From norge@karin.fmq.uh.edu.cu Thu Nov 27 01:37:36 1997 Received: from fax.ceniai.inf.cu for norge@karin.fmq.uh.edu.cu by www.ccl.net (8.8.3/950822.1) id BAA21864; Thu, 27 Nov 1997 01:11:36 -0500 (EST) Received: from ceniai.inf.cu by fax.ceniai.inf.cu with esmtp (Smail3.2) id m0xaxAY-000MTOC; Thu, 27 Nov 1997 01:11:22 -0500 (CST) Received: from fmq.uh.edu.cu by ceniai.inf.cu with bsmtp (Smail3.2) id m0xaxDE-000ApkC; Thu, 27 Nov 1997 01:14:08 -0500 (CST) Received: from ffserver by ffuh with smtp (Smail3.1.29.1 #23 fisuh.fmr.uh.cu ) id m0xatHr-000KdOC; Wed, 26 Nov 97 21:02 CST Received: from karin.fmq.uh.edu.cu by ffserver with smtp (Smail3.1.29.1 #1 fisuh.fmq.uh.edu.cu ) id m0xat1s-0004nYC; Wed, 26 Nov 97 20:46 CST Received: (from norge@localhost) by karin.fmq.uh.edu.cu (8.6.12/8.6.9) id WAA02702; Wed, 26 Nov 1997 22:09:22 -0500 Date: Wed, 26 Nov 1997 22:09:21 -0500 (CST) From: Norge Cruz Hernández To: chemistry@www.ccl.net Subject: Help in Mathematical methods. Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Content-Transfer-Encoding: 8bit Hi, I am trying to solve the minimization of a function whith non linear constrained. I am using the IMSL MATH/LIBRARY in FORTRAN.Version 1.1 December 1989. In that, a routine based on a FORTRAN code developed by Schittkowski(1986). It uses a succesive quadratic programming method to solve the general nonlinear programming problem. But it is not possible for me to solve the problem. I can acces to internet by netscape or by navagator. I can read some WWW page by e-mail. Would any bady said me any web page on IMSL MATH/LIBRARY ? Would any bady said me any web page on NUMERICAL RECIPES ? best regard Norge From barbosa@anne.chemie.unibas.ch Thu Nov 27 05:37:45 1997 Received: from anne.chemie.unibas.ch for barbosa@anne.chemie.unibas.ch by www.ccl.net (8.8.3/950822.1) id FAA23560; Thu, 27 Nov 1997 05:19:45 -0500 (EST) From: Received: by anne.chemie.unibas.ch (AIX 3.2/UCB 5.64/4.03) id AA18731; Thu, 27 Nov 1997 11:09:54 +0100 Message-Id: <9711271009.AA18731@anne.chemie.unibas.ch> Subject: normal mode force constant To: chemistry@www.ccl.net Date: Thu, 27 Nov 1997 11:09:54 +0100 (NFT) X-Mailer: ELM [version 2.4 PL24] Mime-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Dear CCL, I would like to get the normal mode force constant for each bond of a molecule to use them in the equation of Marcus theory. I do not know how to calculate the normal mode force constant for a bond. I would be pleased if somebody could help me to solve this problem. Thank you. Frederique ================================================================================ Frederique BARBOSA Institute for Organic Chemistry University of Basel E-mail : barbosa@anne.chemie.unibas.ch St. Johanns-Ring 19 phone : 061/267 11 57 4056 Basel fax : 061/267 11 05 Switzerland ================================================================================ From jochen@amiga.chemie.uni-konstanz.de Thu Nov 27 07:37:40 1997 Received: from amiga.chemie.uni-konstanz.de for jochen@amiga.chemie.uni-konstanz.de by www.ccl.net (8.8.3/950822.1) id HAA24344; Thu, 27 Nov 1997 07:08:05 -0500 (EST) Received: (from jochen@localhost) by amiga.chemie.uni-konstanz.de (8.8.5/8.6.9) id NAA17749; Thu, 27 Nov 1997 13:09:12 +0100 Date: Thu, 27 Nov 1997 13:09:12 +0100 Message-Id: <199711271209.NAA17749@amiga.chemie.uni-konstanz.de> From: Jochen Buehler To: chemistry@www.ccl.net Subject: G94 E.2 on J90 X-Mailer: VM 6.31 under 20.2 XEmacs Lucid Mime-Version: 1.0 (generated by tm-edit 7.97) Content-Type: multipart/mixed; boundary="Multipart_Thu_Nov_27_13:09:12_1997-1" Content-Transfer-Encoding: 7bit --Multipart_Thu_Nov_27_13:09:12_1997-1 Content-Type: text/plain; charset=US-ASCII Hi, as Gaussian Inc. is not very responsive on this topic, I hope