From chemistry-request@server.ccl.net Wed Dec 11 09:44:00 2002 Received: from ciril.fr ([193.50.27.66]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id gBBEhxi30461 for ; Wed, 11 Dec 2002 09:43:59 -0500 Received: from host20.lctn.uhp-nancy.fr (host20.lctn.uhp-nancy.fr [193.50.239.24]) by ciril.fr (8.12.6/8.12.6/Guy-23-01-2002) with ESMTP id gBBEhvjF010069 for ; Wed, 11 Dec 2002 15:43:57 +0100 (MET) Received: from lctn.uhp-nancy.fr (host23.lctn.uhp-nancy.fr [193.50.239.30]) by host20.lctn.uhp-nancy.fr (AIX4.3/8.9.3/8.9.3) with ESMTP id PAA26548 for ; Wed, 11 Dec 2002 15:43:48 +0100 Sender: assfeld@host20.lctn.uhp-nancy.fr Message-ID: <3DF74EC5.6C0A2C7D@lctn.uhp-nancy.fr> Date: Wed, 11 Dec 2002 15:42:13 +0100 From: Xavier ASSFELD Organization: Chimie Theorique X-Mailer: Mozilla 4.51i [en] (X11; I; AIX 4.3) X-Accept-Language: en MIME-Version: 1.0 To: CCL Subject: Racah parameters Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Scanned-On: arcturus X-Scanned-By: MIMEDefang 2.27 (www . roaringpenguin . com / mimedefang) Dear all, for transition metal electronic states one can use Racah parameters A, B and C. In textbook, one can find that the energy of state X is equal to : A + 22B + 7C for example. I would like to know : 1) The references of Racah's paper dealing with such parameters 2) How one can find the number in front of B and C (22 and 7 in my previous example). Any help would be greatly appreciate. Yours, sincerely. -- ...Xav WARNING ! NEW PHONE AND FAX NUMBER !! Ast. Pr. Xavier Assfeld Xavier.Assfeld@lctn.uhp-nancy.fr Laboratoire de Chimie theorique (T) 33 3 83 68 43 74 Universite Henri Poincare (F) 33 3 83 68 43 71 F-54506 Nancy BP 239 http://www.lctn.uhp-nancy.fr From chemistry-request@server.ccl.net Wed Dec 11 03:46:29 2002 Received: from ciril.fr ([193.50.27.66]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id gBB8kTi11089 for ; Wed, 11 Dec 2002 03:46:29 -0500 Received: from host20.lctn.uhp-nancy.fr (host20.lctn.uhp-nancy.fr [193.50.239.24]) by ciril.fr (8.12.6/8.12.6/Guy-23-01-2002) with ESMTP id gBB8kRjF028396 for ; Wed, 11 Dec 2002 09:46:27 +0100 (MET) Received: from lctn.uhp-nancy.fr (host23.lctn.uhp-nancy.fr [193.50.239.30]) by host20.lctn.uhp-nancy.fr (AIX4.3/8.9.3/8.9.3) with ESMTP id JAA26488 for ; Wed, 11 Dec 2002 09:46:17 +0100 Sender: assfeld@host20.lctn.uhp-nancy.fr Message-ID: <3DF6FAFC.30A1836B@lctn.uhp-nancy.fr> Date: Wed, 11 Dec 2002 09:44:44 +0100 From: Xavier ASSFELD Organization: Chimie Theorique X-Mailer: Mozilla 4.51i [en] (X11; I; AIX 4.3) X-Accept-Language: en MIME-Version: 1.0 To: CCL Subject: Congres Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Scanned-On: arcturus X-Scanned-By: MIMEDefang 2.27 (www . roaringpenguin . com / mimedefang) Dear all, I am very proud to announce : Modelling chemical reactivity: from gas-phase to solution and enzymes. An international conference in honor of Professor Jean-Louis Rivail 16-18 July 2003 Nancy, France The congress will focus on methodological developments and applications of quantum chemistry in reactivity problems, with emphasis put in complex molecular systems in Chemistry and Biology. Reactions involving large molecules in gas-phase, solvent effects and enzymatic catalysis will be the main research domains concerned by this meeting. This Conference is a satellite of the XI ICQC meeting to be held at Bonn (July 20-26 http://www.ICQC.uni-bonn.de/). Invited speakers: J. Bertran (Barcelona), A. D. Buckingham (Cambridge), T. Clark (Erlangen), B. J. Costa-Cabral (Lisboa), C. J. Cramer (Minneapolis), J. P. Daudey (Toulouse), A. Dedieu (Strasbourg), G. Ferenczy (Strasbourg), M. J. Field (Grenoble), F. A. Gianturco (Roma), J. T. Hynes (Boulder, Paris), G. Jansen (Essen), Y. Jean (Orsay), J. C. Rayez (Bordeaux), M. Robb (London), E. Sanchez-Marcos (Sevilla), B. Silvi (Paris), J. Tomasi (Pisa), I. Tunon (Valencia), A. Warshel (Los Angeles) Registration and accomodation forms, invited speakers list and further information are available at the conference web site: http://www.lctn.uhp-nancy.fr/JLR/ Organizing Committee and contact: Manuel Ruiz-Lopez (Manuel.Ruiz@lctn.uhp-nancy.fr) Equipe de Chimie et Biochimie theoriques UMR CNRS-UHP No. 7565, Universite Henri Poincare BP 239, 54506 Vandoeuvre-les-Nancy Cedex, France -- ...Xav WARNING ! NEW PHONE AND FAX NUMBER !! Ast. Pr. Xavier Assfeld Xavier.Assfeld@lctn.uhp-nancy.fr Laboratoire de Chimie theorique (T) 33 3 83 68 43 74 Universite Henri Poincare (F) 33 3 83 68 43 71 F-54506 Nancy BP 239 http://www.lctn.uhp-nancy.fr From chemistry-request@server.ccl.net Wed Dec 11 07:04:54 2002 Received: from amiram13.md.huji.ac.il ([132.64.165.150]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id gBBC4ri27260 for ; Wed, 11 Dec 2002 07:04:53 -0500 Received: from amiram13.md.huji.ac.il (localhost.localdomain [127.0.0.1]) by amiram13.md.huji.ac.il (8.11.6/8.11.6) with ESMTP id gBBBxw331711 for ; Wed, 11 Dec 2002 14:00:03 +0200 Content-Type: text/plain; charset="us-ascii" From: Boris Gorelik To: Subject: energy evaluation programs/functions Date: Wed, 11 Dec 2002 13:59:58 +0200 User-Agent: KMail/1.4.3 MIME-Version: 1.0 Content-Transfer-Encoding: 8bit Message-Id: <200212111359.58905.bgbg@md.huji.ac.il> Hello all, Could anyone suggest a (preferably) free, (preferably) open-source C or C++ program or library for calculating the docking of ligands and of proteins to proteins ? We are mainly unterested in adequate force-fields for docking, All the answers (together with my own findings) will be summarized. Thanks to all in advance, -- Boris Gorelik Wed, 11/Dec/2002, 6 Tevet 5763 ------------------------------------------------- ! Molecular Modelling Group ! ! Pharmacy School, Hadassa Faculty of medicine ! ! The Hebrew University of Jerusalem ! ! http://www.md.huji.ac.il/models/group.html ! ! !------------------------------------------------ From chemistry-request@server.ccl.net Wed Dec 11 05:25:24 2002 Received: from max5.rrze.uni-erlangen.de ([131.188.3.50]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id gBBAPOi25333 for ; Wed, 11 Dec 2002 05:25:24 -0500 Received: from [10.10.59.51] by max5.rrze.uni-erlangen.de; Wed, 11 Dec 2002 11:25:17 +0100 Message-Id: <3.0.5.32.20021211112935.008e7c40@pop.rrze.uni-erlangen.de> X-Sender: bco153@pop.rrze.uni-erlangen.de X-Mailer: QUALCOMM Windows Eudora Light Version 3.0.5 (32) Date: Wed, 11 Dec 2002 11:29:35 +0100 To: "Dr. Daniel Glossman-Mitnik" , From: Ralph Puchta Subject: Re: CCL:program for the calculation of ring centers In-Reply-To: <010c01c29fe4$c16e8200$8400000a@LAQUICOM02> Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Dear Dr. Glossman-Mitnik, I use "Molecule" to calculate the ring centers and all other NICS points. After the NICS-calculation "Molecule" is imho the easiest tool to visualize the NICS-results. Perhaps you have seen them in papers like: Dissected Nucleus-Independent Chemical Shift Analysis of pi-Aromaticity and Antiaromaticity. P. v. R. Schleyer, M. Manoharan, Z.