From chemistry-request@server.ccl.net Mon Oct 2 19:06:14 2000 Received: from chala.q1.fcen.uba.ar (chala.q1.fcen.uba.ar [157.92.31.25]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id TAA02811 for ; Mon, 2 Oct 2000 19:06:12 -0400 Received: from localhost (damian@localhost) by chala.q1.fcen.uba.ar (8.9.3/8.9.3) with ESMTP id WAA13088 for ; Mon, 2 Oct 2000 22:38:35 +0200 Date: Mon, 2 Oct 2000 22:38:35 +0200 (MEST) From: =?X-UNKNOWN?Q?Dami=E1n_Scherlis?= To: chemistry@ccl.net Subject: open shell singlet Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hello. Does anyone know whether an EPR experimet is able to distinguish between open and closed shell singlets ? If it is not: is there any experiment capable of detecting an open shell singlet ? Thanks a lot. -- Damian Scherlis Department of Physical Chemistry Faculty of Sciences University of Buenos Aires From chemistry-request@server.ccl.net Tue Oct 3 02:18:05 2000 Received: from iisc.ernet.in (iisc.ernet.in [144.16.64.3]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id CAA04427 for ; Tue, 3 Oct 2000 02:17:56 -0400 Received: from helix.orgchem.iisc.ernet.in (IDENT:srb@orgchem.iisc.ernet.in [144.16.77.3]) by iisc.ernet.in (8.9.2/8.9.0) with ESMTP id LAA98621 for ; Tue, 3 Oct 2000 11:49:38 +0530 (IST) Received: from localhost (srb@localhost) by helix.orgchem.iisc.ernet.in (8.8.7/8.8.7) with ESMTP id LAA14050 for ; Tue, 3 Oct 2000 11:52:43 +0530 Date: Tue, 3 Oct 2000 11:52:43 +0530 (IST) From: "R.B.Sunoj" To: chemistry@ccl.net Subject: Orbital switching Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear Netters: I am using G94 for performing certain triplet geometry optimizations using B3LYP/6-31G* method. I have tried orbital switching by 'guess=alter' keyword. But always the optimized geometry land up at the previously found minima (ie, before switching the orbitals). Interestingly the out put writes the following, 'Pairs of beta orbitals switched' Again, the MO coefficients tells that the switching is *NOT* done!. (I have a C1 symmetric triplet system). Any suggestions will be appreciated. with regards, Sunoj From chemistry-request@server.ccl.net Tue Oct 3 02:29:41 2000 Received: from tigris.klte.hu (tigris.klte.hu [193.6.138.33]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id CAA04495 for ; Tue, 3 Oct 2000 02:29:40 -0400 Received: from anti07 (193.6.133.59) by tigris.klte.hu (MX V5.1-A Vn6f) with SMTP for ; Tue, 3 Oct 2000 08:28:51 +0200 Message-ID: <000c01c02d03$84d0c480$3b8506c1@chem.klte.hu> From: "Tamas E. Gunda" To: References: Subject: Re: CCL:cross eyes glass Date: Tue, 3 Oct 2000 08:31:09 +0200 MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-2" 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 Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id CAA04496 Hi, I bought a few years ago from Aldrich. Look in the Aldrich catalog. regards Tamas Gunda > I looking for any address for buy a glass (based in mirrors) to look > stereo pictures using cross eyes. > > Thanks a lot! > > Danilo Gonzalez > University of Santiago of Chile > Faculty of Chemistry and Biology > casilla 40, correo 33, > Santiago CHILE > > Fax: 562 - 681 2108 > Dr Tamas E. Gunda Research Group for Antibiotics of the Hungarian Acad. Sci. University of Debrecen, POBox 36 H-4010 Debrecen, Hungary tel.: (+36-52) 316666/2472 fax: (+36-52) 512914 e-mail: tamasgunda@tigris.klte.hu home-page: www.klte.hu/~gundat/gunda.htm From chemistry-request@server.ccl.net Tue Oct 3 03:34:28 2000 Received: from nmr-v.ioc.ac.ru (root@nmr-v.ioc.ac.ru [193.233.3.213]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id DAA04813 for ; Tue, 3 Oct 2000 03:34:27 -0400 Received: from cacr.ioc.ac.ru (val@localhost [127.0.0.1]) by nmr-v.ioc.ac.ru (8.9.3/8.9.3) with ESMTP id LAA21599 for ; Thu, 5 Oct 2000 11:38:02 +0400 Sender: val@nmr-v.ioc.ac.ru Message-ID: <39DC2FDA.DB57757B@cacr.ioc.ac.ru> Date: Thu, 05 Oct 2000 11:38:02 +0400 From: Valentine Ananikov Reply-To: val@cacr.ioc.ac.ru Organization: IOC X-Mailer: Mozilla 4.7 [en] (X11; I; Linux 2.2.13 i686) X-Accept-Language: ru, en MIME-Version: 1.0 To: CCL_post Subject: Second order TS's crossroads Content-Type: text/plain; charset=koi8-r Content-Transfer-Encoding: 7bit Dear CCL'ers, There are two questions concerning second order TS's, which I found being rather contradictory in the literature. So: 1) in some articles one may read something like that: "... we found that reaction proceeds through the second order transition state ... and gives desired products ..." while the other authors state: "... second order saddle points are of no interest for chemical reactions ..." Where is the truth? May a chemical transformation proceed through a second order transition state? 2) Next, If there is a second order TS, does it mean that there are also two independent first order TS's representing each of the imaginary vectors of the former? Is the statement always correct? Any suggestions and references are very welcome. best regards, Valentine. ==================================================================== , , , , Valentine P. Ananikov |\\\\ ////| /////| NMR Group | \\\|/// | ///// | ND Zelinsky Institute of Organic Chemistry | |~~~| | |~~~| | Leninsky Prospect 47 | |===| | |===| | Moscow 117913 | | | | | | | Russia | | A | | | Z | | \ | | / | | / e-mail: val@cacr.ioc.ac.ru \|===|/ |===|/ http://nmr.ioc.ac.ru/Staff/AnanikovVP/ '---' '---' Fax +7 (095)1355328 Phone +7 (095)9383536 ==================================================================== From chemistry-request@server.ccl.net Tue Oct 3 09:04:13 2000 Received: from boris.3dp.com (boris.3dp.com [207.106.4.70]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id JAA07035 for ; Tue, 3 Oct 2000 09:04:12 -0400 Received: from DIMITRIS (dimitris.3dp.com [199.33.182.106]) by boris.3dp.com (8.9.3/8.9.3) with SMTP id JAA26363 for ; Tue, 3 Oct 2000 09:03:56 -0400 (EDT) From: "Dimitris K. Agrafiotis" To: Subject: MMFF Smarts atom type definitions Date: Tue, 3 Oct 2000 09:05:57 -0400 Message-ID: <003001c02d3a$ac5182b0$6ab621c7@DIMITRIS> MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit X-Priority: 3 (Normal) X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook CWS, Build 9.0.2416 (9.0.2911.0) X-MimeOLE: Produced By Microsoft MimeOLE V5.50.4133.2400 Importance: Normal Dear colleagues, Has anyone developed Smarts definitions for the MMFF force field atom types? Thanks in advance, --- Dimitris K. Agrafiotis, PhD | E-mail: dimitris@3dp.com 3-Dimensional Pharmaceuticals, Inc. | Tel: (610) 458-6045 665 Stockton Drive, Suite 104 | Fax: (610) 458-8249 Exton, PA 19341 From chemistry-request@server.ccl.net Tue Oct 3 10:04:25 2000 Received: from rzumail2.unizh.ch (rzumail2.unizh.ch [130.60.128.10]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id KAA07371 for ; Tue, 3 Oct 2000 10:04:25 -0400 Received: from toukie.zzmk.unizh.ch (zzmkfw.unizh.ch [130.60.67.4]) by rzumail2.unizh.ch (8.9.3/8.9.3/07) with ESMTP id QAA03047; Tue, 3 Oct 2000 16:04:12 +0200 (MET DST) Message-Id: <4.3.2.7.0.20001003150508.00a85150@ziaix-imap.unizh.ch> X-Sender: toukie@ziaix-imap.unizh.ch (Unverified) X-Mailer: QUALCOMM Windows Eudora Version 4.3.2 Date: Tue, 03 Oct 2000 15:12:18 +0100 To: chemistry@server.ccl.net From: "Hr. Dr. S. Shapiro" Subject: IR halfband widths Cc: toukie@zui.unizh.ch Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii"; format=flowed Dear Colleagues; I quote from an article published in Spectrochim. Acta 19: 1013 (1963): "Band broadening can also result where a complex polyatomic molecule can exist in different conformational forms. If the centers of conformational isomerism are ultimately involved in the normal vibration responsible for the absorption, it is likely that two separate bands will be resolved, and many cases of this kind are known. However, if centers of conformational isomerism are more remote from the atoms primarily involved in the normal vibration, the perturbation of the steric change on the band frequency may be very small, in which case it will only act to