From chemistry-request@server.ccl.net Wed Feb 27 05:50:53 2002 Received: from tigris.klte.hu ([193.6.138.33]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g1RAoq529287 for ; Wed, 27 Feb 2002 05:50:52 -0500 Received: from anti07 (193.6.133.59) by tigris.klte.hu (MX V5.1-A Vn6f) with SMTP; Wed, 27 Feb 2002 11:49:58 +0100 Message-ID: <002801c1bf7d$2ab05160$3b8506c1@chem.klte.hu> From: "Tamas Gunda" To: "Rowyna" CC: References: <3C7C3C49.8B7D8CF3@vplaces.net> Subject: Re: CCL:calculating dihedral angle Date: Wed, 27 Feb 2002 11:54:44 +0100 MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 5.50.4522.1200 X-MimeOLE: Produced By Microsoft MimeOLE V5.50.4522.1200 Mol2mol can calculate and dump all bond lengths and all angles of a molecule, as well as all of the dihedral angles starting from a selected atom, or within a ring. All possible dihedral angles of a molecule was not implanted, as this can grow to a very large number even in the case of "average-size" molecules. What kind of molecule file format you use? With regards Tamas E. Gunda Dr. Tamas E. Gunda Research Group for Antibiotics Hungarian Academy of Sciences University of Debrecen, POBox 36 H-4010 Debrecen, Hungary tamasgunda@tigris.klte.hu ----- Original Message ----- From: "Rowyna" To: "CCL" Sent: Wednesday, February 27, 2002 2:54 AM Subject: CCL:calculating dihedral angle > Dear CCLers, > > I would be grateful if somebody could suggest any > programs/utilities/scripts which can be used to calculate all the > possible dihedral angles of a given molecule or structure. I'm > interested in using such utilities, hopefully without charge. Maybe I > could write a script for the calculations but I'm not sure how to start > with that so perhaps an existing program would suit me better. > > It would be a lot of help and much thanks in advance. > > Rowyna K. > Institute of Biological Sciences, UM > Malaysia > > -= 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 Wed Feb 27 00:50:08 2002 Received: from jivdhan.unipune.ernet.in ([196.1.114.31]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g1R5o6504222 for ; Wed, 27 Feb 2002 00:50:07 -0500 Received: from chem.unipune.ernet.in (chem.unipune.ernet.in [196.1.114.10]) by jivdhan.unipune.ernet.in (8.11.6/8.11.6) with ESMTP id g1R5tiA14122 for ; Wed, 27 Feb 2002 11:25:44 +0530 Received: from localhost (tcg@localhost) by chem.unipune.ernet.in (8.9.3/8.8.7) with ESMTP id LAA14779 for ; Wed, 27 Feb 2002 11:18:31 +0530 Date: Wed, 27 Feb 2002 11:18:31 +0530 (IST) From: "Students of Dr. S. R. Gadre" To: CCL Subject: Correlation effect on weakly interacting species. Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII CCLer's... Could somebody give me a concrete example of weakly interacting geometrical conformers where the energy trends reverse in correlated methods.( One of the weakly interacting geometrical conformers which was a lower energy minimum at Hartree Fock level should not be a lower energy minimum in a correlated method like MP2 ...a conformer which was not a lower energy minimum in Hartree Fock becoming a lower energy minimum with a correlated method is the kind of situation that i am looking for...the structures should be stationary points on the PES) regards... bala From chemistry-request@server.ccl.net Wed Feb 27 03:01:46 2002 Received: from uni-freiburg.de ([132.230.2.65]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g1R81j526160 for ; Wed, 27 Feb 2002 03:01:46 -0500 Received: from [132.230.171.109] (account oliver.hucke@physchem.uni-freiburg.de HELO physchem.uni-freiburg.de) by uni-freiburg.de (CommuniGate Pro SMTP 3.4.7) with ESMTP-TLS id 5189636 for chemistry@ccl.net; Wed, 27 Feb 2002 09:01:16 +0100 Message-ID: <3C7C938B.8F45918C@physchem.uni-freiburg.de> Date: Wed, 27 Feb 2002 09:06:35 +0100 From: Oliver Hucke X-Mailer: Mozilla 4.79 [en] (WinNT; U) X-Accept-Language: en MIME-Version: 1.0 CC: chemistry@ccl.net Subject: QXP summary References: Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit Dear CCLers, This is the collection of all answers to my question concerning the drug design program QXP. Many thanks to Holger Claussen Joe Leonard Mohan Teran Castaņon, Hugo Gutierrez de David Turner Pieter F.W. Stouten Ya-Jun Zheng for their replies! Kind regards, Oliver ____________________________________________________________________________ Oliver Hucke Inst. fuer Physikalische Chemie II Universitaet Freiburg Albertstr. 23a D-79104 Freiburg Tel. : +49-761-203-5130 (/-6179) Fax. : +49-761-203-6189 email: Oliver.Hucke@physchem.uni-freiburg.de ____________________________________________________________________________ My CCL-message: ================== Dear CCL'ers, we are interested in methods for ligand docking calculations and structure based drug design in general. We have used mainly the ligand docking program FlexX so far, but we would like to be able to treat the binding site as conformationally flexible - FlexX uses a rigid binding pocket. Somebody pointed us to the package QXP, but there is only very few information about it on the internet. Therefore, we would like to ask you for some information about QXP. Do you have any experience with QXP, especially with its ability to perform ligand docking calculations with flexible protein binding site and with the accuracy of predicted binding free energies? Could you point us to some papers describing QXP applications or other sources of information about the program? Thank you very much in advance, Oliver Replies: ==================== --------------------------------------------------------------------------- Hello Oliver, >Do you have any experience with QXP, > Yes. In fact, we think it is so good that we recently concluded a global agreement so that our research sites in St. Louis, Chicago, Kalamazoo (USA) and Nerviano (Italy) have unlimited access and can run an unlimited number of simultaneous QXP jobs. We are in fact in the process of purchasing two Linux clusters with the specific aim to run QXP on them. >especially with its ability to >perform ligand docking calculations with flexible protein binding site >and with the accuracy of predicted binding free energies? > Well, that's the holy grail, isn't it? In order to obtain correlation with experiment, one often has to scale the various energy terms and even then the results are not always satisfactory. Colin McMartin is about ready to release a new scoring function that is based both on crystal structure data and on inhibition data of congeneric sets of compounds. In terms of docking quality (i.e., the ability to reproduce known binding modes), we find that often QXP finds the correct mode (among, say, the best 10-20 poses), but does not score it highest. Both docking and scoring quality also depend to a large extent on the target under consideration. Another docking program you might consider is MolSoft's ICM, whose scoring function has been optimized such that "actives" and "inactives" are separated as much as possible. >Could you point us to some papers describing QXP applications or other >sources of information about the program? > I saw two back-to-back presentations at the 219th ACS meeting in San Francisco (March 2000), one by Dominic Ryan of SKB and one by Venkatraman Mohan of Isis Pharma. They both prominently featured application of QXP and both speakers were quite positive about their experiences. In terms of ease of use QXP/Flo surpasses anything I have seen. It is clearly designed and developed for modellers by a modeller (who got frustrated with generally available tools and decided to build his own). Hope this helps, Pieter Pieter F.W. Stouten, Ph.D. Head, Computational Sciences