my question is sufficiently on topic here... We upgraded from Gaussian94 Rev. D.3 to E.2 as the old version refused to compile on our Cray J90 after an OS update to Unicos 9.x. Now E.2 compiles mostly fine (albeit some warnings show up) but fails on a large variety of the test jobs (e.g. test164[5].com). Now I wonder if there are any success stories running E.2 on J90´s? (All the test jobs run fine on our DEC Alpha system...) Any help appreciated Jochen --Multipart_Thu_Nov_27_13:09:12_1997-1 Content-Type: text/plain; charset=US-ASCII Jochen Buehler EMail: jochen@amiga.chemie.uni-konstanz.de AG Prof. Dr. Daltrozzo buehler@chemie.uni-konstanz.de Fakultaet fuer Chemie Phone: +49-7531-882094 Universitaet Konstanz Fax: +49-7531-883043 --Multipart_Thu_Nov_27_13:09:12_1997-1-- From gbr@NPD.UFPE.BR Thu Nov 27 11:37:42 1997 Received: from NPD1.NPD.UFPE.BR for gbr@NPD.UFPE.BR by www.ccl.net (8.8.3/950822.1) id LAA25452; Thu, 27 Nov 1997 11:31:59 -0500 (EST) Received: from hartree.dqf.ufpe.br by NPD.UFPE.BR (PMDF V5.1-4 #20469) with ESMTP id <01IQI89RD4K0000IFY@NPD.UFPE.BR> for CHEMISTRY@www.ccl.net; Thu, 27 Nov 1997 13:30:32 GMT-3 Date: Thu, 27 Nov 1997 13:29:04 -0200 From: Gerd Bruno da Rocha Subject: cyclodextrin inclusion complexes summary To: CHEMISTRY@www.ccl.net Message-id: <347D91C0.D40A96C1@npd.ufpe.br> Organization: Depto. de Quimica Fundamental - UFPE MIME-version: 1.0 X-Mailer: Mozilla 4.0 [en] (Win95; I) Content-type: text/plain; charset=x-UNICODE-2-0-UTF-7 Content-transfer-encoding: 7bit X-Priority: 3 (Normal) Dear all, Many thanks to those who responded! Here is a brief summary of the responses I received. Best regards, My original question was: Could someone give me any references or suggestions of the most appropriate force field for calculations of cyclodextrin inclusion complexes ? --------------------------------------------------------------------------------------------- summary: Dear Gerd, Your question has no simple answer. It depends very much on what you want to study. In my own experience, MM2 and MM3 force fields do give reasonable results on geometrical data for inclusion of low polar organic molecules. Not much can be said on energetics since no solvent model is included into MM3, although they seem to reproduce correctly the energy differences between bimodal complexes. In contrast, AMBER is able to deal with many more types of molecules, although it is more difficult to use. The energy involved in the inclusion process is highly dependent of the solvent used. So, any force field containing good solvent models is worth thinking if your interest is to study interaction energy. Hope this helps you. -- Carlos JAIME Dept. Quimica, Univ. Autonoma de Barcelona 08193 Bellaterra (Barcelona), SPAIN Phone: ++34-3-581 2591; Fax: ++34-3-581 1265 or ++34-3-581 2477 -------------------------------------------------------------- During my PhD study I have successfully applied the GROMOS forcefield for molecular dynamics simulations of cyclodextrin complexes: J. Biomol. Struct. Dyn. 9(6) 1992 1269-1283 J. Am. Chem. Soc. 116 1994 6293-6302 The GROMOS forcefield can be obtained from Prof. W. van Gunsteren ETH Zentrum CH8092 Zurich Switserland success, Steven ----------------------------------------------------------------------- Dr. Steven P. van Helden E-mail: s.helden@organon.oss.akzonobel.nl CMC group RK2330 Phone: 31-412-661921 NV Organon Fax: 31-412-662539 P.O. Box 20 5340 BH OSS The Netherlands ----------------------------------------------------------------------- Dear Gerd It seems to me that You are planning to perform docking of molecules into cyclodextrin. So intermolecular interactions are predominent and in this case Bill Jorgensen's OPLS force field is the more appropriate to me. regards Gerard