conformational search on ring systems (fwd)

From: Christian Pilger <cpilger |-at-| oc30.uni-paderborn.de>
Subject: conformational search on ring systems (fwd)
Date: Mon, 8 Mar 1999 15:50:09 +0100
 Dear CCL'ers,
 	one week ago, I posted a question about conformational searches on
 ring systems:
 > Dear CCL'ers,
 >
 > 	is anybody aware of a software package that has a conformational
 >search tool applicable to ring-systems ?
 I got several answers on this topic. Thank you very much. Many people
 asked me to summarize the responses:
 ===========================================================================
 From: Jonathan Brecher <jsb |-at-| camsoft.com>
 I believe that Conformer will do this, although I have not tried it myself.
 See http://www.conformer.com
 Jonathan Brecher
 CambidgeSoft Corporation
 jsb |-at-| camsoft.com
 ===========================================================================
 From: Ray Fort Jr. <rcfort |-at-| maine.edu>
 The molecular mechanics program PCModel, which runs on both PCs and UNIX
 boxes, has a search module called GMMX that will do what you want.
 It's available from Serena Software, Box 3076, Bloomington, IN 47402;
 telephone (812)-333-0823.  While not free, it is not terribly expensive.
 ===========================================================================
 From: Curt M. Breneman <brenec |-at-| rpi.edu>
 For ring systems, a stochastic method of conformational searching is
 preferable such as the one described by Prof. Martin Saunders of Yale
 University.
 Curt Breneman
 RPI Chemistry
 ===========================================================================
 From: Chris Williams <chrisw |-at-| chemcomp.com>
 The Molecular Operating Environment (MOE ) from
 Chemical Computing Group (CCG)  offers
 many conformational searching tools, the most
 relevant for your purposes being the RIPS
 conformational search.  Check out the CCG
 website
 http: //www.chemcomp.com
 or contact me directly for more information.
 ===========================================================================
 From: A. Gil Santos <ags |-at-| dq.fct.unl.pt>
 Spartan, from Wave Function, has the possibility of conformational search
 applicable to ring systems. Nevertheless, version 5.1 had several problems
 when runing this kind of jobs. I just got today the last version of this
 package, with the information that a lot of things has been changed, but I
 hadn't the time to test them till now.
 I hope that this information can help you.
 ===========================================================================
 From: "[iso-8859-1] Márcio Cyrillo" <cyrillo |-at-|
 ifi.unicamp.br>
 I can tell you that I developed a software package for PCs that acts as
 an interface for the semi-empirical program MOPAC6. With this program,
 named Chem2Pac, you can perform conformational analysis (sistematic
 only) for one or two variables (bond length, angle or dihedral). It does
 not have a help file and I do not know if I can distribute it now, but
 let me know if you are interested. Grüss aus Brasilien,
 Marcio
 ===========================================================================
 From: Wayne Steinmetz <WSTEINMETZ |-at-| POMONA.EDU>
 Tripos' Sybyl offers a variety of tools that can be used in searching
 the conformational space of cyclic molecules.
 ===========================================================================
 From: Hr. Dr. S. Shapiro <toukie |-at-| zui.unizh.ch>
         For the quality of your binding constants, check out the programme
 SCORE
 [cf. J. Mol. Model. 4: 379 ('98)].  For a programme that will do
 conformational searches on ring systems, check out GMMX by Serena Software.
 (And for an analysis of your obtained ring conformations, you can use the
 programme RICON, freely obtainable from Zefirov's group in Moskau.)
 ===========================================================================
 From: Mark Forster <mforster |-at-| nibsc.ac.uk>
 This is quite a niche topic and few if any packages address it. In terms
 of manual ring conformation adjustment I have used the Biopolymer
 module of the insightII program, this has a very neat interactive ring
 flipping implementation.
 ===========================================================================
 From: Paul D Soper <Paul.D.Soper |-at-| usa.dupont.com>
 I discussed this problem some time ago with Paul Saxe of MSI's San Diego
 office.  He has BTCL scripts for use with Discover 3 which allow one to
 distort rings.  His e-mail address is pws |-at-| msi.com.
 ===========================================================================
 From: Andy Holder <holdera |-at-| umkc.edu>
 Our AMPAC with Graphical User Interface has a simulated annealing method
 that has been quite successful on flexible ring systems.  If you like, I'll
 send out some materials on this aspect of our software.  Let me know.