Department of Chemistry Pharmacia Italia, Nerviano (Mi), Italy Phone: +39-02-4838-5227 (secretary: 3962) Fax: +39-02-4838-3965 Mobile: +39-348-260-3380 ------------------------------------------------------------------------------- Lieber Herr Hucke, in der CCL fragen Sie nach Docking Programmen, die das Docking in flexible Proteinstrukturen erlauben. Ich habe eine Erweiterung f"ur FlexX names FlexE entwickelt, die Proteinflexibilit"at behandeln kann. Im Monet bin ich dabei den Prototypen von FlexE zu "uberarbeiten. Eine kostenlose Demoversion von FlexE soll es demn"achst geben. Ich habe mir erlaubt einen Artikel "uber FlexE anzuh"angen und w"urde Sie informieren, sobald es die Demoversion von FlexE gibt. Viele Gr"usse Holger Claussen ============================================================================= Dr. Holger Claussen Fraunhofer-Institute for Algorithms and Scientific Computing (SCAI) BioSolveIT GmbH Schloss Birlinghoven An der Ziegelei 75 D-53754 Sankt Augustin D-53757 St. Augustin Tel: +49 - 2241 - 14 - 2795 +49 - 2241 - 973 66 65 Fax: +49 - 2241 - 14 - 2656 +49 - 2241 - 973 66 88 E-mail: Holger.Claussen@scai.fraunhofer.de Holger.Claussen@BioSolveIT.de Internet: http://www.scai.fraunhofer.de http://www.BioSolveIT.de ------------------------------------------------------------------------------------- Hello Oliver, Yes, we did use QXP in our group for the docking of ligands on models of GPCRs. The accurancy of the energies is not good, but you can use its energie values for a first ranking of the ligands. The program has a graphical interface (called LZM), which you can use to prepare your docking search (i.e., starting position, flexible sidechains, distance constraints). This last point is crutial for a good search, or in adition you can define a grid for the search, what never worked for me. It has several modules (TFIT for a pharmacophore search, MCDOCK for docking, and DINDOCK for a MC-simulated annealing). I only have experience with the first two. After preparing the files, you can run it on the LZM interface or in shell mode (it works better). Here is the reference of the program: Mcmartin, Journal of Computer-Aided Molecular Design 11(4): 333-344; Jul 1997), and there is another reference (Carrieri et al, Proteins, 43:382 394(2001)), where you will find a good description of a docking with QXP. The program only works for SGI, and you have to order it to the author. I'm afraid the support is not too good. Hope this helps. Fell free for any comments, Best regards Hugo ---------------------------------------------------------------------------------------- Oliver, if you have Tripos/Sybyl Biopolymer's module, you can look at FlexiDock - it's a GA-based docking code which allows for both ligand and protein flexibility. You might also want to look at GOLD, although I'm not sure how one gets it... Joe -- Dave Young wrote: > > Hi, > > A number of CCL members have asked about the book I have been writing. It is now in print and available from Wiley. Here is the publisher's description. > > COMPUTATIONAL CHEMISTRY > Applying Computational Techniques to Real-World Problems > > David Young, Cytoclonal Pharmaceutics, Dallas > > 0-471-33368-9 Pub Date: 2/16/01 416 pages $69.95 > > As the field of computational chemistry continues to expand, experimental chemists are expected to know how to utilize techniques that are becoming available at the desktop level through commercial software packages. This book provides a much-needed basic guide to computational chemistry software and tools available today. A practical, easily accessible reference for chemists, this text focuses on accurately applying computational chemistry techniques to everyday chemistry problems. Techniques for handling problem cases, such as SCF convergence problems, are also discussed. > > To order, please call (800) 225-5945 or visit http://www.amazon.com/exec/obidos/ASIN/0471333689 > It is also available through Barnes & Noble (http://www.barnesandnoble.com/), which has the table of contents listed on the web. > > Dave Young > dave.young@springmail.com > > -= 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 -- Hi Oliver: Here is the QXP reference: C. McMartin & R.S. Bohacek J. Comput.