-X. Wang, B. Kiran, H. Jiao, R. Puchta, N.J.R. van Eikema Hommes, Org. Lett.,2001, 3, 2465-2468. Molecule was designed for Apple-Macintosh, but you can run it on a PC with the ARDI's Executor. More Infos you can find at http://www.chemie.uni-erlangen.de/hommes/molecule/index.html Greetings Ralph Puchta From chemistry-request@server.ccl.net Wed Dec 11 05:42:12 2002 Received: from mailstudenti.unimi.it ([159.149.10.4]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id gBBAgCi25613 for ; Wed, 11 Dec 2002 05:42:12 -0500 Received: from smtp.unimi.it (smtp.unimi.it [159.149.10.3]) by mailstudenti.unimi.it (iPlanet Messaging Server 5.1 (built May 7 2001)) with ESMTP id <0H6Y0012FAYNNX@mailstudenti.unimi.it> for chemistry@ccl.net; Wed, 11 Dec 2002 11:40:00 +0100 (MET) Received: from Villa (villa.farma.unimi.it [159.149.79.66]) by smtp.unimi.it (iPlanet Messaging Server 5.1 (built May 7 2001)) with SMTP id <0H6Y008P4AXVGA@smtp.unimi.it> for chemistry@ccl.net; Wed, 11 Dec 2002 11:40:01 +0100 (MET) Date: Wed, 11 Dec 2002 11:42:22 +0100 From: Giulio Vistoli Subject: Announcing VEGA1.4.3 To: CCL Message-id: <001c01c2a102$03b38b60$424f959f@Villa> Organization: =?iso-8859-1?Q?Universit=E0_di_Milano?= MIME-version: 1.0 X-MIMEOLE: Produced By Microsoft MimeOLE V6.00.2800.1106 X-Mailer: Microsoft Outlook Express 6.00.2800.1106 Content-type: text/plain; charset=iso-8859-1 Content-transfer-encoding: 7BIT X-Priority: 3 X-MSMail-priority: Normal Dear collegues, As a christmas gift, we are glad to announce the new release of VEGA1.4.3 (http://www.ddl.unimi.it/) our well known program to convert, manage and visualize of 3D structures for several platforms (Win32, Linux, Irix, AmigaOs). New features of release 1.4.3: - Alchemy loader & saver. - MDL Molfile saver. - CSV and Raw surface format. - Gromacs .xtc support for the trajectory analysis. - Multi-model PDB support for the trajectory analysis. - ILM calculation in the trajectory analysis. - The IFF file format was expanded in order to support the surface maps. - Win32: new geometry transformation engine. - Win32: added By segment coloring method. - Win32: surface calculation for selected atoms. - Win32: trajectory analysis for selected atoms. - Win32: interactive selection of the conformations trough the graph editor. - Win32: added the Data De/compressor Engine support in the graph editor. - Win32: now the graph editor supports Gromacs log files. - Win32: REBOL/View instead of REBOL/Core scripting language. - Win32: new extended commands (BioDock, GraphAdd, GraphCalc, GraphClose, GraphDelete, GraphGet, GraphLabelX, GraphLabelY, GraphLoad, GraphNew, GraphOpen, GraphSave, GraphSet, GraphTitle, GraphWin, MonitorPower). - Win32: new system variables (CPUs, GLRenderer, GLVendor, GLVersion, GraphLabelX, GraphLabelY, GraphPoints, GraphPosX, GraphPosY, GraphSizeX, GraphSizeY, GraphTitle, GraphVisible, TmpFile, TmpDir). - Win32: WinDD 1.4. Giulio Vistoli & Alessandro Pedretti --------------- Giulio Vistoli Istituto di Chimica Farmaceutica e Tossicologica Viale Abruzzi, 42 I-20131 Milano Italia Tel. +39-02-50317545 Fax +39-02-50317565 giulio.vistoli@unimi.it http://www.ddl.unimi.it From chemistry-request@server.ccl.net Tue Dec 10 17:04:41 2002 Received: from mxout5.cac.washington.edu ([140.142.32.135]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id gBAM4fi31576 for ; Tue, 10 Dec 2002 17:04:41 -0500 Received: from mailscan-out1.cac.washington.edu (mailscan-out1.cac.washington.edu [140.142.32.138]) by mxout5.cac.washington.edu (8.12.1+UW01.12/8.12.1+UW02.11) with SMTP id gBAM4XpB001867 for ; Tue, 10 Dec 2002 14:04:33 -0800 Received: FROM smtp.washington.edu BY mailscan-out1.cac.washington.edu ; Tue Dec 10 14:04:33 2002 -0800 Received: from donald ([128.95.128.116]) by smtp.washington.edu (8.12.1+UW01.12/8.12.1+UW02.11) with SMTP id gBAM4XmX008595 for ; Tue, 10 Dec 2002 14:04:33 -0800 Message-ID: <005d01c2a097$6b4c8d00$74805f80@donald> From: "Carsten Detering" To: Subject: Amber7 and partial charges Date: Tue, 10 Dec 2002 22:59:31 +0100 Organization: University of Washington MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_005A_01C2A09F.CCFD1EE0" X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 