[MMTK] adding bonds between molecules

david.evans at ulsop.ac.uk david.evans at ulsop.ac.uk
Wed Jan 12 16:43:16 CET 2005

Thanks for the info, I should be able to make it work by defining a
new 'nucleotide'.

If anyone is interested, I'm close to having Amber99 combined with
the gaff forcefield implemented within MMTK, which should be useful
ultimately for ligand binding calculations.


---- Message from konrad.hinsen at laposte.net at 2005-01-11 17:50:41
>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
>> 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
>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
>an object without a specific database entry, but that would be more 
>effort (though also more general). One advantage to the database
>method is that it lets you specify modified charges and atom types
>the combined item, which in practice will be necessary in most cases.
>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: hinsen at llb.saclay.cea.fr

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