-Aided Mol. Des. vol 11, 333, 1997. McMartin's e-mail address: cmcma@ix.netcom.com His telephone number: 860 379 5502 Let me know if you need any additional info. Cheers, -mohan -------------- Hi again, You could also get information on QXP at http://uwmml.pharmacy.wisc.edu/Flo/floindx.html -mohan --------------- Ya-Jun Zheng wrote: > > Oliver, > > QXP is part of Flo99, which is a program developed by Colin McMartin and > Regine Bohacek. There are a number of papers describing the modeling > results using Flo. Please see the recent papers by Dan Rich in J. Med. > Chem. (in 2002) and Organic Letters (in 2001) and also papers by Regine > Bohacek and coworkers from ARIAD Pharmaceuticals (works on SH3 domain > inhibitors, some appeared on covers of J. Med. Chem last year). Regine > also developed a de novo design program (called AlleGrow) recently. Here > is Colin's contact info: > > Phone: 860-379-5502 and e-mail: cmcma@ix.netcom.com > > Yajun Zheng From chemistry-request@server.ccl.net Wed Feb 27 03:47:23 2002 Received: from mailstudenti.unimi.it ([159.149.10.4]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g1R8lN527408 for ; Wed, 27 Feb 2002 03:47:23 -0500 Received: from vega (smtp.unimi.it [159.149.10.3]) by mailstudenti.unimi.it (iPlanet Messaging Server 5.1 (built May 7 2001)) with SMTP id <0GS600DN9OE7SU@mailstudenti.unimi.it> for chemistry@ccl.net; Wed, 27 Feb 2002 09:46:56 +0100 (MET) Date: Wed, 27 Feb 2002 09:48:14 +0100 From: Giulio Vistoli Subject: Re: CCL:calculating dihedral angle To: Rowyna , CCL Message-id: <002101c1bf6b$7eaa9940$204f959f@farma.unimi.it.farma.unimi.it> Organization: Ist. Chimica Farmaceutica MIME-version: 1.0 X-MIMEOLE: Produced By Microsoft MimeOLE V5.50.4522.1200 X-Mailer: Microsoft Outlook Express 5.50.4522.1200 Content-type: text/plain; charset=iso-8859-1 Content-transfer-encoding: 7BIT X-Priority: 3 X-MSMail-priority: Normal References: <3C7C3C49.8B7D8CF3@vplaces.net> Dear Rowyna, Our program VEGA can calculate the dihedral angles (along with other measures like distances, angles, dipole, etc)of a molecule and can calculate this property also on the frames saved in a tralectory. VEGA is free download at http://users.unimi.it/~ddl Best regards Giulio Vistoli -- Dr. Giulio Vistoli Ist. di Chimica Farmaceutica e Tossicologica Viale Abruzzi, 42 I-20131 Milano (Italy) Tel. +39 02 503 17522 Fax +39 02 503 17565 E-Mail: giulio.vistoli@unimi.it WWW: http://users.unimi.it/~ddl From chemistry-request@server.ccl.net Wed Feb 27 08:41:44 2002 Received: from chinon.cnrs-orleans.fr ([163.9.6.107]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g1RDfe531891 for ; Wed, 27 Feb 2002 08:41:40 -0500 Received: (from hinsen@localhost) by chinon.cnrs-orleans.fr (8.11.2/8.11.2) id g1RDfEH22106; Wed, 27 Feb 2002 14:41:14 +0100 Date: Wed, 27 Feb 2002 14:41:14 +0100 Message-Id: <200202271341.g1RDfEH22106@chinon.cnrs-orleans.fr> X-Authentication-Warning: chinon.cnrs-orleans.fr: hinsen set sender to hinsen@cnrs-orleans.fr using -f From: Konrad Hinsen To: chemistry@ccl.net Subject: Re: CCL:Normal Modes for large proteins Ben Carrington writes: > Can anyone suggest how I go about performing normal modes calculations > on large systems - protein complexes to be exact. At the moment I cannot > get any programs to run due to the large amount of memory needed. Can I > split this calculation up? There are various techniques to calculate normal modes for large