[MMTK] adding bonds between molecules

konrad.hinsen at laposte.net konrad.hinsen at laposte.net
Tue Jan 11 17:50:41 CET 2005


On Jan 11, 2005, at 16:32, david.evans at ulsop.ac.uk wrote:

> Is is possible to add a chemical bond between two atoms which are
> defined as part of different Molecule objects? For example between a
> DNA nucleotide and a small molecule.
>
No. A Molecule object is not supposed to have chemical bonds to the 
outside world. There are a couple of places in the code where this 
property is silently assumed, so it is better not to try to work around 
it.

The most straightforward correct way to handle a nucleotide with a 
covalently attached ligand is to create a new database entry for the 
combined object. It is possible to write Python code that creates such 
an object without a specific database entry, but that would be more 
effort (though also more general). One advantage to the database file 
method is that it lets you specify modified charges and atom types for 
the combined item, which in practice will be necessary in most cases.

Konrad.
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