6.00.2600.0000 X-MIMEOLE: Produced By Microsoft MimeOLE V6.00.2600.0000 This is a multi-part message in MIME format. ------=_NextPart_000_005A_01C2A09F.CCFD1EE0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Hi folks, We just got the new Amber7 package, and, being new to amber, I am = struggling with assigning partial charges, which is my only interest at = the moment. I have several RNA pdb files, to which I would like to = assign partial charges and convert them to mol2 files on the fly. = Following the manual, this can obviously be done with antechamber, = however, the program core dumps every time I use it and secondly, it = tells me that the Kollman charges (esp) are only to be used for = Gaussian. Can anybody tell me a quick and dirty method to simply assign the = partial charges? Thanks a lot in advance, Carsten ~~~~~~~~~~~~~~~~~~~~~~~~~~~ Carsten Detering, Ph.D. University of Washington Seattle, WA 98195 Phone 206-543-5081 Fax 206-685-8665 email detering@u.washington.edu ~~~~~~~~~~~~~~~~~~~~~~~~~~~ ------=_NextPart_000_005A_01C2A09F.CCFD1EE0 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable
Hi folks,
 
We just got the new Amber7 package, and, being new to amber, I am=20 struggling with assigning partial charges, which is my only interest at = the=20 moment. I have several RNA pdb files, to which I would like to = assign=20 partial charges and convert them to mol2 files on the fly. Following the = manual,=20 this can obviously be done with antechamber, however, the program core = dumps=20 every time I use it and secondly, it tells me that the Kollman charges = (esp) are=20 only to be used for Gaussian.
Can anybody tell me a quick and dirty method to simply assign the = partial=20 charges?
Thanks a lot in advance,
 
Carsten
 
~~~~~~~~~~~~~~~~~~~~~~~~~~~
Carsten Detering, = Ph.D.
University of=20 Washington
Seattle, WA 98195
Phone 206-543-5081
Fax=20 206-685-8665
email detering@u.washington.edu~~~~~~~~~~~~~~~~~~~~~~~~~~~
------=_NextPart_000_005A_01C2A09F.CCFD1EE0-- From chemistry-request@server.ccl.net Wed Dec 11 12:09:15 2002 Received: from f04n01.cac.psu.edu ([128.118.141.31]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id gBBH9Fi02602 for ; Wed, 11 Dec 2002 12:09:15 -0500 Received: from psu.edu (cornea.chem.psu.edu [128.118.172.87]) by f04n01.cac.psu.edu (8.9.3/8.9.3) with ESMTP id MAA138532 for ; Wed, 11 Dec 2002 12:09:10 -0500 Message-ID: <3DF77136.EE540A3@psu.edu> Date: Wed, 11 Dec 2002 12:09:10 -0500 From: Ed Brothers Reply-To: enb108@psu.edu Organization: PSU Merz Group X-Mailer: Mozilla 4.61 (Macintosh; I; PPC) X-Accept-Language: en,pdf MIME-Version: 1.0 To: chemistry@ccl.net Subject: DIIS in CPHF convergence. Content-Type: text/plain; charset=us-ascii; x-mac-type="54455854"; x-mac-creator="4D4F5353" Content-Transfer-Encoding: 7bit I am currently implementing the CPHF in oreder to calculate an analytical hessian. I have previously used DIIS for SCF convergence acceleration. In DIIS-SCF, the error is defined as FDS-SDF, where F is the fock matrix, D is the density matrix, and S is the overlap matrix. How do I set up the error values in CPHF to accelerate convergence? Thanks for any help you can give me. Ed Brothers. Merz Group Penn State From chemistry-request@server.ccl.net Wed Dec 11 12:59:59 2002 Received: from mailrelay1.lanl.gov ([128.165.4.101]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id gBBHxwi03855 for ; Wed, 11 Dec 2002 12:59:58 -0500 Received: from swan.lanl.gov (localhost.localdomain [127.0.0.1]) by mailrelay1.lanl.gov (8.12.3/8.12.3/(ccn-5)) with ESMTP id gBBHxw9i019125 for ; Wed, 11 Dec 2002 10:59:58 -0700 Received: from heron.lanl.gov (heron.lanl.gov [128.165.96.39]) by swan.lanl.gov (8.12.1/8.12.1) with