systems, approximately and/or iteratively. It all depends on what you need the normal modes for. If you are interested in low-frequency modes for large systems, I can propose a method described in K. Hinsen Analysis of domain motions by approximate normal mode calculations Proteins 33(3), 417-429 (1998) and implemented in the Molecular Modelling Toolkit: http://dirac.cnrs-orleans.fr/MMTK/ as well as in an interactive domain motion analysis tool: http://dirac.cnrs-orleans.fr/DomainFinder/ For some applications, see K. Hinsen, A. Thomas, M.J. Field Analysis of domain motions in large proteins, Proteins 34(3), 369-382 (1999) -- ------------------------------------------------------------------------------- Konrad Hinsen | E-Mail: hinsen@cnrs-orleans.fr Centre de Biophysique Moleculaire (CNRS) | Tel.: +33-2.38.25.56.24 Rue Charles Sadron | Fax: +33-2.38.63.15.17 45071 Orleans Cedex 2 | Deutsch/Esperanto/English/ France | Nederlands/Francais ------------------------------------------------------------------------------- From chemistry-request@server.ccl.net Wed Feb 27 10:00:45 2002 Received: from maple.sucs.soton.ac.uk ([152.78.128.16]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g1RF0j501322 for ; Wed, 27 Feb 2002 10:00:45 -0500 Received: from poplar.sucs.soton.ac.uk (poplar.sucs.soton.ac.uk [152.78.128.30]) by maple.sucs.soton.ac.uk (8.10.0/8.10.0) with ESMTP id g1RF09H25656 for ; Wed, 27 Feb 2002 15:00:09 GMT Received: from willow.sucs.soton.ac.uk (willow.sucs.soton.ac.uk [152.78.128.20]) by poplar.sucs.soton.ac.uk (8.10.0/8.10.0) with ESMTP id g1RExlg00655 for ; Wed, 27 Feb 2002 14:59:47 GMT Date: Wed, 27 Feb 2002 14:59:24 +0000 (GMT) From: "F.TOSCHI" Sender: F.TOSCHI@soton.ac.uk To: chemistry@ccl.net Subject: Tanimoto Coefficient Calculation Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-MailScanner: Believed to be clean Dear CCL, I am looking for a fast algorithm/software (possibly free) to compute the Tanimoto coefficient and/or other similarity/distance indices. Any references or pointers to source code would be very welcome. Many thanks in advance, Francesca Toschi f.toschi@soton.ac.uk Chemistry Department University of Southampton SO17 1BJ Southampton, UK From chemistry-request@server.ccl.net Wed Feb 27 12:43:14 2002 Received: from mxout1.cac.washington.edu ([140.142.32.5]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g1RHhE504560 for ; Wed, 27 Feb 2002 12:43:14 -0500 Received: from mailscan-out3.cac.washington.edu (mailscan-out3.cac.washington.edu [140.142.32.18]) by mxout1.cac.washington.edu (8.12.1+UW01.12/8.12.1+UW02.01) with SMTP id g1RHgixY026379 for ; Wed, 27 Feb 2002 09:42:48 -0800 Received: FROM mailhost1.u.washington.edu BY mailscan-out3.cac.washington.edu ; Wed Feb 27 09:42:44 2002 -0800 Received: from donald ([128.95.128.116]) by mailhost1.u.washington.edu (8.12.1+UW01.12/8.12.1+UW02.01) with SMTP id g1RHghgK022155 for ; Wed, 27 Feb 2002 09:42:43 -0800 From: "Carsten Detering" To: "ChemistryList" Subject: autodock, atom types Date: Wed, 27 Feb 2002 18:29:26 +0100 Message-ID: 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 IMO, Build 9.0.2416 (9.0.2910.0) X-MimeOLE: Produced By Microsoft MimeOLE V5.00.2615.200 Importance: Normal Dear CCl'ers, I am currently trying to add another atom type to AutoDock, n, to decide between nitrogen as a hydrogen bond donor and nitrogen as an acceptor. Does anyone of you have experience with that? I added this particular atom type, n, to the dpf3gen.awk and gpf3gen.awk files, and everything works fine for the latter. For the built .dpf file, autodock gives an errormessage "ERROR: 7 atom types declared in "", S_line "C/.../autodock3: Aborting" in my case the ligand has atom types CANOPHn. Also, in the gpf3gen.awk file, it is said that PROTEIN_ATOMTYPES should be set to the same string as ATOMTYPE in autogrid.h, but