broaden the band. NO EXAMPLES OF SUCH AN EFFECT HAVE YET BEEN POSITIVELY DEMONSTRATED ...." [Emphasis by capitalisation added.] I would be very interested in hearing from anyone who can supply me with references definitively demonstrating conformational IR band broadening of the type that, as of 1963, still had not been positively demonstrated. Thanks in advance to all responders, S. Shapiro toukie@zui.unizh.ch From chemistry-request@server.ccl.net Tue Oct 3 10:11:40 2000 Received: from rzumail2.unizh.ch (rzumail2.unizh.ch [130.60.128.10]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id KAA07416 for ; Tue, 3 Oct 2000 10:11:40 -0400 Received: from toukie.zzmk.unizh.ch (zzmkfw.unizh.ch [130.60.67.4]) by rzumail2.unizh.ch (8.9.3/8.9.3/07) with ESMTP id QAA04739; Tue, 3 Oct 2000 16:11:26 +0200 (MET DST) Message-Id: <4.3.2.7.0.20001003151843.00a9da70@ziaix-imap.unizh.ch> X-Sender: toukie@ziaix-imap.unizh.ch X-Mailer: QUALCOMM Windows Eudora Version 4.3.2 Date: Tue, 03 Oct 2000 15:19:36 +0100 To: chemistry@server.ccl.net From: "Hr. Dr. S. Shapiro" Subject: ? re H-bonding Cc: toukie@zui.unizh.ch Mime-Version: 1.0 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 KAA07417 Dear Colleagues; Consider a phenolic molecule residing in the vicinity of an external hydrogen bond (:B) acceptor such that an intermolecular hydrogen bond is formed between the phenol and the external hydrogen bond acceptor C6H5-O-H --- :B Now, let a hydrogen bond donor (H-O-A) migrate into the vicinity of the phenolic oxygen atom such that a second hydrogen bond can form with the phenolic oxygen atom: C6H5-O-H --- :B ¦ ¦ H-O-A Under such circumstances, would formation of a second hydrogen bond between H-O-A and C6H5OH lead to a weakening of the hydrogen bond strength between C6H5-O-H and the hydrogen bond acceptor :B? Any references or experimental data with which you can provide me that will shed light on this question would be most sincerely appreciated. Thanks in advance to all responders, S. Shapiro toukie@zui.unizh.ch From chemistry-request@server.ccl.net Tue Oct 3 11:16:53 2000 Received: from gw-chimie.math.unibuc.ro (gw-chimie.math.unibuc.ro [193.226.51.14]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id LAA07876 for ; Tue, 3 Oct 2000 11:16:49 -0400 Received: from localhost (andreir@localhost) by gw-chimie.math.unibuc.ro (8.8.7/8.8.7) with SMTP id RAA02467 for ; Tue, 3 Oct 2000 17:19:39 +0300 Date: Tue, 3 Oct 2000 17:19:38 +0300 (EEST) From: Andrei Ionescu To: chemistry@ccl.net Subject: gamess problem Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear all, I am trying to optimize the geometry for an excited state. I was surprised to find that even the example provided by the user manual did not work. Here is the input and the error message given by the output: I did make a setenv line for the DAFL30 file in the rungms script. $CONTRL SCFTYP=GVB CITYP=GUGA RUNTYP=TRUDGE COORD=HINT $END $BASIS GBASIS=N31 NGAUSS=6 $END $SCF DIRSCF=.TRUE. $END $GUGDIA NSTATE=5 $END $GUGDM IROOT=3 $END $DATA Methylene TCSCF+CISD geometry optimization CNV 2 C 6. LC 0.00 0.0 0.00 - O K H 1. PCC 1.00 53. 0.00 + O K I $END $SCF NCO=3 NPAIR=1 $END $TRUDGE OPTMIZ=GEOMETRY NPAR=2 IEX(1)=21,22 P(1)=1.08 $END $CIDRT GROUP=C1 SOCI=.TRUE. NFZC=1 NDOC=3 NVAL=1 NEXT=-1 $END --------------------------------------- MULLIKEN AND LOWDIN POPULATION ANALYSES --------------------------------------- *** ERROR *** ATTEMPT TO READ A DAF RECORD THAT WAS NEVER WRITTEN. RECORD NUMBER 70 OF LENGTH 13 DOES NOT EXIST. CHECK -PROG.DOC- FOR A LIST OF DIRECT ACCESS FILE CONTENTS EXECUTION OF GAMESS TERMINATED ABNORMALLY AT Sun Jul 23 00:38:28 2000 STEP CPU TIME = .01 TOTAL CPU TIME = 2.1 ( .0 MIN) TOTAL WALL CLOCK TIME= 2.0 SECONDS, CPU UTILIZATION IS 105.00% 121410 WORDS OF DYNAMIC MEMORY USED IF YOU WANT A CORE FILE, SET COREFL=.TRUE. IN $SYSTEM. STOP IN ABRT statement executed I will really appreciate any clue. Regards. ------------------------------------------------------------------------- ANDREI RADU IONESCU