Vergoten vergoten@chouia.univ-lille1.fr -------------------------------------------------------------------- Dear Gerd, I'm working on cyclodextrins too and use the AMBER force field with the GLYCAM implementation. Have a look for it at: http://www.amber.ucsf.edu/amber/ff94_glycam.html Hope it helps regards Bruno Dr Bruno Manunza DISAABA (Dept. of Agricultural Environm. Sci) University of Sassari V.le Italia 39 07100 Sassari, ITALY phone: 39 79 229215 fax: 39 79 229276 e-mail: bruno@antas.agraria.uniss.it e-mail: bruno@tharros.dipchim.uniss.it e-mail: gx6bot81@cray.cineca.it web: http://antas.agraria.uniss.it -- *********************************************************************** Universidade Federal de Pernambuco Centro de Ciencias Exatas e da Natureza Departamento de Quimica Fundamental http://www.dqf.ufpe.br Recife - PE - Brazil Gerd Bruno da Rocha E-Mail : gbr@npd.ufpe.br : gerd@dqf.ufpe.br MSc Student in Computational Chemistry *********************************************************************** From rvenable@deimos.cber.nih.gov Thu Nov 27 12:37:44 1997 Received: from deimos.cber.nih.gov for rvenable@deimos.cber.nih.gov by www.ccl.net (8.8.3/950822.1) id MAA25727; Thu, 27 Nov 1997 12:35:58 -0500 (EST) Received: from localhost by deimos.cber.nih.gov with SMTP (1.37.109.14/16.2) id AA260691451; Thu, 27 Nov 1997 12:24:11 -0500 Date: Thu, 27 Nov 1997 12:24:10 -0500 (EST) From: Rick Venable Reply-To: Rick Venable To: Norge Cruz Hernandez Cc: CHEMISTRY@www.ccl.net Subject: Re: CCL:Help in Mathematical methods. In-Reply-To: Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII On Wed, 26 Nov 1997, Norge Cruz Hernandez wrote: > I am trying to solve the minimization of a function whith non linear > constrained. First, let me highly recommend that you look at the code available at NETLIB; it has the following attributes: o It is mature, well tested, stable code; the linear algebra library (BLAS) is the basis for most vendor implementations, and the LINPACK suite used to benchmark floating point performance is also here o It is public domain code, with no restrictions on re-use o It is highly efficient, well optimized code; for inversion of large matrices, I observed a ca. 50-fold speedup in switching from N.R. routines to those in NETLIB o The web site is fairly well organized, and allows you to download just the source files you need http://www.netlib.org Note: use your vendor supplied blas.a library, if available; the routines are often hand-tuned and optimized for the machine architecture. > Would any bady said me any web page on IMSL MATH/LIBRARY ? The IMSL subroutines are commercially available (only) from Visual Numerics, Inc.; their homepage is at http://www.vni.com > Would any bady said me any web page on NUMERICAL RECIPES ? The Numerical Recipes routines are copyrighted, and are generally for personal use if you've bought the book. There are restrictions against distributing code which contains N.R. routines. Nonetheless, routines and documentation are available at http://nr.harvard.edu/numerical-recipes Finally, a good pointer to many useful freely available (and commercial) Fortran libraries and programs is at http://kumo.swcp.com/fortran/ -- Rick Venable =====\ |=| "Eschew Obfuscation" FDA/CBER Biophysics Lab |____/ |=| Bethesda, MD U.S.A. | \ / |=| ( Not an official statement or rvenable@deimos.cber.nih.gov | \ / |=| position of the FDA; for that, http://nmr1.cber.nih.gov/ \/ |=| see http://www.fda.gov ) From h332262@sirius.cab.u-szeged.hu Thu Nov 27 13:37:43 1997 Received: from sirius.cab.u-szeged.hu for h332262@sirius.cab.u-szeged.hu by www.ccl.net (8.8.3/950822.1) id MAA25868; Thu, 27 Nov 1997 12:52:31 -0500 (EST) Received: by sirius.cab.u-szeged.hu (SMI-8.6/SMI-SVR4) id SAA04571; Thu, 27 Nov 1997 