there is no such variable ATOMTYPE in that library file. I tried to change ATOMTYPE in autocomm.h and recompile the autodock executable, but another error mesage occurs: "writeStateOfPDBQ is undefined". I am using an SGI with IRIX 6.5. Could anybody help me with this problem?? Thanks in advance, with best regards, Carsten ------------------------ Carsten Detering, Ph.D. University of Washington Seattle, WA 98195 email: detering@u.washington.edu From chemistry-request@server.ccl.net Wed Feb 27 23:20:42 2002 Received: from igcar.ernet.in ([202.141.82.2]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g1S4Kf519391 for ; Wed, 27 Feb 2002 23:20:41 -0500 Received: from igcar.ernet.in (localhost.localdomain [127.0.0.1]) by igcar.ernet.in (8.9.3/8.9.3) with ESMTP id JAA17202 for ; Thu, 28 Feb 2002 09:54:07 +0530 Received: from [203.199.205.25] ([203.199.205.25]) by igcar.ernet.in (8.9.3/8.9.3) with SMTP id JAA17173 for ; Thu, 28 Feb 2002 09:54:02 +0530 Received: from [10.1.1.100] by [203.199.205.25] via smtpd (for mail.igcar.ernet.in [202.141.82.2]) with SMTP; 28 Feb 2002 04:21:12 UT Received: (from Urcl@localhost) by igcmail.igcar.ernet.in (8.9.3+Sun/8.9.1) id JAA27233 for chemistry@ccl.net; Thu, 28 Feb 2002 09:51:14 -0500 (GMT) X-Authentication-Warning: igcmail.igcar.ernet.in: Urcl set sender to vvenkat@igcar.ernet.in using -f >Received: from localhost by rcl.igcar.ernet.in (8.9.1b+Sun/SMI-SVR4) id JAA17413; Thu, 28 Feb 2002 09:49:42 -0500 (GMT) Date: Thu, 28 Feb 2002 09:49:42 -0500 (GMT) From: "V.Venkatesan" X-Sender: vvenkat@rcl To: chemistry@ccl.net Subject: Gaussian AIM Calculation Failure Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII HAI I am trying to perform an Atoms in Molecules analysis on quite a small molecule (dimethoxymethane-B3LYP/6-31++G**) using Gaussian 94. Unfortunately, the calculation bombs out with the message: ********************************************************************** Properties of atoms in molecules using the SCF density. ********************************************************************** I. ATTRACTORS ------------------------------------------------------------------------------- Attr. Cartesian Coordinates Nucleus Density X Y Z (Distance) Total Spin ------------------------------------------------------------------------------- 1 4.130505 -.476845 .194551 C ( .000005) .11758E+03 .00000E+00 2 1.614715 -.558569 -.718313 O ( .000010) .28990E+03 .00000E+00 3 .049437 1.315179 .385209 C ( .000006) .11759E+03 .00000E+00 4 -2.398134 1.087801 -.520545 O ( .000010) .28984E+03 .00000E+00 5 -3.663983 -1.163077 .253213 C ( .000005) .11759E+03 .00000E+00 6 .690561 3.177301 -.138876 H ( .039163) .44008E+00 .00000E+00 7 .103250 1.110778 2.431796 H ( .037508) .43815E+00 .00000E+00 8 -3.663849 -1.329676 2.287304 H ( .038120) .43277E+00 .00000E+00 9 -5.570301 -1.001109 -.403137 H ( .039758) .43428E+00 .00000E+00 10 -2.798330 -2.810052 -.556131 H ( .039611) .43252E+00 .00000E+00 11 4.208662 -.782156 2.212897 H ( .038039) .43258E+00 .00000E+00 12 5.024959 1.309062 -.231056 H ( .038114) .43269E+00 .00000E+00 13 5.145607 -1.957823 -.737185 H ( .039841) .43326E+00 .00000E+00 ------------------------------------------------------------------------------- II. CRITICAL POINTS ON ATTRACTOR INTERACTION LINES ------------------------------------------------------------------------------- Line Attractors Cartesian Coordinates Density A B X Y Z Total Spin ------------------------------------------------------------------------------- 1 2 1 3.256872 -.479338 -.097775 .25743E+00 .00000E+00 2 3 2 .620234 .659640 .012929 .26590E+00 .00000E+00 3 4 3 -.785923 1.199318 .088428 .28336E+00 .00000E+00 4 5 4 -3.199128 -.395092 .010638 .25150E+00 .00000E+00 5 6 3 .470177 2.522798 .041728 .28938E+00 .00000E+00 6 7 3 .083449 1.175462 1.705193 .28194E+00 .00000E+00 