andreir@gw-chimie.math.unibuc.ro Department of Physical Chemistry at the University of Bucharest Bd. Elisabeta 4-12, 70346 Bucharest, Romania Phone: +40/01/3131120 Fax: +40/01/3159249 http://gw-chimie.math.unibuc.ro From chemistry-request@server.ccl.net Tue Oct 3 13:01:08 2000 Received: from Mercury.acs.unt.edu (mercury.acs.unt.edu [129.120.220.1]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id NAA08757 for ; Tue, 3 Oct 2000 13:00:46 -0400 Received: from jove.acs.unt.edu (10759@jove.acs.unt.edu [129.120.220.41]) by Mercury.acs.unt.edu (8.8.8/8.8.8) with ESMTP id MAA11607 for ; Tue, 3 Oct 2000 12:00:28 -0500 (CDT) Received: from localhost (tdp0006@localhost) by jove.acs.unt.edu (8.8.8/8.8.8) with ESMTP id MAA22455 for ; Tue, 3 Oct 2000 12:00:12 -0500 (CDT) Date: Tue, 3 Oct 2000 12:00:11 -0500 (CDT) From: TREVOR D POWER To: CCL_post Subject: Re: CCL:Second order TS's crossroads In-Reply-To: <39DC2FDA.DB57757B@cacr.ioc.ac.ru> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Valentine, I actually ran into this head first when I was doing modeling of organolithium reactions about a year ago. Many theoreticians will tell you that a second-order transition state is a theoretical entity and cannot be called a transition state nor a molecule anyway. If fact the only correct designation would probably be a second-order saddle point. When one is looking for a transition state that describes a particular reaction and they instead find such a maximum, this usually means that the reaction they are trying to model is actually not concerted and may go through two transition states and 1 intermediate. I would think that one needs to go to extreme measures to find a second-order saddle point; such as symmetry or geometry restrictions (a partial optimization --- which does not make a lot of sense). I would expect that those papers describing a reaction to go through second-order saddle points are in journals not set up to rigorously review computational manuscripts (like J. Org. Chem. for example). You would do well to find papers on this subject in J. Phys. Chem or J. Chem. Phys. Alan Isaacson, Miami University, wrote a few papers (none are reviews though) that began my literature search on this topic. I would agree with the "other authors" as stated below. The principle of least motion is violated in a second-order saddle point. Hope my posting does not spark too many fires out there. Regards, Trevor D. Power Department of Chemistry University of North Texas NT Station, Box 305070 Denton, Tx 76201-5070 tdp0006@unt.edu On Thu, 5 Oct 2000, Valentine Ananikov wrote: > > Dear CCL'ers, > > There are two questions concerning second order TS's, which I > found being rather contradictory in the literature. So: > > 1) in some articles one may read something like that: "... we > found that reaction proceeds through the second order transition > state ... and gives desired products ..." > > while the other authors state: "... second order saddle points > are of no interest for chemical reactions ..." > > Where is the truth? May a chemical transformation proceed through > a second order transition state? > > 2) Next, > > If there is a second order TS, does it mean that there are > also two independent first order TS's representing each of the > imaginary vectors of the former? Is the statement always correct? > > > Any suggestions and references are very welcome. > > best regards, > Valentine. > > > ==================================================================== > , , , , > Valentine P. Ananikov |\\\\ ////| /////| > NMR Group | \\\|/// | ///// | > ND Zelinsky Institute of Organic Chemistry | |~~~| | |~~~| | > Leninsky Prospect 47 | |===| | |===| | > Moscow 117913 | | | | | | | > Russia | | A | | | Z | | > \ | | / | | / > e-mail: val@cacr.ioc.ac.ru \|===|/ |===|/ > http://nmr.ioc.ac.ru/Staff/AnanikovVP/ '---' '---' > Fax +7 (095)1355328 Phone +7 (095)9383536 > ==================================================================== > > > -= 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 > > > > > > From chemistry-request@server.ccl.net Tue Oct 3 13:52:04 2000 Received: from web3403.mail.yahoo.com (web3403.mail.yahoo.com [204.71.203.57]) by server.ccl.net (8.8.7/8.8.7) with SMTP id NAA08940 for ; Tue, 3 Oct 2000 13:52:04 -0400 Message-ID: <20001003174944.25063.qmail@web3403.mail.yahoo.com> Received: from [136.142.109.103] by web3403.mail.yahoo.com; Tue, 03 Oct 2000 10:49:44 PDT Date: Tue, 3 Oct 2000 10:49:44 -0700 (PDT) From: Mary Boyden Subject: program to calc. internal coordinates and PED To: chemistry@ccl.net MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Dear CCL: I would like to find a program which will accept the normal mode Cartesian coordinates from a Gaussian 98 output file, convert them to internal coordinates, and find the potential energy distribution for one of the normal modes. Are there any (preferably free) programs available that will accomplish this? I am a beginner and really appreciate all help. Thanks! Mary Boyden Department of Chemistry Unversity of Pittsburgh __________________________________________________ Do You Yahoo!? Yahoo! Photos - 35mm Quality Prints, Now Get 15 Free! http://photos.yahoo.com/ From chemistry-request@server.ccl.net Tue Oct 3 15:13:48 2000 Received: from qtp.ufl.edu (zwart.qtp.ufl.edu [128.227.89.3]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id PAA09197 for ; Tue, 3 Oct 2000 15:13:48 -0400 Received: from pc1 (pc1 [128.227.192.187]) by qtp.ufl.edu (8.9.1a/8.9.1) with SMTP id PAA22359 for ; Tue, 3 Oct 2000 15:13:56 -0400 (EDT) Message-ID: <010701c02d6e$6f84cac0$bbc0e380@qtp.ufl.edu> From: "Stefan Fau" To: "CCL - all" Subject: Re: Second order TS's crossroads Date: Tue, 3 Oct 2000 15:16:30 -0400 MIME-Version: 1.0 Content-Type: text/plain; charset="koi8-r" 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 Valentine, to 1) I think that 2nd order TSs are of little importance, chemically. If you have a 2nd order TS with one imaginary mode connecting your reactants and products, you can optimize along the other imaginary mode and get a 1st order TS that should still connect your reactants and products. (I don't know of any exceptions to that, but maybe there are a few.) Due to the optimization, the energy of this 1st order TS is lower, and therefore more reacting molecules should pass along here (assuming that the effects of nuclear motion are small enough). Classically, every point (geometry) on the potential energy hypersurface which is below the molecules energy is accessible by that molecule. So if you supply your molecule with lots of energy lots of geometries are possible. If you give just enough energy to keep a very slow reaction going virtually all product molecules will have passed the 1st order TS. to 2) A 2nd order TS is not generally connected to four 1st order TSs (two for each imaginary mode). I once had a 2nd order TS connected to two mirror-symmetric 1st order TSs and two minima. The first order TSs connected the same minima. I think that this scheme might be common with 2nd order TSs of higher symmetry. The example is published in S. Fau, G. Frenking, Theochem - J. Mol. Struct. 1995, 338, 117-130. I think the 2nd order TS was a C2v structure of B2CH4, the 1st order TS was non-planar Cs and the minimum was planar Cs. 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 Tue Oct 3 17:39:25 2000 Received: from unlserve.unl.edu (unlserve.unl.edu [129.93.1.130]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id RAA10033 for ; Tue, 3 Oct 2000 17:39:25 -0400 Received: from localhost (jmazlo@localhost) by unlserve.unl.edu (8.9.1a/8.9.2) with SMTP id QAA75966 for ; Tue, 3 Oct 2000 16:28:48 -0500 Date: Tue, 3 Oct 2000 16:28:48 -0500 (CDT) From: Johanna Mazlo To: chemistry@server.ccl.net Subject: autodock: max_tors Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear CCL members, I am a new user of AUTODOCK. I am trying to dock a peptide to a fab portion of an antibody. I am having difficulty with the step: autodock3 -p lig.macro.dpf -l