 In the meantime, the following references describe the SA method.
 1. Bokisch, F.; Liotard, D.; Rayez, J. C.; Duguay, B. Intl. J. Quant. Chem.
 1992, 44,  619.
 ===========================================================================
 From: Patrick Bultinck <Patrick.Bultinck |-at-| rug.ac.be>
 Stochastic searching is implemented in MM3, obtainable from QCPE (object
 code). I use it very regularly on crown ethers and other macrocycles. If
 you want I can send a reprint (when I get them...).
 ===========================================================================
 From: Tamas Gunda <tamasgunda |-at-| tigris.klte.hu>
 If you mean on "conformational search tool applicable to
 ring-systems" the calculation of ring-puckering data,
 distances from least-square planes, torsional angles in rings,
 different pyramidality indices of atoms,
 then have a look on Mol2mol at
 www.compuchem.com/mol2mol.htm
 ===========================================================================
 From: Patrick Bultinck <Patrick.Bultinck |-at-| rug.ac.be>
 Have a look at B.P. Hay et al., J. Mol. Struct. (THEOCHEM), 337 (1995) 34-47
 It nicely illustrates the use of MM3 conformational searching. MM3 can be
 obtained from QCPE for LOW cost, but without graphical interface, but you
 can check results with all kinds of graphical programs. If you want I can
 also send a proof of my own work, which is mainly on ab initio
 calculations.
 ===========================================================================
 From: Cikui Liang <cikui |-at-| ese.ogi.edu>
 You can find information on CONFLEX from:
 http://sun.icrs.tohoku.ac.jp/~gotoh/CONFLEX/conflex_manual.htm
 Oxford Molecular Group (www.oxmol.com) has implemented CONFLEX with their
 CAChe software.  It is going to be available for the next CAChe release.
 Hope this helps.
 ===========================================================================
 From: Chris Williams <chrisw |-at-| chemcomp.com>
 The application in MOE most suited for your
 problem of ring system conformational searching
 is the RIPS (Random Incremental Pulse Search)
 application.  The RIPS application is based on a
 paper by Ferguson et.al.
 (J. Am. Chem. Soc., 111,  p4371-4378, (1989))
 The implementation of this algorithm MOE has an
 additional chiral constraining force than ensures
 the correct diastereomer of a given compound  is generated
 upon minimization of the perturbed structure.
 Other conformational searching tools in MOE include
 molcular dynamics (MD), a hybrid MD/Monte Carlo conformational
 search and a fast rotatable bond search.  Of these, only the
 fast rotatable bond search is not applicable to ring searches.
 If you need more specific information, please
 contact me at either the e-mail address or the
 telephone number below.
 ===========================================================================
 From: trevor.howe |-at-| pharma.Novartis.com
 MacroModel is excellent for this although the analysis tools are pretty
 hopeless but I would say this is the industry standard for ring systems.
 QUNATA, does a similar job with CHARMm as the force field.
 ===========================================================================
 From: Jens Sadowski <sadowski |-at-| zhs4.zh.basf-ag.de>
 the 3D-structure generator corina is capable of generating multiple
 conformations for ring systems up to ring size 8. Look at
    http://www2.ccc.uni-erlangen.de/services/3d.html
 ===========================================================================
 From: Mark Forster <mforster |-at-| nibsc.ac.uk>
 I'll address this in two parts
     1) Code to measure ring conformation parameters.
     2) Software to manipulate ring conformations interactively.
 1) For six membered rings our Unix/X11 code called mdXvu is available from
 the Quantum Chemistry Program Exchange (QCPE) and one of its
 features is the measurement of the Cremer Pople ring puckering
 parameters.
 2) The Biopolymer module of insightII (from MSI) has a nice tool
 for 'ring flapping' i.e. selecting two atoms in a ring and pivoting the
 intermediate ring atoms about the selected pair while maintaining the
 bond lengths and angles. This works for 5,6,7.... membered rings.
 ===========================================================================
 Regards,
 Christian
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  Dipl.-Chem. Christian Pilger          Uni-GH Paderborn
                                        FB 13 - Organische Chemie
                                        Warburger Str. 100
                                        D-33098 Paderborn/Germany
  Tel.: 05251-60279/-602183
  Fax : 05251-603245         email: cpilger |-at-| oc30.uni-paderborn.de
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