[MMTK] simplied peptide model

[khinsen at cea.fr]

On Feb 21, 2005, at 15:53, Shirley Siu wrote:

> I am trying to use MMTK for constructing a peptide, to be used
> in simulation afterwards. I am completely new to MMTK, and wondering if
> anybody do the same before? and what is the proper way of building the
> model, if I am given only the residue sequence.
>
Building the model is rather easy:

	from MMTK.Proteins import PeptideChain
	chain = PeptideChain(['ala', 'gly', 'ile', 'pro'])

However, you cannot do much with such a model. Most operations provided 
in MMTK require atomic coordinates. If you are looking for a tool that 
will generate atomic coordinates for you, MMTK is not the right one, at 
least not at the moment. However, you can use some molecular builder to 
create an initial configuration, and then load the result back into 
MMTK for simulation purposes.

Konrad.
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Konrad Hinsen
Laboratoire Léon 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: khinsen at cea.fr
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