Subject: conformational search on ring systems (fwd)

From: Christian Pilger <[email-masked]>
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 <[email-masked]>

I believe that Conformer will do this, although I have not tried it myself.
See http://www.conformer.com

Jonathan Brecher
CambidgeSoft Corporation
[email-masked]
===========================================================================
From: Ray Fort Jr. <[email-masked]>
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 <[email-masked]>
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 <[email-masked]>
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 <[email-masked]>
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" <[email-masked]>
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 <[email-masked]>
Tripos' Sybyl offers a variety of tools that can be used in searching
the conformational space of cyclic molecules.
===========================================================================
From: Hr. Dr. S. Shapiro <[email-masked]>
        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 <[email-masked]>
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 <[email-masked]>
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 [email-masked].
===========================================================================
From: Andy Holder <[email-masked]>
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 <[email-masked]>
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 <[email-masked]>
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 <[email-masked]>
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 <[email-masked]>
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 <[email-masked]>
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: [email-masked]
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 <[email-masked]>
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 <[email-masked]>
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: [email-masked]
 
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