7 8 5 -3.657837 -1.263358 1.556588 .27937E+00 .00000E+00 8 9 5 -4.893078 -1.055459 -.170942 .28648E+00 .00000E+00 9 10 5 -3.100697 -2.226752 -.270939 .28529E+00 .00000E+00 10 11 1 4.172814 -.670408 1.488526 .27909E+00 .00000E+00 11 12 1 4.696754 .671492 -.078745 .27945E+00 .00000E+00 12 13 1 4.783788 -1.434115 -.408339 .28621E+00 .00000E+00 ------------------------------------------------------------------------------- ------------------------------------------------------------------------------- Line Density Ellipticity Hessian eigenvalues and eigenvectors Laplacian Eig X Y Z ------------------------------------------------------------------------------- 1 -.4811E+00 .1195E-01 -.4763E+00 .22836 -.77236 -.59272 -.4707E+00 .24542 .63481 -.73266 .4659E+00 .94214 .02184 .33452 2 -.6338E+00 .1731E+00 -.5713E+00 -.76701 -.34732 -.53950 -.4870E+00 .22926 .63697 -.73601 .4245E+00 -.59927 .68822 .40894 3 -.6032E+00 .1204E+00 -.6175E+00 .25879 -.84009 -.47674 -.5511E+00 .23980 .53398 -.81078 .5654E+00 .93570 .09550 .33964 4 -.4695E+00 .1730E-01 -.4597E+00 -.72342 .18949 -.66390 -.4519E+00 -.49520 .52765 .69019 .4421E+00 -.48109 -.82806 .28787 5 -.1072E+01 .2135E-01 -.8017E+00 .93906 -.33635 -.07100 -.7849E+00 .14907 .21234 .96576 .5151E+00 -.30976 -.91749 .24954 6 -.9987E+00 .2408E-01 -.7658E+00 -.90058 .42997 .06389 -.7477E+00 .43372 .89862 .06603 .5148E+00 -.02902 .08718 -.99577 7 -.9775E+00 .4502E-01 -.7514E+00 .49205 .86647 .08439 -.7190E+00 .87052 -.49067 -.03784 .4929E+00 .00862 .09209 -.99571 8 -.1044E+01 .4374E-01 -.7850E+00 .21178 .88315 -.41858 -.7521E+00 -.25364 .46328 .84914 .4931E+00 .94383 -.07366 .32211 9 -.1032E+01 .4270E-01 -.7805E+00 .64813 .57399 -.50047 -.7486E+00 -.63657 .04765 -.76974 .4969E+00 -.41798 .81748 .39627 10 -.9743E+00 .4430E-01 -.7501E+00 -.98998 -.13814 .02942 -.7182E+00 -.13193 .97883 .15645 .4940E+00 -.05041 .15100 -.98725 11 -.9776E+00 .4440E-01 -.7518E+00 -.81486 .30358 -.49381 -.7198E+00 .36698 -.38925 -.84487 .4940E+00 -.44870 -.86967 .20577 12 -.1043E+01 .4136E-01 -.7838E+00 -.82596 -.26022 -.50008 -.7527E+00 -.24622 -.63148 .73526 .4932E+00 -.50712 .73043 .45750 ------------------------------------------------------------------------------- ------------------------------------------------------------------------------- Line Buckling Distance to attractor A Distance to attractor B Angle dev. Arc Line Differ. Arc Line Differ. A B ------------------------------------------------------------------------------- 1 .0346 1.75777 1.75728 .00050 .92129 .92125 .00004 4.07 2.53 2 .0258 .94561 .94559 .00002 1.73480 1.73428 .00051 1.46 3.80 3 .0402 1.72776 1.72699 .00077 .89413 .89405 .00008 4.96 3.27 4 .0382 .92998 .92991 .00007 1.76780 1.76712 .00067 2.83 4.65 5 .0056 .71384 .71384 .00000 1.32447 1.32414 .00033 .45 1.92 6 .0079 .72975 .72975 .00000 1.32833 1.32779 .00054 .65 2.52 7 .0088 .73374 .73374 .00000 1.30774 1.30724 .00050 .72 2.45 8 .0033 .71798 .71798 .00000 1.30488 1.30467 .00021 .22 1.61 9 .0038 .71624 .71624 .00000 1.31312 1.31279 .00033 .08 1.89 10 .0081 .73382 .73382 .00000 1.30946 1.30906 .00040 .67 2.22 11 .0080 .73309 .73308 .00000 1.30959 1.30920 .00039 .66 2.18 12 .0027 .71647 .71646 .00000 1.30656 1.30638 .00018 .15 1.47 ------------------------------------------------------------------------------- 13 attractors - 12 bond point(s) + 0 ring point(s) - 0 cage point(s) = 1 FATAL ERROR: TOO MANY INTEGRATION DOMAINS Error termination via Lnk1e in C:\G94W\l609.exe. Can anyone suggest a cure? ******************************************************************************* NAME:V.VENKATESAN ADDRESS:MATERIALS CHEMISTRY DIVISION RADIOCHEMICAL LABORATORY INDIRA GANDHI CENTRE FOR ATOMIC RESEACH KALPAKKAM-603102 TAMILNADU INDIA E-MAIL ID:vvenkat@igcar.ernet.in *******************************************************************************