lig.macro.dlg & The peptide has more than the default for MAX_TORS of 32, therefore this step does not successfully complete and it says that the MAX_TORS has exceeded the limit (32) thus change constant.h. I have changed the constant.h to 100. I have also done what the manual suggests which is the change the MAX_TORS in autodock.h to 100 and recompile. I have gone back and done all the steps including making the pdqs, autotors, etc. However, it still says that the MAX_TORS of 32 has been exceeded and will not complete the docking using autodock3. I am hoping someone could tell me what I am doing wrong. Thank you for your help. Johanna Mazlo University of Nebraska Lincoln, Nebraska 68588-0304 jmazlo@unlserve.unl.edu From chemistry-request@server.ccl.net Tue Oct 3 18:00:23 2000 Received: from schrodinger.com (root@thermidore.schrodinger.com [199.245.177.4]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id SAA10152 for ; Tue, 3 Oct 2000 18:00:22 -0400 Received: from schrodinger.com (natasha.schrodinger.com [192.156.98.136]) by schrodinger.com (8.8.5/8.8.5) with ESMTP id OAA28435; Tue, 3 Oct 2000 14:59:47 -0700 Message-ID: <39DA55EB.FDD04A12@schrodinger.com> Date: Tue, 03 Oct 2000 14:55:55 -0700 From: George Vacek Organization: Schrodinger, Inc. X-Mailer: Mozilla 4.72 [en] (WinNT; I) X-Accept-Language: en MIME-Version: 1.0 To: TREVOR D POWER CC: CCL_post Subject: Re: CCL:Second order TS's crossroads References: Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit TREVOR D POWER wrote: > Many theoreticians will tell you > that a second-order transition state is a theoretical entity and cannot > be called a transition state nor a molecule anyway. If fact the only > correct designation would probably be a second-order saddle point. When > one is looking for a transition state that describes a particular reaction > and they instead find such a maximum, this usually means that the reaction > they are trying to model is actually not concerted and may go through two > transition states and 1 intermediate. I would think that one needs to go > to extreme measures to find a second-order saddle point; A well stated response Trevor. A couple papers where theoreticians concede that experimentalists may have seen evidence of a second order saddle point are: ``The Anomalous Behavior of the Zeeman Anticrossing Spectra of \~A $^1A_u$ Acetylene: Theoretical Considerations,'' G. Vacek, C. D. Sherrill, Y. Yamaguchi and H. F. Schaefer, {\it J. Chem. Phys.} {\bf 104}, 1774-8 (1996). ``The \~A $^1A_u$ State and the $T_2$ Potential Surface of Acetylene: Implications for Triplet Perturbations in the Flourescence Spectra of the \~A State,'' C. D. Sherrill, G. Vacek, Y. Yamaguchi, H. F. Schaefer, J. F. Stanton and J. Gauss, {\it J. Chem. Phys.} {\bf 104}, 8507-15 (1996). Regards, George Vacek =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=- vacek@schrodinger.com (503)299-1150 http://www.schrodinger.com/~vacek/ Schrodinger, Inc., 1500 SW First Ave., Suite 1180, Portland, OR 97201 Every culture that has lost myth has lost, by the same token, its natural, healthy creativity. -- Friedrich Nietzsche "The Birth of Tragedy" 1872 =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=- From chemistry-request@server.ccl.net Tue Oct 3 18:47:47 2000 Received: from asnmail.asc.edu (asnmail.asc.edu [129.66.12.7]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id SAA10462 for ; Tue, 3 Oct 2000 18:47:47 -0400 Received: from localhost (asnmaz01@localhost) by asnmail.asc.edu (8.9.3/8.9.3) with ESMTP id SAA29028 for ; Tue, 3 Oct 2000 18:02:58 -0500 Date: Tue, 3 Oct 2000 18:02:58 -0500 (CDT) From: "Mark A. Zottola" To: CCL Subject: Fractional to Cartesian converter Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII I regret that this is problably an overly-answered question. However, I can not get to the CCL web site to search this out. I am looking for a converter which will take a space group and a set of fractional coordinates and convert them into cartesian coordinates. Thanks, Mark