Subject: Re: CCL:FREE SOFTWARE

From: "Joerg K. Wegner" <wegnerj~at~informatik.uni-tuebingen.de>
Date: Fri, 30 Apr 2004 09:52:33 +0200

Hi,

Overview:
http://zeus.polsl.gliwice.pl/~nikodem/linux4chemistry.html

Docking (academics):
Autodock (Linux only)
http://www.scripps.edu/pub/olson-web/doc/autodock/

Ghemical (includes Mopac) (+ OELib,OpenBabel, conformer generation !):
http://www.uku.fi/~thassine/ghemical/

QSAR:
JOELib
http://www-ra.informatik.uni-tuebingen.de/software/joelib/

Kind regards, Joerg

-- 
Dipl. Chem. Joerg K. Wegner
Center of Bioinformatics Tuebingen (ZBIT)
Department of Computer Architecture
Univ. Tuebingen, Sand 1, D-72076 Tuebingen, Germany
Phone: (+49/0) 7071 29 78970
Fax: (+49/0) 7071 29 5091
E-Mail: mailto:wegnerj~at~informatik.uni-tuebingen.de
WWW:    http://www-ra.informatik.uni-tuebingen.de
--
Never mistake motion for action.
                                     (E. Hemingway)

Never mistake action for meaningful action.
                                (Hugo Kubinyi,2004)

---

From: "Peter Gannett" <pgannett:at:hsc.wvu.edu>
Date: Thu, 29 Apr 2004 15:38:05 -0400

Miguel:

While not so good for manipulation and docking, the programs NAMD and
VMD are very good for MM/MD and visualization with some post MD run
processing.  Versions are available for Unix/Linux/Win.  

Pete Gannett

>>> "E.L. Willighagen" <egonw:at:sci.kun.nl> 4/29/2004 3:48:27 AM >>>

On Wednesday 28 April 2004 23:13, Miguel Romero wrote:
> This is the first time I write to the CCL. I am starting a new
molecular
> modeling project in a new research group. I've used comercial
modeling
> software for many time but now I have to switch to something else,
> preferably a FREE or reasonably priced software. I
>
> I am going to work with ligand-protein complexes and I need
manipulation
> software, doking and molecular mechanics (geometry optimization and
> molecular dynamics) software. It can work under linux or windows
sistems.
>
> Can anybody help me.
> thanks in advance for any help!

I'm not sure which programming language you plan to use (I guess C, C++
or 
even fortran...), but for visualization I do recommend Jmol 
(http://www.jmol.org) which is open source and has a very good 3D 
visualization of proteins which is even being improved every day by an

international group of programmers and users.

And since Java can easily bind to C/C++ code, it is quite
straightforward to 
combine it with your code.

I hope this helps,

Egon

- -- 
egonw:at:sci.kun.nl 
PhD on Molecular Representation in Chemometrics
Nijmegen University
http://www.cac.sci.kun.nl/people/egonw/ 
GPG: 1024D/D6336BA6

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---

From: Konrad Hinsen <hinsen$at$cnrs-orleans.fr>
Date: Fri, 30 Apr 2004 10:38:46 +0200

On Apr 28, 2004, at 23:13, Miguel Romero wrote:

> molecular modeling project in a new research group. I've used 
> comercial modeling software for many time but now I have to switch to 
> something else, preferably a FREE or reasonably priced software. I
>
> manipulation software, doking and molecular mechanics (geometry 
> optimization and molecular dynamics) software. It can work under linux 
> or windows sistems.

Have a look at

	http://dirac.cnrs-orleans.fr/MMTK/

You probably have to write some code yourself (docking for example), 
but that should be easy given that a lot of support code is there.
---------------------------------------------------------------------
Konrad Hinsen
Laboratoire Lion Brillouin, CEA Saclay,
91191 Gif-sur-Yvette Cedex, France
Tel.: +33-1 69 08 79 25
Fax: +33-1 69 08 82 61
E-Mail: hinsen$at$llb.saclay.cea.fr
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