thu, 1 Aug 2002 10:08:36 -0400 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2653.19) Content-Type: text/plain; charset="iso-8859-1" Yes, we have seen this as well. The problem is that shared memory is not released when a job is killed. You need to release it manually using ipcrm. You can see which need to be removed with ipcs. The command we use is ipcrm shm `ipcs -m |grep -i 0x0 | awk '{print $2;}'` It just automates selecting the shared memory addresses. Dom Dominic M. Di Toro Donald J. O'Connor Professor of Environmental Engineering 4513 Manhattan College Parkway Manhattan College Riverdale, NY 10471 Tel: 718-862-7276 FAX: 718-862-8018 dditoro@manhattan.edu -----Original Message----- From: Yubo Fan [mailto:yubofan@mail.chem.tamu.edu] Sent: Tuesday, July 30, 2002 12:31 PM To: CHEMISTRY@ccl.net Subject: CCL:share memory problem for G98 on Linux Hi, everyone, A share memory problem has always been bothering me for a long time since I ran G98 jobs on Linux boxes. Often, I have to kill running jobs manually to stop optimizations to wrong geometries. I just use "kill -9 'IDs of G98 job'". But, if I killed many times, I couldn't run parallel jobs any more. Share memory cannot be available at all. I have to restart the system to clean memory. Any advice. Thanks in advance Yubo -- ============================================================ Yubo Fan Email: yubofan@mail.chem.tamu.edu Department of Chemistry Tel: 1-979-845-7222 Texas A&M University College Station, TX 77843 ============================================================ -= 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 Thu Aug 1 01:27:24 2002 Received: from sina.com ([202.108.35.244]) by server.ccl.net (8.11.6/8.11.0) with SMTP id g715RNf05958 for ; Thu, 1 Aug 2002 01:27:24 -0400 Received: (qmail 13833 invoked by uid 99); 1 Aug 2002 05:26:50 -0000 Message-ID: <20020801052650.13831.qmail@sina.com> From: kzong To: chemistry@ccl.net Subject: Question about charmm MIME-Version: 1.0 Date: Thu, 01 Aug 2002 13:26:50 +0800 X-Mailer: SinaMail 3.0Beta (FireToad) X-Priority: 3 Dear All, I have some trouble with charmm. I want to do molecular dynamics simulation with periodic boundary condiction(detail is in the following), so I put serveral moleculars in a cubic box and execute simulation in vacuum(just do a test), after the simulation when I observe the output coor file I find that moleculars separate gradually and system's size becomes more and more big. How can I resolve it? The part of periodic boundary condiction setup in my input file is following: Crystal define cubic @boxsize @boxsize @boxsize 90 90 90 crystal build cutoff @cutoff noper 0 crystal write card unit 6 image byres xcen 0.0 ycen 0.0 zcen 0.0 select all end =================================================================== From chemistry-request@server.ccl.net Thu Aug 1 06:43:16 2002 Received: from mail9.messagelabs.com ([194.205.110.133]) by server.ccl.net (8.11.6/8.11.0) with SMTP id g71AhFf14089 for ; Thu, 1 Aug 2002 06:43:15 -0400 X-VirusChecked: Checked Received: (qmail 32004 invoked from network); 1 Aug 2002 10:37:46 -0000 Received: from mailhost.biofocus.com (HELO srcmail1.biofocus-domain1.com) (62.189.105.145) by server-11.tower-9.messagelabs.com with SMTP; 1 Aug 2002 10:37:46 -0000 content-class: urn:content-classes:message MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Subject: Gamess and HOMO / LUMO energies X-MimeOLE: Produced By Microsoft Exchange V6.0.5762.3 Date: Thu, 1 Aug 2002 11:43:20 +0100 Message-ID: X-MS-Has-Attach: X-MS-TNEF-Correlator: Thread-Topic: Gamess and HOMO / LUMO energies Thread-Index: AcI5SDnTjzGrfaMBEday+gAw8RMaDQ== From: "Adrian Stevens" To: Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id g71AhGf14090 Hi All, Sorry for a QM-newbie question, but I've just obtained a copy of PC-Gamess and wanted to calculate and compare a set of HOMO-LUMO energies. However, I haven't been able to find the right function yet in the manual. Any help appreciated. Many thanks, A. ================================================== Dr Adrian Stevens Research Fellow, Computational Chemistry Group, Molecular Informatics Department, BioFocus plc. Sittingbourne Research Centre, Sittingbourne, Kent, ME9 8AZ Tel. +44/0 1795 412300 Fax. +44/0 1795 471123 e-mail: astevens@biofocus.co.uk Web: _____________________________________________________________________ This e-mail and any attachments are confidential. They may contain privileged information and are intended for the named addressee(s) only. If you are not the intended recipient, please notify us immediately and do not disclose, distribute, or retain this e-mail or any part of it. Unless expressly stated, opinions in this email are those of the individual sender, and not of BioFocus plc. BioFocus plc reserves the right to monitor all e-mail communications through its network. This e-mail has been scanned for all known viruses by MessageLabs. From chemistry-request@server.ccl.net Thu Aug 1 14:52:17 2002 Received: from brass.metals.hope.edu ([198.110.98.36]) by server.ccl.net (8.11.6/8.11.0) with SMTP id g71IqHf30902 for ; Thu, 1 Aug 2002 14:52:17 -0400 Received: from hope.edu ([198.110.98.17]) by brass.metals.hope.edu (NAVGW 2.5.2.11) with SMTP id M2002080114523131890 for ; Thu, 01 Aug 2002 14:52:31 -0400 Received: from hope.edu [198.110.99.18] (matthew.zwier@hope.edu) by hope.edu; Thu, 1 Aug 2002 14:52:19 -0400 X-WM-Posted-At: hope.edu; Thu, 1 Aug 02 14:52:19 -0400 Message-ID: <3D498360.9090902@hope.edu> Date: Thu, 01 Aug 2002 14:52:16 -0400 From: Matt Zwier Reply-To: matthew.zwier@hope.edu User-Agent: Mozilla/5.0 (Windows; U; Windows NT 5.0; en-US; rv:1.0.0) Gecko/20020530 X-Accept-Language: en-us, en MIME-Version: 1.0 To: chemistry@ccl.net Subject: Visualization of G98 normal modes Content-Type: text/plain; charset=us-ascii; format=flowed Content-Transfer-Encoding: 7bit Hey all, I'm working on looking at normal mode vibrations of fairly-complex dye molecules. I'm currently using WebMO to view the FREQ calculation output, and that works very well, but it cannot, for instance, animate the motion of the molecule for each normal mode. Does anyone know of a piece of software that can accomplish this? Thanks, Matt Zwier matthew.zwier@hope.edu Hope College Dept. of Chemistry