ESMTP id gBBIwdFj011866 for ; Wed, 11 Dec 2002 11:58:39 -0700 Received: from localhost (tamulis@localhost) by heron.lanl.gov (8.12.1/8.12.1) with ESMTP id gBBAsT2k003880 for ; Wed, 11 Dec 2002 03:54:29 -0700 Date: Wed, 11 Dec 2002 03:54:29 -0700 (MST) From: "Temporary Guest Account;CNLS;7-1444;9999999" To: Subject: Formulae of Fermi Contact in G98 Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear Netters, would you please to give me exact formulae how it is calculating Isotropic Fermi Contact Couplings constants in the G98 ? Maybe you can give me exact reference on article which was the origing writing codes of this part of G98? The best variant should be if you will send me pdf (ps) file of these formulae or this article. Enclosed please find part of my resulting file of radical molecule calculations while I wish to understand how these numbers were obtained in G98: Atom a.u. MegaHertz Gauss 10(-4) cm-1 6 N(14) 0.10574 34.16484 12.19087 11.39616 17 O(17) 0.06247 -37.87121 -13.51339 -12.63247 Thank you in advance. Regards, Arvydas Tamulis ******************************************************************* Arvydas Tamulis Temporal address until 28 February 2003: Los Alamos National Laboratory Center for Nonlinear Studies P.O. Box 1663, Mail Stop B258 Los Alamos, New Mexico 87545 Work Phone: (505) 667-7278 Fax: (505) 665-2659 e-mail: tamulis@cnls.lanl.gov ******************************************************************* From chemistry-request@server.ccl.net Wed Dec 11 14:46:21 2002 Received: from f04n07.cac.psu.edu ([128.118.141.35]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id gBBJkLi05733 for ; Wed, 11 Dec 2002 14:46:21 -0500 Received: from ra.chem.psu.edu (ra.chem.psu.edu [128.118.199.40]) by f04n07.cac.psu.edu (8.9.3/8.9.3) with ESMTP id OAA72628 for ; Wed, 11 Dec 2002 14:46:16 -0500 Content-Type: text/plain; charset="us-ascii" From: Rajarshi Guha Reply-To: rajarshi@presidency.com To: Subject: plotting molecular surfaces Date: Wed, 11 Dec 2002 14:44:20 -0500 X-Mailer: KMail [version 1.4] MIME-Version: 1.0 Content-Transfer-Encoding: 8bit Message-Id: <200212111444.24969.rajarshi@presidency.com> -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 Hi, I have used Molekel for plotting surfaces made of electrostatic potentials. I'd like to do this for a similar problem - rather than atomic charges, I want to plot atomic hydrophobicities. I have a program which reads Hyperchem HIN files and caluclates the hydrophobicity values. The resultant output consists of atom type, value. I also have at hand the x,y,z coordinates of the atoms (from the hin file). Essentially this is analogous to plotting an electrostatic potential surface - Molekel reads in Gaussian cube format. Thus if I could put my data in this format Molekel should be able to do the job. Is the format spec available anywhere? But apart from the Molekel route does anybody have any pointers as to how I could go about visualizing my data using freely available code. Thanks, - -- - ------------------------------------------------------------------- Rajarshi Guha GPG Fingerprint: 0CCA 8EE2 2EEB 25E2 AB04 06F7 1BB9 E634 9B87 56EE - ------------------------------------------------------------------- Alcohol, an alternative to your self - 'Alcohol' by the Bare Naked Ladies -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.0.7 (GNU/Linux) iD8DBQE995WYG7nmNJuHVu4RArkxAJ9dYOTpIQOKr16MB5TG7RujumcaIQCgnmCq CQWDz31KuiVugyZcnSDSpAM= =fBX2 -----END PGP SIGNATURE----- From chemistry-request@server.ccl.net Wed Dec 11 12:11:51 2002 Received: from mtiwmhc11.worldnet.att.net ([204.127.131.115]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id gBBHBpi02686 for ; Wed, 11 Dec 2002 12:11:51 -0500 Received: from hal ([12.86.37.130]) by mtiwmhc11.worldnet.att.net (InterMail vM.5.01.05.12 201-253-122-126-112-20020820) with ESMTP id <20021211171149.XTMR9286.mtiwmhc11.worldnet.att.net@hal>; Wed, 11 Dec 2002 17:11:49 +0000 Message-Id: <4.2.0.58.20021211100626.02023370@postoffice.worldnet.att.net> X-Sender: mrmopac@postoffice.worldnet.att.net X-Mailer: QUALCOMM Windows Eudora Pro Version 4.2.0.58 Date: Wed, 11 Dec 2002 10:08:07 -0700 To: Xavier ASSFELD , CCL From: "James J. P. Stewart" Subject: Re: CCL:Racah parameters In-Reply-To: <3DF74EC5.6C0A2C7D@lctn.uhp-nancy.fr> Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii"; format=flowed Please see http://www.cachesoftware.com/mopac/Mopac2002manual/node485.html Racah's reference is: Phys Rev, 61, 186 (1942) At 03:42 PM 12/11/2002 +0100, Xavier ASSFELD wrote: >Dear all, > >for transition metal electronic states one can use Racah >parameters A, B and C. >In textbook, one can find that the energy of state X is >equal to : A + 22B + 7C for example. >I would like to know : >1) The references of Racah's paper dealing with such parameters >2) How one can find the number in front of B and C (22 and >7 in my previous example). >Any help would be greatly appreciate. > >Yours, sincerely. > > >-- > > ...Xav > >WARNING ! NEW PHONE AND FAX NUMBER !! > >Ast. Pr. Xavier Assfeld Xavier.Assfeld@lctn.uhp-nancy.fr >Laboratoire de Chimie theorique (T) 33 3 83 68 43 74 >Universite Henri Poincare (F) 33 3 83 68 43 71 >F-54506 Nancy BP 239 http://www.lctn.uhp-nancy.fr > >-= 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 > > > ( @ @ ) .-------------oOOo----(_)----oOOo-------------------------------------. | James J. P. Stewart | | | Stewart Computational Chemistry | E-mail: jstewart@fujitsu.com | | 15210 Paddington Circle | 39/03/15 N, 104/49/29 W | | Colorado Springs CO 80921-2512 | | | USA .ooo0 | Phone: USA +(719) 488-9416 | | ( ) Oooo. | | .--------------------\ (----( )-------------------------------------. \_) ) / (_/ From chemistry-request@server.ccl.net Wed Dec 11 10:18:22 2002 Received: from nomina.net.lu.se ([130.235.132.90]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id gBBFILi31575 for ; Wed, 11 Dec 2002 10:18:21 -0500 Received: from csxp (CS-XP1800.mig.lu.se [130.235.104.90]) by nomina.net.lu.se (8.9.3/8.9.0) with SMTP id QAA15647 for ; Wed, 11 Dec 2002 16:18:55 +0100 (MET) Message-ID: <001901c2a129$05a13fe0$5a68eb82@csxp> From: =?iso-8859-1?Q?Emanuel_Bj=F6rne?= To: Subject: Rating in AutoDock3. Date: Wed, 11 Dec 2002 16:21:47 +0100 MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_0016_01C2A131.6703D8D0" 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_0016_01C2A131.6703D8D0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Dear all, How come that AutoDock 3.0 rates its simulation results according to = Energy instead of Free Energy of Binding? As far as I have understood = the entropic contributions from the assumed restriction of torsion = angles are not included in the Final Docked Energy but they are in the = Free Energy of binding.Or is it possible to chose what results to use in = the rating? Regards, Emanuel Bj=F6rne ------=_NextPart_000_0016_01C2A131.6703D8D0 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable
Dear all,
 
How come that AutoDock 3.0 rates its = simulation=20 results according to Energy instead of Free Energy of Binding? As far as = I have=20 understood the entropic contributions from the assumed restriction of = torsion=20 angles are not included in the Final Docked Energy but they are in the = Free=20 Energy of binding.Or is it possible to chose what results to = use in=20 the rating?
 
Regards,
 
Emanuel Bj=F6rne
 
 
 
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