18:52:29 +0100 Date: Thu, 27 Nov 1997 18:52:28 +0100 (MET) From: Kiss Gergo X-Sender: h332262@sirius To: chemistry@www.ccl.net Subject: Summary: Tinker outputs Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi everybody, I posted this question some days ago to the list: >I use the Tinker package for some calculations on peptides. The problem >is, that the output is in Tinker's xyz format. Rasmol, Molmol and Molden >can't read this. If I use the included xyzpdb.x program for converting to >pdb, Rasmol and Molden reads the file, but none of them can perform >backbone calculations. >Do you know about a graphical software, which can read Tinker's xyz >format, or about a converter, which can turn this file into usable form. >Please help me, I will summarize the answers. > The answers I got: 1.----------------------------------------------------------------------- Hi, My gOpenMol program can read both Tinker single coordinate and multi coordinate files. The release 1.0 (with the Tinker reader) is will be ready in a few days. Address: http://laaksonen.csc.fi/gopenmol/ Regards, -leif laaksonen 2.-------------------------------------------------------------------- Dear Gergo Kiss, If your molecule is a peptide/protein, then xyzpdb should write a PDB file that is "correct" in all respects and will be able to do backbone calculations, etc. in Rasmol, and so on. In order for the correct PDB file to be created by xyzpdb, you must have a TINKER sequence file (.seq file) present during the conversion process so that xyzpdb will know it is dealing with a protein and will correctly parse the xyz file looking for the correct sequence of amino acids. The sequence file is created automatically by the pdbxyz program whenever a PDB file is translated to xyz format, and also when the protein program is used to build an arbitrary structure from a sequence and set of phi-psi-chi angles. If the sequence file is not present during xyzpdb, then the program will assume that your system is nonpeptide and will write a PDB file that follows the PDB format, but does not use standard residue names, atom names and such that Rasmol and other programs expect. The recent version of TINKER should be able to handle xyz <--> PDB conversions for multiple chains of peptide/protein optionally followed at the bottom of the file by water molecules and/or ligands. We have recently added the ability to handle a limited selection of "capping residues" for the polypeptide chains. This last feature will be added to the distribution version on http://dasher.wustl.edu/tinker/ shortly. In addition, you might look into the Babel software. This is a public domain molecule file format converter. While I have not yet done so, it should be a fairly simple matter to write a TINKER module for Bable that will allow conversion of TINKER xyz to/from PDB and other formats. Hope this helps. Best wishes, Jay Ponder 3.----------------------------------------------------------------------- Dear Kiss Gergo, About molden. First there is already a tinker xyz routine in molden, but it is only accessible from the z-matrix editor mapxyz/optimise option. I will add a commandline flag to force tinker xyz reading. But still there is a way to accomplish what you want in molden: - use the xyzpdb.x program for converting to pdb - start molden with the -f commandline flag. Regards, Gijs ------------------------------------------------------------------------- So these were the answers. My problem was that I didn't have the .seq file in the working directory. Copying it there helped the problem. Grateful thanks for everybody who sent me suggestions. I hop this summary will help some of you in using Tinker, which is a very powerful software package. Kiss, Gergo h332262@sirius.cab.u-szeged.hu