[MMTK] Nucleotide Sequences, Solvation question

khinsen at cea.fr khinsen at cea.fr
Thu Mar 31 10:29:46 CEST 2005


On 30.03.2005, at 17:09, Justin Lemkul wrote:

> nucleotides/peptides, etc.)  I was reading up about how to construct a
> nucleotide chain,
> but I can't seem to get the syntax right.  Can someone show me how to  
> create,
> for example, a very short chain of, say, CAGT?

from MMTK.NucleicAcids import NucleotideChain
chain = NucleotideChain(['dc', 'da', 'dg', 'dt'])

This creates all the objects, but the objects have undefined positions,  
so you cannot do much with it. The DNA support currently available in  
MMTK is intended for constructing DNA-containing systems from PDB  
files, not from scratch. There is no support for generating helices,  
adding counterions, etc.

There is, however, all the infrastructure to implement such functions,  
so someone with sufficient knowledge of DNA could write them with  
little effort.

Konrad.
--
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Konrad Hinsen
Laboratoire Leon 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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